| 3 |
|
|
| 4 |
|
@ARTICLE{Torre2003, |
| 5 |
|
author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez |
| 6 |
< |
and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez}, |
| 6 |
> |
and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez}, |
| 7 |
|
title = {Calculation of the solution properties of flexible macromolecules: |
| 8 |
< |
methods and applications}, |
| 8 |
> |
methods and applications}, |
| 9 |
|
journal = {European Biophysics Journal with Biophysics Letters}, |
| 10 |
|
year = {2003}, |
| 11 |
|
volume = {32}, |
| 13 |
|
number = {5}, |
| 14 |
|
month = {Aug}, |
| 15 |
|
abstract = {While the prediction of hydrodynamic properties of rigid particles |
| 16 |
< |
is nowadays feasible using simple and efficient computer programs, |
| 17 |
< |
the calculation of such properties and, in general, the dynamic |
| 18 |
< |
behavior of flexible macromolecules has not reached a similar situation. |
| 19 |
< |
Although the theories are available, usually the computational work |
| 20 |
< |
is done using solutions specific for each problem. We intend to |
| 21 |
< |
develop computer programs that would greatly facilitate the task |
| 22 |
< |
of predicting solution behavior of flexible macromolecules. In this |
| 23 |
< |
paper, we first present an overview of the two approaches that are |
| 24 |
< |
most practical: the Monte Carlo rigid-body treatment, and the Brownian |
| 25 |
< |
dynamics simulation technique. The Monte Carlo procedure is based |
| 26 |
< |
on the calculation of properties for instantaneous conformations |
| 27 |
< |
of the macromolecule that are regarded as if they were instantaneously |
| 28 |
< |
rigid. We describe how a Monte Carlo program can be interfaced to |
| 29 |
< |
the programs in the HYDRO suite for rigid particles, and provide |
| 30 |
< |
an example of such calculation, for a hypothetical particle: a protein |
| 31 |
< |
with two domains connected by a flexible linker. We also describe |
| 32 |
< |
briefly the essentials of Brownian dynamics, and propose a general |
| 33 |
< |
mechanical model that includes several kinds of intramolecular interactions, |
| 34 |
< |
such as bending, internal rotation, excluded volume effects, etc. |
| 35 |
< |
We provide an example of the application of this methodology to |
| 36 |
< |
the dynamics of a semiflexible, wormlike DNA.}, |
| 16 |
> |
is nowadays feasible using simple and efficient computer programs, |
| 17 |
> |
the calculation of such properties and, in general, the dynamic |
| 18 |
> |
behavior of flexible macromolecules has not reached a similar situation. |
| 19 |
> |
Although the theories are available, usually the computational work |
| 20 |
> |
is done using solutions specific for each problem. We intend to |
| 21 |
> |
develop computer programs that would greatly facilitate the task |
| 22 |
> |
of predicting solution behavior of flexible macromolecules. In this |
| 23 |
> |
paper, we first present an overview of the two approaches that are |
| 24 |
> |
most practical: the Monte Carlo rigid-body treatment, and the Brownian |
| 25 |
> |
dynamics simulation technique. The Monte Carlo procedure is based |
| 26 |
> |
on the calculation of properties for instantaneous conformations |
| 27 |
> |
of the macromolecule that are regarded as if they were instantaneously |
| 28 |
> |
rigid. We describe how a Monte Carlo program can be interfaced to |
| 29 |
> |
the programs in the HYDRO suite for rigid particles, and provide |
| 30 |
> |
an example of such calculation, for a hypothetical particle: a protein |
| 31 |
> |
with two domains connected by a flexible linker. We also describe |
| 32 |
> |
briefly the essentials of Brownian dynamics, and propose a general |
| 33 |
> |
mechanical model that includes several kinds of intramolecular interactions, |
| 34 |
> |
such as bending, internal rotation, excluded volume effects, etc. |
| 35 |
> |
We provide an example of the application of this methodology to |
| 36 |
> |
the dynamics of a semiflexible, wormlike DNA.}, |
| 37 |
|
annote = {724XK Times Cited:6 Cited References Count:64}, |
| 38 |
|
issn = {0175-7571}, |
| 39 |
|
uri = {<Go to ISI>://000185513400011}, |
| 42 |
|
@ARTICLE{Alakent2005, |
| 43 |
|
author = {B. Alakent and M. C. Camurdan and P. Doruker}, |
| 44 |
|
title = {Hierarchical structure of the energy landscape of proteins revisited |
| 45 |
< |
by time series analysis. II. Investigation of explicit solvent effects}, |
| 45 |
> |
by time series analysis. II. Investigation of explicit solvent effects}, |
| 46 |
|
journal = {Journal of Chemical Physics}, |
| 47 |
|
year = {2005}, |
| 48 |
|
volume = {123}, |
| 50 |
|
number = {14}, |
| 51 |
|
month = {Oct 8}, |
| 52 |
|
abstract = {Time series analysis tools are employed on the principal modes obtained |
| 53 |
< |
from the C-alpha trajectories from two independent molecular-dynamics |
| 54 |
< |
simulations of alpha-amylase inhibitor (tendamistat). Fluctuations |
| 55 |
< |
inside an energy minimum (intraminimum motions), transitions between |
| 56 |
< |
minima (interminimum motions), and relaxations in different hierarchical |
| 57 |
< |
energy levels are investigated and compared with those encountered |
| 58 |
< |
in vacuum by using different sampling window sizes and intervals. |
| 59 |
< |
The low-frequency low-indexed mode relationship, established in |
| 60 |
< |
vacuum, is also encountered in water, which shows the reliability |
| 61 |
< |
of the important dynamics information offered by principal components |
| 62 |
< |
analysis in water. It has been shown that examining a short data |
| 63 |
< |
collection period (100 ps) may result in a high population of overdamped |
| 64 |
< |
modes, while some of the low-frequency oscillations (< 10 cm(-1)) |
| 65 |
< |
can be captured in water by using a longer data collection period |
| 66 |
< |
(1200 ps). Simultaneous analysis of short and long sampling window |
| 67 |
< |
sizes gives the following picture of the effect of water on protein |
| 68 |
< |
dynamics. Water makes the protein lose its memory: future conformations |
| 69 |
< |
are less dependent on previous conformations due to the lowering |
| 70 |
< |
of energy barriers in hierarchical levels of the energy landscape. |
| 71 |
< |
In short-time dynamics (< 10 ps), damping factors extracted from |
| 72 |
< |
time series model parameters are lowered. For tendamistat, the friction |
| 73 |
< |
coefficient in the Langevin equation is found to be around 40-60 |
| 74 |
< |
cm(-1) for the low-indexed modes, compatible with literature. The |
| 75 |
< |
fact that water has increased the friction and that on the other |
| 76 |
< |
hand has lubrication effect at first sight contradicts. However, |
| 77 |
< |
this comes about because water enhances the transitions between |
| 78 |
< |
minima and forces the protein to reduce its already inherent inability |
| 79 |
< |
to maintain oscillations observed in vacuum. Some of the frequencies |
| 80 |
< |
lower than 10 cm(-1) are found to be overdamped, while those higher |
| 81 |
< |
than 20 cm(-1) are slightly increased. As for the long-time dynamics |
| 82 |
< |
in water, it is found that random-walk motion is maintained for |
| 83 |
< |
approximately 200 ps (about five times of that in vacuum) in the |
| 84 |
< |
low-indexed modes, showing the lowering of energy barriers between |
| 85 |
< |
the higher-level minima.}, |
| 53 |
> |
from the C-alpha trajectories from two independent molecular-dynamics |
| 54 |
> |
simulations of alpha-amylase inhibitor (tendamistat). Fluctuations |
| 55 |
> |
inside an energy minimum (intraminimum motions), transitions between |
| 56 |
> |
minima (interminimum motions), and relaxations in different hierarchical |
| 57 |
> |
energy levels are investigated and compared with those encountered |
| 58 |
> |
in vacuum by using different sampling window sizes and intervals. |
| 59 |
> |
The low-frequency low-indexed mode relationship, established in |
| 60 |
> |
vacuum, is also encountered in water, which shows the reliability |
| 61 |
> |
of the important dynamics information offered by principal components |
| 62 |
> |
analysis in water. It has been shown that examining a short data |
| 63 |
> |
collection period (100 ps) may result in a high population of overdamped |
| 64 |
> |
modes, while some of the low-frequency oscillations (< 10 cm(-1)) |
| 65 |
> |
can be captured in water by using a longer data collection period |
| 66 |
> |
(1200 ps). Simultaneous analysis of short and long sampling window |
| 67 |
> |
sizes gives the following picture of the effect of water on protein |
| 68 |
> |
dynamics. Water makes the protein lose its memory: future conformations |
| 69 |
> |
are less dependent on previous conformations due to the lowering |
| 70 |
> |
of energy barriers in hierarchical levels of the energy landscape. |
| 71 |
> |
In short-time dynamics (< 10 ps), damping factors extracted from |
| 72 |
> |
time series model parameters are lowered. For tendamistat, the friction |
| 73 |
> |
coefficient in the Langevin equation is found to be around 40-60 |
| 74 |
> |
cm(-1) for the low-indexed modes, compatible with literature. The |
| 75 |
> |
fact that water has increased the friction and that on the other |
| 76 |
> |
hand has lubrication effect at first sight contradicts. However, |
| 77 |
> |
this comes about because water enhances the transitions between |
| 78 |
> |
minima and forces the protein to reduce its already inherent inability |
| 79 |
> |
to maintain oscillations observed in vacuum. Some of the frequencies |
| 80 |
> |
lower than 10 cm(-1) are found to be overdamped, while those higher |
| 81 |
> |
than 20 cm(-1) are slightly increased. As for the long-time dynamics |
| 82 |
> |
in water, it is found that random-walk motion is maintained for |
| 83 |
> |
approximately 200 ps (about five times of that in vacuum) in the |
| 84 |
> |
low-indexed modes, showing the lowering of energy barriers between |
| 85 |
> |
the higher-level minima.}, |
| 86 |
|
annote = {973OH Times Cited:1 Cited References Count:33}, |
| 87 |
|
issn = {0021-9606}, |
| 88 |
|
uri = {<Go to ISI>://000232532000064}, |
| 89 |
|
} |
| 90 |
|
|
| 91 |
+ |
@BOOK{Alexander1987, |
| 92 |
+ |
title = {A Pattern Language: Towns, Buildings, Construction}, |
| 93 |
+ |
publisher = {Oxford University Press}, |
| 94 |
+ |
year = {1987}, |
| 95 |
+ |
author = {C. Alexander}, |
| 96 |
+ |
address = {New York}, |
| 97 |
+ |
} |
| 98 |
+ |
|
| 99 |
|
@BOOK{Allen1987, |
| 100 |
|
title = {Computer Simulations of Liquids}, |
| 101 |
|
publisher = {Oxford University Press}, |
| 107 |
|
@ARTICLE{Allison1991, |
| 108 |
|
author = {S. A. Allison}, |
| 109 |
|
title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application |
| 110 |
< |
to Polarized Dynamic Light-Scattering}, |
| 110 |
> |
to Polarized Dynamic Light-Scattering}, |
| 111 |
|
journal = {Macromolecules}, |
| 112 |
|
year = {1991}, |
| 113 |
|
volume = {24}, |
| 115 |
|
number = {2}, |
| 116 |
|
month = {Jan 21}, |
| 117 |
|
abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments |
| 118 |
< |
of rigid macromolecules. It is applied to polarized dynamic light |
| 119 |
< |
scattering from rodlike sturctures and from a model of a DNA fragment |
| 120 |
< |
(762 base pairs). A number of rod cases are examined in which the |
| 121 |
< |
translational anisotropy is increased form zero to a large value. |
| 122 |
< |
Simulated first cumulants as well as amplitudes and lifetimes of |
| 123 |
< |
the dynamic form factor are compared with predictions of analytic |
| 124 |
< |
theories and found to be in very good agreement with them. For DNA |
| 125 |
< |
fragments 762 base pairs in length or longer, translational anisotropy |
| 126 |
< |
does not contribute significantly to dynamic light scattering. In |
| 127 |
< |
a comparison of rigid and flexible simulations on semistiff models |
| 128 |
< |
of this fragment, it is shown directly that flexing contributes |
| 129 |
< |
to the faster decay processes probed by light scattering and that |
| 130 |
< |
the flexible model studies are in good agreement with experiment.}, |
| 118 |
> |
of rigid macromolecules. It is applied to polarized dynamic light |
| 119 |
> |
scattering from rodlike sturctures and from a model of a DNA fragment |
| 120 |
> |
(762 base pairs). A number of rod cases are examined in which the |
| 121 |
> |
translational anisotropy is increased form zero to a large value. |
| 122 |
> |
Simulated first cumulants as well as amplitudes and lifetimes of |
| 123 |
> |
the dynamic form factor are compared with predictions of analytic |
| 124 |
> |
theories and found to be in very good agreement with them. For DNA |
| 125 |
> |
fragments 762 base pairs in length or longer, translational anisotropy |
| 126 |
> |
does not contribute significantly to dynamic light scattering. In |
| 127 |
> |
a comparison of rigid and flexible simulations on semistiff models |
| 128 |
> |
of this fragment, it is shown directly that flexing contributes |
| 129 |
> |
to the faster decay processes probed by light scattering and that |
| 130 |
> |
the flexible model studies are in good agreement with experiment.}, |
| 131 |
|
annote = {Eu814 Times Cited:8 Cited References Count:32}, |
| 132 |
|
issn = {0024-9297}, |
| 133 |
|
uri = {<Go to ISI>://A1991EU81400029}, |
| 136 |
|
@ARTICLE{Andersen1983, |
| 137 |
|
author = {H. C. Andersen}, |
| 138 |
|
title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics |
| 139 |
< |
Calculations}, |
| 139 |
> |
Calculations}, |
| 140 |
|
journal = {Journal of Computational Physics}, |
| 141 |
|
year = {1983}, |
| 142 |
|
volume = {52}, |
| 150 |
|
@ARTICLE{Auerbach2005, |
| 151 |
|
author = {A. Auerbach}, |
| 152 |
|
title = {Gating of acetylcholine receptor channels: Brownian motion across |
| 153 |
< |
a broad transition state}, |
| 153 |
> |
a broad transition state}, |
| 154 |
|
journal = {Proceedings of the National Academy of Sciences of the United States |
| 155 |
< |
of America}, |
| 155 |
> |
of America}, |
| 156 |
|
year = {2005}, |
| 157 |
|
volume = {102}, |
| 158 |
|
pages = {1408-1412}, |
| 159 |
|
number = {5}, |
| 160 |
|
month = {Feb 1}, |
| 161 |
|
abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between |
| 162 |
< |
stable #closed# and #open# conformations. In patch clamp recordings, |
| 163 |
< |
diliganded AChR gating appears to be a simple, two-state reaction. |
| 164 |
< |
However, mutagenesis studies indicate that during gating dozens |
| 165 |
< |
of residues across the protein move asynchronously and are organized |
| 166 |
< |
into rigid body gating domains (#blocks#). Moreover, there is an |
| 167 |
< |
upper limit to the apparent channel opening rate constant. These |
| 168 |
< |
observations suggest that the gating reaction has a broad, corrugated |
| 169 |
< |
transition state region, with the maximum opening rate reflecting, |
| 170 |
< |
in part, the mean first-passage time across this ensemble. Simulations |
| 171 |
< |
reveal that a flat, isotropic energy profile for the transition |
| 172 |
< |
state can account for many of the essential features of AChR gating. |
| 173 |
< |
With this mechanism, concerted, local structural transitions that |
| 174 |
< |
occur on the broad transition state ensemble give rise to fractional |
| 175 |
< |
measures of reaction progress (Phi values) determined by rate-equilibrium |
| 176 |
< |
free energy relationship analysis. The results suggest that the |
| 177 |
< |
coarse-grained AChR gating conformational change propagates through |
| 178 |
< |
the protein with dynamics that are governed by the Brownian motion |
| 179 |
< |
of individual gating blocks.}, |
| 162 |
> |
stable #closed# and #open# conformations. In patch clamp recordings, |
| 163 |
> |
diliganded AChR gating appears to be a simple, two-state reaction. |
| 164 |
> |
However, mutagenesis studies indicate that during gating dozens |
| 165 |
> |
of residues across the protein move asynchronously and are organized |
| 166 |
> |
into rigid body gating domains (#blocks#). Moreover, there is an |
| 167 |
> |
upper limit to the apparent channel opening rate constant. These |
| 168 |
> |
observations suggest that the gating reaction has a broad, corrugated |
| 169 |
> |
transition state region, with the maximum opening rate reflecting, |
| 170 |
> |
in part, the mean first-passage time across this ensemble. Simulations |
| 171 |
> |
reveal that a flat, isotropic energy profile for the transition |
| 172 |
> |
state can account for many of the essential features of AChR gating. |
| 173 |
> |
With this mechanism, concerted, local structural transitions that |
| 174 |
> |
occur on the broad transition state ensemble give rise to fractional |
| 175 |
> |
measures of reaction progress (Phi values) determined by rate-equilibrium |
| 176 |
> |
free energy relationship analysis. The results suggest that the |
| 177 |
> |
coarse-grained AChR gating conformational change propagates through |
| 178 |
> |
the protein with dynamics that are governed by the Brownian motion |
| 179 |
> |
of individual gating blocks.}, |
| 180 |
|
annote = {895QF Times Cited:9 Cited References Count:33}, |
| 181 |
|
issn = {0027-8424}, |
| 182 |
|
uri = {<Go to ISI>://000226877300030}, |
| 185 |
|
@ARTICLE{Baber1995, |
| 186 |
|
author = {J. Baber and J. F. Ellena and D. S. Cafiso}, |
| 187 |
|
title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined |
| 188 |
< |
Using H-2 Nmr and H-1-H-1 Noe Spectroscopy}, |
| 188 |
> |
Using H-2 Nmr and H-1-H-1 Noe Spectroscopy}, |
| 189 |
|
journal = {Biochemistry}, |
| 190 |
|
year = {1995}, |
| 191 |
|
volume = {34}, |
| 193 |
|
number = {19}, |
| 194 |
|
month = {May 16}, |
| 195 |
|
abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane |
| 196 |
< |
on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine |
| 197 |
< |
membranes in the liquid crystalline phase was investigated using |
| 198 |
< |
H-2 NMR. Upon the addition of the anesthetics, the first five methylene |
| 199 |
< |
units near the interface generally show a very small increase in |
| 200 |
< |
segmental order, while segments deeper within the bilayer show a |
| 201 |
< |
small decrease in segmental order. From the H-2 NMR results, the |
| 202 |
< |
chain length for the perdeuterated palmitoyl chain in the absence |
| 203 |
< |
of anesthetic was found to be 12.35 Angstrom. Upon the addition |
| 204 |
< |
of halothane enflurane, or isoflurane, the acyl chain undergoes |
| 205 |
< |
slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively, |
| 206 |
< |
at 50 mol % anesthetic. A simple model was used to estimate the |
| 207 |
< |
relative amounts of anesthetic located near the interface and deeper |
| 208 |
< |
in the bilayer hydrocarbon region, and only a slight preference |
| 209 |
< |
for an interfacial location was observed. Intermolecular H-1-H-1 |
| 210 |
< |
nuclear Overhauser effects (NOEs) were measured between phospholipid |
| 211 |
< |
and halothane protons. These NOEs are consistent with the intramembrane |
| 212 |
< |
location of the anesthetics suggested by the H-2 NMR data. In addition, |
| 213 |
< |
the NOE data indicate that anesthetics prefer the interfacial and |
| 214 |
< |
hydrocarbon regions of the membrane and are not found in high concentrations |
| 215 |
< |
in the phospholipid headgroup.}, |
| 196 |
> |
on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine |
| 197 |
> |
membranes in the liquid crystalline phase was investigated using |
| 198 |
> |
H-2 NMR. Upon the addition of the anesthetics, the first five methylene |
| 199 |
> |
units near the interface generally show a very small increase in |
| 200 |
> |
segmental order, while segments deeper within the bilayer show a |
| 201 |
> |
small decrease in segmental order. From the H-2 NMR results, the |
| 202 |
> |
chain length for the perdeuterated palmitoyl chain in the absence |
| 203 |
> |
of anesthetic was found to be 12.35 Angstrom. Upon the addition |
| 204 |
> |
of halothane enflurane, or isoflurane, the acyl chain undergoes |
| 205 |
> |
slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively, |
| 206 |
> |
at 50 mol % anesthetic. A simple model was used to estimate the |
| 207 |
> |
relative amounts of anesthetic located near the interface and deeper |
| 208 |
> |
in the bilayer hydrocarbon region, and only a slight preference |
| 209 |
> |
for an interfacial location was observed. Intermolecular H-1-H-1 |
| 210 |
> |
nuclear Overhauser effects (NOEs) were measured between phospholipid |
| 211 |
> |
and halothane protons. These NOEs are consistent with the intramembrane |
| 212 |
> |
location of the anesthetics suggested by the H-2 NMR data. In addition, |
| 213 |
> |
the NOE data indicate that anesthetics prefer the interfacial and |
| 214 |
> |
hydrocarbon regions of the membrane and are not found in high concentrations |
| 215 |
> |
in the phospholipid headgroup.}, |
| 216 |
|
annote = {Qz716 Times Cited:38 Cited References Count:37}, |
| 217 |
|
issn = {0006-2960}, |
| 218 |
|
uri = {<Go to ISI>://A1995QZ71600035}, |
| 221 |
|
@ARTICLE{Banerjee2004, |
| 222 |
|
author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray}, |
| 223 |
|
title = {Solution of quantum Langevin equation: Approximations, theoretical |
| 224 |
< |
and numerical aspects}, |
| 224 |
> |
and numerical aspects}, |
| 225 |
|
journal = {Journal of Chemical Physics}, |
| 226 |
|
year = {2004}, |
| 227 |
|
volume = {120}, |
| 229 |
|
number = {19}, |
| 230 |
|
month = {May 15}, |
| 231 |
|
abstract = {Based on a coherent state representation of noise operator and an |
| 232 |
< |
ensemble averaging procedure using Wigner canonical thermal distribution |
| 233 |
< |
for harmonic oscillators, a generalized quantum Langevin equation |
| 234 |
< |
has been recently developed [Phys. Rev. E 65, 021109 (2002); 66, |
| 235 |
< |
051106 (2002)] to derive the equations of motion for probability |
| 236 |
< |
distribution functions in c-number phase-space. We extend the treatment |
| 237 |
< |
to explore several systematic approximation schemes for the solutions |
| 238 |
< |
of the Langevin equation for nonlinear potentials for a wide range |
| 239 |
< |
of noise correlation, strength and temperature down to the vacuum |
| 240 |
< |
limit. The method is exemplified by an analytic application to harmonic |
| 241 |
< |
oscillator for arbitrary memory kernel and with the help of a numerical |
| 242 |
< |
calculation of barrier crossing, in a cubic potential to demonstrate |
| 243 |
< |
the quantum Kramers' turnover and the quantum Arrhenius plot. (C) |
| 244 |
< |
2004 American Institute of Physics.}, |
| 232 |
> |
ensemble averaging procedure using Wigner canonical thermal distribution |
| 233 |
> |
for harmonic oscillators, a generalized quantum Langevin equation |
| 234 |
> |
has been recently developed [Phys. Rev. E 65, 021109 (2002); 66, |
| 235 |
> |
051106 (2002)] to derive the equations of motion for probability |
| 236 |
> |
distribution functions in c-number phase-space. We extend the treatment |
| 237 |
> |
to explore several systematic approximation schemes for the solutions |
| 238 |
> |
of the Langevin equation for nonlinear potentials for a wide range |
| 239 |
> |
of noise correlation, strength and temperature down to the vacuum |
| 240 |
> |
limit. The method is exemplified by an analytic application to harmonic |
| 241 |
> |
oscillator for arbitrary memory kernel and with the help of a numerical |
| 242 |
> |
calculation of barrier crossing, in a cubic potential to demonstrate |
| 243 |
> |
the quantum Kramers' turnover and the quantum Arrhenius plot. (C) |
| 244 |
> |
2004 American Institute of Physics.}, |
| 245 |
|
annote = {816YY Times Cited:8 Cited References Count:35}, |
| 246 |
|
issn = {0021-9606}, |
| 247 |
|
uri = {<Go to ISI>://000221146400009}, |
| 259 |
|
@ARTICLE{Barth1998, |
| 260 |
|
author = {E. Barth and T. Schlick}, |
| 261 |
|
title = {Overcoming stability limitations in biomolecular dynamics. I. Combining |
| 262 |
< |
force splitting via extrapolation with Langevin dynamics in LN}, |
| 262 |
> |
force splitting via extrapolation with Langevin dynamics in LN}, |
| 263 |
|
journal = {Journal of Chemical Physics}, |
| 264 |
|
year = {1998}, |
| 265 |
|
volume = {109}, |
| 267 |
|
number = {5}, |
| 268 |
|
month = {Aug 1}, |
| 269 |
|
abstract = {We present an efficient new method termed LN for propagating biomolecular |
| 270 |
< |
dynamics according to the Langevin equation that arose fortuitously |
| 271 |
< |
upon analysis of the range of harmonic validity of our normal-mode |
| 272 |
< |
scheme LIN. LN combines force linearization with force splitting |
| 273 |
< |
techniques and disposes of LIN'S computationally intensive minimization |
| 274 |
< |
(anharmonic correction) component. Unlike the competitive multiple-timestepping |
| 275 |
< |
(MTS) schemes today-formulated to be symplectic and time-reversible-LN |
| 276 |
< |
merges the slow and fast forces via extrapolation rather than impulses; |
| 277 |
< |
the Langevin heat bath prevents systematic energy drifts. This combination |
| 278 |
< |
succeeds in achieving more significant speedups than these MTS methods |
| 279 |
< |
which are Limited by resonance artifacts to an outer timestep less |
| 280 |
< |
than some integer multiple of half the period of the fastest motion |
| 281 |
< |
(around 4-5 fs for biomolecules). We show that LN achieves very |
| 282 |
< |
good agreement with small-timestep solutions of the Langevin equation |
| 283 |
< |
in terms of thermodynamics (energy means and variances), geometry, |
| 284 |
< |
and dynamics (spectral densities) for two proteins in vacuum and |
| 285 |
< |
a large water system. Significantly, the frequency of updating the |
| 286 |
< |
slow forces extends to 48 fs or more, resulting in speedup factors |
| 287 |
< |
exceeding 10. The implementation of LN in any program that employs |
| 288 |
< |
force-splitting computations is straightforward, with only partial |
| 289 |
< |
second-derivative information required, as well as sparse Hessian/vector |
| 290 |
< |
multiplication routines. The linearization part of LN could even |
| 291 |
< |
be replaced by direct evaluation of the fast components. The application |
| 292 |
< |
of LN to biomolecular dynamics is well suited for configurational |
| 293 |
< |
sampling, thermodynamic, and structural questions. (C) 1998 American |
| 294 |
< |
Institute of Physics.}, |
| 270 |
> |
dynamics according to the Langevin equation that arose fortuitously |
| 271 |
> |
upon analysis of the range of harmonic validity of our normal-mode |
| 272 |
> |
scheme LIN. LN combines force linearization with force splitting |
| 273 |
> |
techniques and disposes of LIN'S computationally intensive minimization |
| 274 |
> |
(anharmonic correction) component. Unlike the competitive multiple-timestepping |
| 275 |
> |
(MTS) schemes today-formulated to be symplectic and time-reversible-LN |
| 276 |
> |
merges the slow and fast forces via extrapolation rather than impulses; |
| 277 |
> |
the Langevin heat bath prevents systematic energy drifts. This combination |
| 278 |
> |
succeeds in achieving more significant speedups than these MTS methods |
| 279 |
> |
which are Limited by resonance artifacts to an outer timestep less |
| 280 |
> |
than some integer multiple of half the period of the fastest motion |
| 281 |
> |
(around 4-5 fs for biomolecules). We show that LN achieves very |
| 282 |
> |
good agreement with small-timestep solutions of the Langevin equation |
| 283 |
> |
in terms of thermodynamics (energy means and variances), geometry, |
| 284 |
> |
and dynamics (spectral densities) for two proteins in vacuum and |
| 285 |
> |
a large water system. Significantly, the frequency of updating the |
| 286 |
> |
slow forces extends to 48 fs or more, resulting in speedup factors |
| 287 |
> |
exceeding 10. The implementation of LN in any program that employs |
| 288 |
> |
force-splitting computations is straightforward, with only partial |
| 289 |
> |
second-derivative information required, as well as sparse Hessian/vector |
| 290 |
> |
multiplication routines. The linearization part of LN could even |
| 291 |
> |
be replaced by direct evaluation of the fast components. The application |
| 292 |
> |
of LN to biomolecular dynamics is well suited for configurational |
| 293 |
> |
sampling, thermodynamic, and structural questions. (C) 1998 American |
| 294 |
> |
Institute of Physics.}, |
| 295 |
|
annote = {105HH Times Cited:29 Cited References Count:49}, |
| 296 |
|
issn = {0021-9606}, |
| 297 |
|
uri = {<Go to ISI>://000075066300006}, |
| 300 |
|
@ARTICLE{Batcho2001, |
| 301 |
|
author = {P. F. Batcho and T. Schlick}, |
| 302 |
|
title = {Special stability advantages of position-Verlet over velocity-Verlet |
| 303 |
< |
in multiple-time step integration}, |
| 303 |
> |
in multiple-time step integration}, |
| 304 |
|
journal = {Journal of Chemical Physics}, |
| 305 |
|
year = {2001}, |
| 306 |
|
volume = {115}, |
| 308 |
|
number = {9}, |
| 309 |
|
month = {Sep 1}, |
| 310 |
|
abstract = {We present an analysis for a simple two-component harmonic oscillator |
| 311 |
< |
that compares the use of position-Verlet to velocity-Verlet for |
| 312 |
< |
multiple-time step integration. The numerical stability analysis |
| 313 |
< |
based on the impulse-Verlet splitting shows that position-Verlet |
| 314 |
< |
has enhanced stability, in terms of the largest allowable time step, |
| 315 |
< |
for cases where an ample separation of time scales exists. Numerical |
| 316 |
< |
investigations confirm the advantages of the position-Verlet scheme |
| 317 |
< |
when used for the fastest time scales of the system. Applications |
| 318 |
< |
to a biomolecule. a solvated protein, for both Newtonian and Langevin |
| 319 |
< |
dynamics echo these trends over large outer time-step regimes. (C) |
| 320 |
< |
2001 American Institute of Physics.}, |
| 311 |
> |
that compares the use of position-Verlet to velocity-Verlet for |
| 312 |
> |
multiple-time step integration. The numerical stability analysis |
| 313 |
> |
based on the impulse-Verlet splitting shows that position-Verlet |
| 314 |
> |
has enhanced stability, in terms of the largest allowable time step, |
| 315 |
> |
for cases where an ample separation of time scales exists. Numerical |
| 316 |
> |
investigations confirm the advantages of the position-Verlet scheme |
| 317 |
> |
when used for the fastest time scales of the system. Applications |
| 318 |
> |
to a biomolecule. a solvated protein, for both Newtonian and Langevin |
| 319 |
> |
dynamics echo these trends over large outer time-step regimes. (C) |
| 320 |
> |
2001 American Institute of Physics.}, |
| 321 |
|
annote = {469KV Times Cited:6 Cited References Count:30}, |
| 322 |
|
issn = {0021-9606}, |
| 323 |
|
uri = {<Go to ISI>://000170813800005}, |
| 326 |
|
@ARTICLE{Bates2005, |
| 327 |
|
author = {M. A. Bates and G. R. Luckhurst}, |
| 328 |
|
title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation |
| 329 |
< |
study}, |
| 329 |
> |
study}, |
| 330 |
|
journal = {Physical Review E}, |
| 331 |
|
year = {2005}, |
| 332 |
|
volume = {72}, |
| 334 |
|
number = {5}, |
| 335 |
|
month = {Nov}, |
| 336 |
|
abstract = {Inspired by recent claims that compounds composed of V-shaped molecules |
| 337 |
< |
can exhibit the elusive biaxial nematic phase, we have developed |
| 338 |
< |
a generic simulation model for such systems. This contains the features |
| 339 |
< |
of the molecule that are essential to its liquid crystal behavior, |
| 340 |
< |
namely the anisotropies of the two arms and the angle between them. |
| 341 |
< |
The behavior of the model has been investigated using Monte Carlo |
| 342 |
< |
simulations for a wide range of these structural parameters. This |
| 343 |
< |
allows us to establish the relationship between the V-shaped molecule |
| 344 |
< |
and its ability to form a biaxial nematic phase. Of particular importance |
| 345 |
< |
are the criteria of geometry and the relative anisotropy necessary |
| 346 |
< |
for the system to exhibit a Landau point, at which the biaxial nematic |
| 347 |
< |
is formed directly from the isotropic phase. The simulations have |
| 348 |
< |
also been used to determine the orientational order parameters for |
| 349 |
< |
a selection of molecular axes. These are especially important because |
| 350 |
< |
they reveal the phase symmetry and are connected to the experimental |
| 351 |
< |
determination of this. The simulation results show that, whereas |
| 352 |
< |
some positions are extremely sensitive to the phase biaxiality, |
| 353 |
< |
others are totally blind to this.}, |
| 337 |
> |
can exhibit the elusive biaxial nematic phase, we have developed |
| 338 |
> |
a generic simulation model for such systems. This contains the features |
| 339 |
> |
of the molecule that are essential to its liquid crystal behavior, |
| 340 |
> |
namely the anisotropies of the two arms and the angle between them. |
| 341 |
> |
The behavior of the model has been investigated using Monte Carlo |
| 342 |
> |
simulations for a wide range of these structural parameters. This |
| 343 |
> |
allows us to establish the relationship between the V-shaped molecule |
| 344 |
> |
and its ability to form a biaxial nematic phase. Of particular importance |
| 345 |
> |
are the criteria of geometry and the relative anisotropy necessary |
| 346 |
> |
for the system to exhibit a Landau point, at which the biaxial nematic |
| 347 |
> |
is formed directly from the isotropic phase. The simulations have |
| 348 |
> |
also been used to determine the orientational order parameters for |
| 349 |
> |
a selection of molecular axes. These are especially important because |
| 350 |
> |
they reveal the phase symmetry and are connected to the experimental |
| 351 |
> |
determination of this. The simulation results show that, whereas |
| 352 |
> |
some positions are extremely sensitive to the phase biaxiality, |
| 353 |
> |
others are totally blind to this.}, |
| 354 |
|
annote = {Part 1 988LQ Times Cited:0 Cited References Count:38}, |
| 355 |
|
issn = {1539-3755}, |
| 356 |
|
uri = {<Go to ISI>://000233603100030}, |
| 366 |
|
number = {5}, |
| 367 |
|
month = {Nov 1}, |
| 368 |
|
abstract = {We introduce an unbiased protocol for performing rotational moves |
| 369 |
< |
in rigid-body dynamics simulations. This approach - based on the |
| 370 |
< |
analytic solution for the rotational equations of motion for an |
| 371 |
< |
orthogonal coordinate system at constant angular velocity - removes |
| 372 |
< |
deficiencies that have been largely ignored in Brownian dynamics |
| 373 |
< |
simulations, namely errors for finite rotations that result from |
| 374 |
< |
applying the noncommuting rotational matrices in an arbitrary order. |
| 375 |
< |
Our algorithm should thus replace standard approaches to rotate |
| 376 |
< |
local coordinate frames in Langevin and Brownian dynamics simulations.}, |
| 369 |
> |
in rigid-body dynamics simulations. This approach - based on the |
| 370 |
> |
analytic solution for the rotational equations of motion for an |
| 371 |
> |
orthogonal coordinate system at constant angular velocity - removes |
| 372 |
> |
deficiencies that have been largely ignored in Brownian dynamics |
| 373 |
> |
simulations, namely errors for finite rotations that result from |
| 374 |
> |
applying the noncommuting rotational matrices in an arbitrary order. |
| 375 |
> |
Our algorithm should thus replace standard approaches to rotate |
| 376 |
> |
local coordinate frames in Langevin and Brownian dynamics simulations.}, |
| 377 |
|
annote = {736UA Times Cited:0 Cited References Count:11}, |
| 378 |
|
issn = {0006-3495}, |
| 379 |
|
uri = {<Go to ISI>://000186190500018}, |
| 382 |
|
@ARTICLE{Beloborodov1998, |
| 383 |
|
author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev}, |
| 384 |
|
title = {Effect of coupling between rotational and translational Brownian |
| 385 |
< |
motions on NMR spin relaxation: Consideration using green function |
| 386 |
< |
of rigid body diffusion}, |
| 385 |
> |
motions on NMR spin relaxation: Consideration using green function |
| 386 |
> |
of rigid body diffusion}, |
| 387 |
|
journal = {Journal of Magnetic Resonance}, |
| 388 |
|
year = {1998}, |
| 389 |
|
volume = {132}, |
| 391 |
|
number = {2}, |
| 392 |
|
month = {Jun}, |
| 393 |
|
abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein, |
| 394 |
< |
Biopolymers 33, 409-436, 1993), it was analytically shown that coupling |
| 395 |
< |
between translation and rotation diffusion degrees of freedom does |
| 396 |
< |
not affect the correlation functions relevant to the NMR intramolecular |
| 397 |
< |
relaxation. It follows that spectral densities usually used for |
| 398 |
< |
the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37, |
| 399 |
< |
647-654, 1962) can be regarded as exact in respect to the rotation-translation |
| 400 |
< |
coupling for the spin system connected with a rigid body. (C) 1998 |
| 401 |
< |
Academic Press.}, |
| 394 |
> |
Biopolymers 33, 409-436, 1993), it was analytically shown that coupling |
| 395 |
> |
between translation and rotation diffusion degrees of freedom does |
| 396 |
> |
not affect the correlation functions relevant to the NMR intramolecular |
| 397 |
> |
relaxation. It follows that spectral densities usually used for |
| 398 |
> |
the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37, |
| 399 |
> |
647-654, 1962) can be regarded as exact in respect to the rotation-translation |
| 400 |
> |
coupling for the spin system connected with a rigid body. (C) 1998 |
| 401 |
> |
Academic Press.}, |
| 402 |
|
annote = {Zu605 Times Cited:2 Cited References Count:6}, |
| 403 |
|
issn = {1090-7807}, |
| 404 |
|
uri = {<Go to ISI>://000074214800017}, |
| 407 |
|
@ARTICLE{Berardi1996, |
| 408 |
|
author = {R. Berardi and S. Orlandi and C. Zannoni}, |
| 409 |
|
title = {Antiphase structures in polar smectic liquid crystals and their molecular |
| 410 |
< |
origin}, |
| 410 |
> |
origin}, |
| 411 |
|
journal = {Chemical Physics Letters}, |
| 412 |
|
year = {1996}, |
| 413 |
|
volume = {261}, |
| 415 |
|
number = {3}, |
| 416 |
|
month = {Oct 18}, |
| 417 |
|
abstract = {We demonstrate that the overall molecular dipole organization in a |
| 418 |
< |
smectic liquid crystal formed of polar molecules can be strongly |
| 419 |
< |
influenced by the position of the dipole in the molecule. We study |
| 420 |
< |
by large scale Monte Carlo simulations systems of attractive-repulsive |
| 421 |
< |
''Gay-Berne'' elongated ellipsoids with an axial dipole at the center |
| 422 |
< |
or near the end of the molecule and we show that monolayer smectic |
| 423 |
< |
liquid crystals and modulated antiferroelectric bilayer stripe domains |
| 424 |
< |
similar to the experimentally observed ''antiphase'' structures |
| 425 |
< |
are obtained in the two cases.}, |
| 418 |
> |
smectic liquid crystal formed of polar molecules can be strongly |
| 419 |
> |
influenced by the position of the dipole in the molecule. We study |
| 420 |
> |
by large scale Monte Carlo simulations systems of attractive-repulsive |
| 421 |
> |
''Gay-Berne'' elongated ellipsoids with an axial dipole at the center |
| 422 |
> |
or near the end of the molecule and we show that monolayer smectic |
| 423 |
> |
liquid crystals and modulated antiferroelectric bilayer stripe domains |
| 424 |
> |
similar to the experimentally observed ''antiphase'' structures |
| 425 |
> |
are obtained in the two cases.}, |
| 426 |
|
annote = {Vn637 Times Cited:49 Cited References Count:26}, |
| 427 |
|
issn = {0009-2614}, |
| 428 |
|
uri = {<Go to ISI>://A1996VN63700023}, |
| 431 |
|
@ARTICLE{Berkov2005, |
| 432 |
|
author = {D. V. Berkov and N. L. Gorn}, |
| 433 |
|
title = {Magnetization precession due to a spin-polarized current in a thin |
| 434 |
< |
nanoelement: Numerical simulation study}, |
| 434 |
> |
nanoelement: Numerical simulation study}, |
| 435 |
|
journal = {Physical Review B}, |
| 436 |
|
year = {2005}, |
| 437 |
|
volume = {72}, |
| 439 |
|
number = {9}, |
| 440 |
|
month = {Sep}, |
| 441 |
|
abstract = {In this paper a detailed numerical study (in frames of the Slonczewski |
| 442 |
< |
formalism) of magnetization oscillations driven by a spin-polarized |
| 443 |
< |
current through a thin elliptical nanoelement is presented. We show |
| 444 |
< |
that a sophisticated micromagnetic model, where a polycrystalline |
| 445 |
< |
structure of a nanoelement is taken into account, can explain qualitatively |
| 446 |
< |
all most important features of the magnetization oscillation spectra |
| 447 |
< |
recently observed experimentally [S. I. Kiselev , Nature 425, 380 |
| 448 |
< |
(2003)], namely, existence of several equidistant spectral bands, |
| 449 |
< |
sharp onset and abrupt disappearance of magnetization oscillations |
| 450 |
< |
with increasing current, absence of the out-of-plane regime predicted |
| 451 |
< |
by a macrospin model, and the relation between frequencies of so-called |
| 452 |
< |
small-angle and quasichaotic oscillations. However, a quantitative |
| 453 |
< |
agreement with experimental results (especially concerning the frequency |
| 454 |
< |
of quasichaotic oscillations) could not be achieved in the region |
| 455 |
< |
of reasonable parameter values, indicating that further model refinement |
| 456 |
< |
is necessary for a complete understanding of the spin-driven magnetization |
| 457 |
< |
precession even in this relatively simple experimental situation.}, |
| 442 |
> |
formalism) of magnetization oscillations driven by a spin-polarized |
| 443 |
> |
current through a thin elliptical nanoelement is presented. We show |
| 444 |
> |
that a sophisticated micromagnetic model, where a polycrystalline |
| 445 |
> |
structure of a nanoelement is taken into account, can explain qualitatively |
| 446 |
> |
all most important features of the magnetization oscillation spectra |
| 447 |
> |
recently observed experimentally [S. I. Kiselev , Nature 425, 380 |
| 448 |
> |
(2003)], namely, existence of several equidistant spectral bands, |
| 449 |
> |
sharp onset and abrupt disappearance of magnetization oscillations |
| 450 |
> |
with increasing current, absence of the out-of-plane regime predicted |
| 451 |
> |
by a macrospin model, and the relation between frequencies of so-called |
| 452 |
> |
small-angle and quasichaotic oscillations. However, a quantitative |
| 453 |
> |
agreement with experimental results (especially concerning the frequency |
| 454 |
> |
of quasichaotic oscillations) could not be achieved in the region |
| 455 |
> |
of reasonable parameter values, indicating that further model refinement |
| 456 |
> |
is necessary for a complete understanding of the spin-driven magnetization |
| 457 |
> |
precession even in this relatively simple experimental situation.}, |
| 458 |
|
annote = {969IT Times Cited:2 Cited References Count:55}, |
| 459 |
|
issn = {1098-0121}, |
| 460 |
|
uri = {<Go to ISI>://000232228500058}, |
| 463 |
|
@ARTICLE{Berkov2005a, |
| 464 |
|
author = {D. V. Berkov and N. L. Gorn}, |
| 465 |
|
title = {Stochastic dynamic simulations of fast remagnetization processes: |
| 466 |
< |
recent advances and applications}, |
| 466 |
> |
recent advances and applications}, |
| 467 |
|
journal = {Journal of Magnetism and Magnetic Materials}, |
| 468 |
|
year = {2005}, |
| 469 |
|
volume = {290}, |
| 470 |
|
pages = {442-448}, |
| 471 |
|
month = {Apr}, |
| 472 |
|
abstract = {Numerical simulations of fast remagnetization processes using stochastic |
| 473 |
< |
dynamics are widely used to study various magnetic systems. In this |
| 474 |
< |
paper, we first address several crucial methodological problems |
| 475 |
< |
of such simulations: (i) the influence of finite-element discretization |
| 476 |
< |
on simulated dynamics, (ii) choice between Ito and Stratonovich |
| 477 |
< |
stochastic calculi by the solution of micromagnetic stochastic equations |
| 478 |
< |
of motion and (iii) non-trivial correlation properties of the random |
| 479 |
< |
(thermal) field. Next, we discuss several examples to demonstrate |
| 480 |
< |
the great potential of the Langevin dynamics for studying fast remagnetization |
| 481 |
< |
processes in technically relevant applications: we present numerical |
| 482 |
< |
analysis of equilibrium magnon spectra in patterned structures, |
| 483 |
< |
study thermal noise effects on the magnetization dynamics of nanoelements |
| 484 |
< |
in pulsed fields and show some results for a remagnetization dynamics |
| 485 |
< |
induced by a spin-polarized current. (c) 2004 Elsevier B.V. All |
| 486 |
< |
rights reserved.}, |
| 473 |
> |
dynamics are widely used to study various magnetic systems. In this |
| 474 |
> |
paper, we first address several crucial methodological problems |
| 475 |
> |
of such simulations: (i) the influence of finite-element discretization |
| 476 |
> |
on simulated dynamics, (ii) choice between Ito and Stratonovich |
| 477 |
> |
stochastic calculi by the solution of micromagnetic stochastic equations |
| 478 |
> |
of motion and (iii) non-trivial correlation properties of the random |
| 479 |
> |
(thermal) field. Next, we discuss several examples to demonstrate |
| 480 |
> |
the great potential of the Langevin dynamics for studying fast remagnetization |
| 481 |
> |
processes in technically relevant applications: we present numerical |
| 482 |
> |
analysis of equilibrium magnon spectra in patterned structures, |
| 483 |
> |
study thermal noise effects on the magnetization dynamics of nanoelements |
| 484 |
> |
in pulsed fields and show some results for a remagnetization dynamics |
| 485 |
> |
induced by a spin-polarized current. (c) 2004 Elsevier B.V. All |
| 486 |
> |
rights reserved.}, |
| 487 |
|
annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25}, |
| 488 |
|
issn = {0304-8853}, |
| 489 |
|
uri = {<Go to ISI>://000228837600109}, |
| 492 |
|
@ARTICLE{Berkov2002, |
| 493 |
|
author = {D. V. Berkov and N. L. Gorn and P. Gornert}, |
| 494 |
|
title = {Magnetization dynamics in nanoparticle systems: Numerical simulation |
| 495 |
< |
using Langevin dynamics}, |
| 495 |
> |
using Langevin dynamics}, |
| 496 |
|
journal = {Physica Status Solidi a-Applied Research}, |
| 497 |
|
year = {2002}, |
| 498 |
|
volume = {189}, |
| 500 |
|
number = {2}, |
| 501 |
|
month = {Feb 16}, |
| 502 |
|
abstract = {We report on recent progress achieved by the development of numerical |
| 503 |
< |
methods based on the stochastic (Langevin) dynamics applied to systems |
| 504 |
< |
of interacting magnetic nanoparticles. The method enables direct |
| 505 |
< |
simulations of the trajectories of magnetic moments taking into |
| 506 |
< |
account (i) all relevant interactions, (ii) precession dynamics, |
| 507 |
< |
and (iii) temperature fluctuations included via the random (thermal) |
| 508 |
< |
field. We present several novel results obtained using new methods |
| 509 |
< |
developed for the solution of the Langevin equations. In particular, |
| 510 |
< |
we have investigated magnetic nanodots and disordered granular systems |
| 511 |
< |
of single-domain magnetic particles. For the first case we have |
| 512 |
< |
calculated the spectrum and the spatial distribution of spin excitations. |
| 513 |
< |
For the second system the complex ac susceptibility chi(omega, T) |
| 514 |
< |
for various particle concentrations and particle anisotropies were |
| 515 |
< |
computed and compared with numerous experimental results.}, |
| 503 |
> |
methods based on the stochastic (Langevin) dynamics applied to systems |
| 504 |
> |
of interacting magnetic nanoparticles. The method enables direct |
| 505 |
> |
simulations of the trajectories of magnetic moments taking into |
| 506 |
> |
account (i) all relevant interactions, (ii) precession dynamics, |
| 507 |
> |
and (iii) temperature fluctuations included via the random (thermal) |
| 508 |
> |
field. We present several novel results obtained using new methods |
| 509 |
> |
developed for the solution of the Langevin equations. In particular, |
| 510 |
> |
we have investigated magnetic nanodots and disordered granular systems |
| 511 |
> |
of single-domain magnetic particles. For the first case we have |
| 512 |
> |
calculated the spectrum and the spatial distribution of spin excitations. |
| 513 |
> |
For the second system the complex ac susceptibility chi(omega, T) |
| 514 |
> |
for various particle concentrations and particle anisotropies were |
| 515 |
> |
computed and compared with numerous experimental results.}, |
| 516 |
|
annote = {526TF Times Cited:4 Cited References Count:37}, |
| 517 |
|
issn = {0031-8965}, |
| 518 |
|
uri = {<Go to ISI>://000174145200026}, |
| 521 |
|
@ARTICLE{Bernal1980, |
| 522 |
|
author = {J.M. Bernal and J. G. {de la Torre}}, |
| 523 |
|
title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules |
| 524 |
< |
with Arbitrary Shape}, |
| 524 |
> |
with Arbitrary Shape}, |
| 525 |
|
journal = {Biopolymers}, |
| 526 |
|
year = {1980}, |
| 527 |
|
volume = {19}, |
| 528 |
|
pages = {751-766}, |
| 529 |
|
} |
| 530 |
|
|
| 531 |
+ |
@ARTICLE{Brenner1967, |
| 532 |
+ |
author = {H. Brenner }, |
| 533 |
+ |
title = {Coupling between the Translational and Rotational Brownian Motions |
| 534 |
+ |
of Rigid Particles of Arbitrary shape}, |
| 535 |
+ |
journal = {J. Collid. Int. Sci.}, |
| 536 |
+ |
year = {1967}, |
| 537 |
+ |
volume = {23}, |
| 538 |
+ |
pages = {407-436}, |
| 539 |
+ |
} |
| 540 |
+ |
|
| 541 |
+ |
@ARTICLE{Brooks1983, |
| 542 |
+ |
author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States |
| 543 |
+ |
and S. Swaminathan and M. Karplus}, |
| 544 |
+ |
title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics |
| 545 |
+ |
Calculations}, |
| 546 |
+ |
journal = {Journal of Computational Chemistry}, |
| 547 |
+ |
year = {1983}, |
| 548 |
+ |
volume = {4}, |
| 549 |
+ |
pages = {187-217}, |
| 550 |
+ |
number = {2}, |
| 551 |
+ |
annote = {Qp423 Times Cited:6414 Cited References Count:96}, |
| 552 |
+ |
issn = {0192-8651}, |
| 553 |
+ |
uri = {<Go to ISI>://A1983QP42300010}, |
| 554 |
+ |
} |
| 555 |
+ |
|
| 556 |
|
@ARTICLE{Brunger1984, |
| 557 |
|
author = {A. Brunger and C. L. Brooks and M. Karplus}, |
| 558 |
|
title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations |
| 559 |
< |
of St2 Water}, |
| 559 |
> |
of St2 Water}, |
| 560 |
|
journal = {Chemical Physics Letters}, |
| 561 |
|
year = {1984}, |
| 562 |
|
volume = {105}, |
| 570 |
|
@ARTICLE{Budd1999, |
| 571 |
|
author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell}, |
| 572 |
|
title = {Self-similar numerical solutions of the porous-medium equation using |
| 573 |
< |
moving mesh methods}, |
| 573 |
> |
moving mesh methods}, |
| 574 |
|
journal = {Philosophical Transactions of the Royal Society of London Series |
| 575 |
< |
a-Mathematical Physical and Engineering Sciences}, |
| 575 |
> |
a-Mathematical Physical and Engineering Sciences}, |
| 576 |
|
year = {1999}, |
| 577 |
|
volume = {357}, |
| 578 |
|
pages = {1047-1077}, |
| 579 |
|
number = {1754}, |
| 580 |
|
month = {Apr 15}, |
| 581 |
|
abstract = {This paper examines a synthesis of adaptive mesh methods with the |
| 582 |
< |
use of symmetry to study a partial differential equation. In particular, |
| 583 |
< |
it considers methods which admit discrete self-similar solutions, |
| 584 |
< |
examining the convergence of these to the true self-similar solution |
| 585 |
< |
as well as their stability. Special attention is given to the nonlinear |
| 586 |
< |
diffusion equation describing flow in a porous medium.}, |
| 582 |
> |
use of symmetry to study a partial differential equation. In particular, |
| 583 |
> |
it considers methods which admit discrete self-similar solutions, |
| 584 |
> |
examining the convergence of these to the true self-similar solution |
| 585 |
> |
as well as their stability. Special attention is given to the nonlinear |
| 586 |
> |
diffusion equation describing flow in a porous medium.}, |
| 587 |
|
annote = {199EE Times Cited:4 Cited References Count:14}, |
| 588 |
|
issn = {1364-503X}, |
| 589 |
|
uri = {<Go to ISI>://000080466800005}, |
| 599 |
|
number = {21}, |
| 600 |
|
month = {Dec 1}, |
| 601 |
|
abstract = {Fluids of hard bent-core molecules have been studied using theory |
| 602 |
< |
and computer simulation. The molecules are composed of two hard |
| 603 |
< |
spherocylinders, with length-to-breadth ratio L/D, joined by their |
| 604 |
< |
ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20 |
| 605 |
< |
degrees, the simulations show isotropic, nematic, smectic, and solid |
| 606 |
< |
phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic, |
| 607 |
< |
and solid phases are in evidence, which suggests that there is a |
| 608 |
< |
nematic-smectic-solid triple point at an angle in the range 20 degrees |
| 609 |
< |
< gamma < 30 degrees. In all of the orientationally ordered fluid |
| 610 |
< |
phases the order is purely uniaxial. For gamma = 10 degrees and |
| 611 |
< |
20 degrees, at the studied densities, the solid is also uniaxially |
| 612 |
< |
ordered, whilst for gamma = 30 degrees the solid layers are biaxially |
| 613 |
< |
ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find |
| 614 |
< |
no spontaneous orientational ordering. This is shown to be due to |
| 615 |
< |
the interlocking of dimer pairs which precludes alignment. We find |
| 616 |
< |
similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial |
| 617 |
< |
nematic transition is predicted by Onsager theory. Simulations in |
| 618 |
< |
the biaxial nematic phase show it to be at least mechanically stable |
| 619 |
< |
with respect to the isotropic phase, however. We have compared the |
| 620 |
< |
quasi-exact simulation results in the isotropic phase with the predicted |
| 621 |
< |
equations of state from three theories: the virial expansion containing |
| 622 |
< |
the second and third virial coefficients; the Parsons-Lee equation |
| 623 |
< |
of state; an application of Wertheim's theory of associating fluids |
| 624 |
< |
in the limit of infinite attractive association energy. For all |
| 625 |
< |
of the molecule elongations and geometries we have simulated, the |
| 626 |
< |
Wertheim theory proved to be the most accurate. Interestingly, the |
| 627 |
< |
isotropic equation of state is virtually independent of the dimer |
| 628 |
< |
bond angle-a feature that is also reflected in the lack of variation |
| 629 |
< |
with angle of the calculated second and third virial coefficients. |
| 630 |
< |
(C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].}, |
| 602 |
> |
and computer simulation. The molecules are composed of two hard |
| 603 |
> |
spherocylinders, with length-to-breadth ratio L/D, joined by their |
| 604 |
> |
ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20 |
| 605 |
> |
degrees, the simulations show isotropic, nematic, smectic, and solid |
| 606 |
> |
phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic, |
| 607 |
> |
and solid phases are in evidence, which suggests that there is a |
| 608 |
> |
nematic-smectic-solid triple point at an angle in the range 20 degrees |
| 609 |
> |
< gamma < 30 degrees. In all of the orientationally ordered fluid |
| 610 |
> |
phases the order is purely uniaxial. For gamma = 10 degrees and |
| 611 |
> |
20 degrees, at the studied densities, the solid is also uniaxially |
| 612 |
> |
ordered, whilst for gamma = 30 degrees the solid layers are biaxially |
| 613 |
> |
ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find |
| 614 |
> |
no spontaneous orientational ordering. This is shown to be due to |
| 615 |
> |
the interlocking of dimer pairs which precludes alignment. We find |
| 616 |
> |
similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial |
| 617 |
> |
nematic transition is predicted by Onsager theory. Simulations in |
| 618 |
> |
the biaxial nematic phase show it to be at least mechanically stable |
| 619 |
> |
with respect to the isotropic phase, however. We have compared the |
| 620 |
> |
quasi-exact simulation results in the isotropic phase with the predicted |
| 621 |
> |
equations of state from three theories: the virial expansion containing |
| 622 |
> |
the second and third virial coefficients; the Parsons-Lee equation |
| 623 |
> |
of state; an application of Wertheim's theory of associating fluids |
| 624 |
> |
in the limit of infinite attractive association energy. For all |
| 625 |
> |
of the molecule elongations and geometries we have simulated, the |
| 626 |
> |
Wertheim theory proved to be the most accurate. Interestingly, the |
| 627 |
> |
isotropic equation of state is virtually independent of the dimer |
| 628 |
> |
bond angle-a feature that is also reflected in the lack of variation |
| 629 |
> |
with angle of the calculated second and third virial coefficients. |
| 630 |
> |
(C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].}, |
| 631 |
|
annote = {255TC Times Cited:24 Cited References Count:38}, |
| 632 |
|
issn = {0021-9606}, |
| 633 |
|
uri = {<Go to ISI>://000083685400056}, |
| 643 |
|
number = {11}, |
| 644 |
|
month = {Nov}, |
| 645 |
|
abstract = {A review is presented of molecular and mesoscopic computer simulations |
| 646 |
< |
of liquid crystalline systems. Molecular simulation approaches applied |
| 647 |
< |
to such systems are described, and the key findings for bulk phase |
| 648 |
< |
behaviour are reported. Following this, recently developed lattice |
| 649 |
< |
Boltzmann approaches to the mesoscale modelling of nemato-dynanics |
| 650 |
< |
are reviewed. This paper concludes with a discussion of possible |
| 651 |
< |
areas for future development in this field.}, |
| 646 |
> |
of liquid crystalline systems. Molecular simulation approaches applied |
| 647 |
> |
to such systems are described, and the key findings for bulk phase |
| 648 |
> |
behaviour are reported. Following this, recently developed lattice |
| 649 |
> |
Boltzmann approaches to the mesoscale modelling of nemato-dynanics |
| 650 |
> |
are reviewed. This paper concludes with a discussion of possible |
| 651 |
> |
areas for future development in this field.}, |
| 652 |
|
annote = {989TU Times Cited:2 Cited References Count:258}, |
| 653 |
|
issn = {0034-4885}, |
| 654 |
|
uri = {<Go to ISI>://000233697600004}, |
| 657 |
|
@ARTICLE{Carrasco1999, |
| 658 |
|
author = {B. Carrasco and J. G. {de la Torre}}, |
| 659 |
|
title = {Hydrodynamic properties of rigid particles: Comparison of different |
| 660 |
< |
modeling and computational procedures}, |
| 660 |
> |
modeling and computational procedures}, |
| 661 |
|
journal = {Biophysical Journal}, |
| 662 |
|
year = {1999}, |
| 663 |
|
volume = {76}, |
| 665 |
|
number = {6}, |
| 666 |
|
month = {Jun}, |
| 667 |
|
abstract = {The hydrodynamic properties of rigid particles are calculated from |
| 668 |
< |
models composed of spherical elements (beads) using theories developed |
| 669 |
< |
by Kirkwood, Bloomfield, and their coworkers. Bead models have usually |
| 670 |
< |
been built in such a way that the beads fill the volume occupied |
| 671 |
< |
by the particles. Sometimes the beads are few and of varying sizes |
| 672 |
< |
(bead models in the strict sense), and other times there are many |
| 673 |
< |
small beads (filling models). Because hydrodynamic friction takes |
| 674 |
< |
place at the molecular surface, another possibility is to use shell |
| 675 |
< |
models, as originally proposed by Bloomfield. In this work, we have |
| 676 |
< |
developed procedures to build models of the various kinds, and we |
| 677 |
< |
describe the theory and methods for calculating their hydrodynamic |
| 678 |
< |
properties, including approximate methods that may be needed to |
| 679 |
< |
treat models with a very large number of elements. By combining |
| 680 |
< |
the various possibilities of model building and hydrodynamic calculation, |
| 681 |
< |
several strategies can be designed. We have made a quantitative |
| 682 |
< |
comparison of the performance of the various strategies by applying |
| 683 |
< |
them to some test cases, for which the properties are known a priori. |
| 684 |
< |
We provide guidelines and computational tools for bead modeling.}, |
| 668 |
> |
models composed of spherical elements (beads) using theories developed |
| 669 |
> |
by Kirkwood, Bloomfield, and their coworkers. Bead models have usually |
| 670 |
> |
been built in such a way that the beads fill the volume occupied |
| 671 |
> |
by the particles. Sometimes the beads are few and of varying sizes |
| 672 |
> |
(bead models in the strict sense), and other times there are many |
| 673 |
> |
small beads (filling models). Because hydrodynamic friction takes |
| 674 |
> |
place at the molecular surface, another possibility is to use shell |
| 675 |
> |
models, as originally proposed by Bloomfield. In this work, we have |
| 676 |
> |
developed procedures to build models of the various kinds, and we |
| 677 |
> |
describe the theory and methods for calculating their hydrodynamic |
| 678 |
> |
properties, including approximate methods that may be needed to |
| 679 |
> |
treat models with a very large number of elements. By combining |
| 680 |
> |
the various possibilities of model building and hydrodynamic calculation, |
| 681 |
> |
several strategies can be designed. We have made a quantitative |
| 682 |
> |
comparison of the performance of the various strategies by applying |
| 683 |
> |
them to some test cases, for which the properties are known a priori. |
| 684 |
> |
We provide guidelines and computational tools for bead modeling.}, |
| 685 |
|
annote = {200TT Times Cited:46 Cited References Count:57}, |
| 686 |
|
issn = {0006-3495}, |
| 687 |
|
uri = {<Go to ISI>://000080556700016}, |
| 690 |
|
@ARTICLE{Chandra1999, |
| 691 |
|
author = {A. Chandra and T. Ichiye}, |
| 692 |
|
title = {Dynamical properties of the soft sticky dipole model of water: Molecular |
| 693 |
< |
dynamics simulations}, |
| 693 |
> |
dynamics simulations}, |
| 694 |
|
journal = {Journal of Chemical Physics}, |
| 695 |
|
year = {1999}, |
| 696 |
|
volume = {111}, |
| 698 |
|
number = {6}, |
| 699 |
|
month = {Aug 8}, |
| 700 |
|
abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water |
| 701 |
< |
are calculated by means of molecular dynamics simulations. Since |
| 702 |
< |
this is not a simple point model, the forces and torques arising |
| 703 |
< |
from the SSD potential are derived here. Simulations are carried |
| 704 |
< |
out in the microcanonical ensemble employing the Ewald method for |
| 705 |
< |
the electrostatic interactions. Various time correlation functions |
| 706 |
< |
and dynamical quantities associated with the translational and rotational |
| 707 |
< |
motion of water molecules are evaluated and compared with those |
| 708 |
< |
of two other commonly used models of liquid water, namely the transferable |
| 709 |
< |
intermolecular potential-three points (TIP3P) and simple point charge/extended |
| 710 |
< |
(SPC/E) models, and also with experiments. The dynamical properties |
| 711 |
< |
of the SSD water model are found to be in good agreement with the |
| 712 |
< |
experimental results and appear to be better than the TIP3P and |
| 713 |
< |
SPC/E models in most cases, as has been previously shown for its |
| 714 |
< |
thermodynamic, structural, and dielectric properties. Also, molecular |
| 715 |
< |
dynamics simulations of the SSD model are found to run much faster |
| 716 |
< |
than TIP3P, SPC/E, and other multisite models. (C) 1999 American |
| 717 |
< |
Institute of Physics. [S0021-9606(99)51430-X].}, |
| 701 |
> |
are calculated by means of molecular dynamics simulations. Since |
| 702 |
> |
this is not a simple point model, the forces and torques arising |
| 703 |
> |
from the SSD potential are derived here. Simulations are carried |
| 704 |
> |
out in the microcanonical ensemble employing the Ewald method for |
| 705 |
> |
the electrostatic interactions. Various time correlation functions |
| 706 |
> |
and dynamical quantities associated with the translational and rotational |
| 707 |
> |
motion of water molecules are evaluated and compared with those |
| 708 |
> |
of two other commonly used models of liquid water, namely the transferable |
| 709 |
> |
intermolecular potential-three points (TIP3P) and simple point charge/extended |
| 710 |
> |
(SPC/E) models, and also with experiments. The dynamical properties |
| 711 |
> |
of the SSD water model are found to be in good agreement with the |
| 712 |
> |
experimental results and appear to be better than the TIP3P and |
| 713 |
> |
SPC/E models in most cases, as has been previously shown for its |
| 714 |
> |
thermodynamic, structural, and dielectric properties. Also, molecular |
| 715 |
> |
dynamics simulations of the SSD model are found to run much faster |
| 716 |
> |
than TIP3P, SPC/E, and other multisite models. (C) 1999 American |
| 717 |
> |
Institute of Physics. [S0021-9606(99)51430-X].}, |
| 718 |
|
annote = {221EN Times Cited:14 Cited References Count:66}, |
| 719 |
|
issn = {0021-9606}, |
| 720 |
|
uri = {<Go to ISI>://000081711200038}, |
| 744 |
|
number = {1-2}, |
| 745 |
|
month = {Jan}, |
| 746 |
|
abstract = {We investigate the asymptotic behavior of systems of nonlinear differential |
| 747 |
< |
equations and introduce a family of mixed methods from combinations |
| 748 |
< |
of explicit Runge-Kutta methods. These methods have better stability |
| 749 |
< |
behavior than traditional Runge-Kutta methods and generally extend |
| 750 |
< |
the range of validity of the calculated solutions. These methods |
| 751 |
< |
also give a way of determining if the numerical solutions are real |
| 752 |
< |
or spurious. Emphasis is put on examples coming from mathematical |
| 753 |
< |
models in ecology. (C) 2002 IMACS. Published by Elsevier Science |
| 754 |
< |
B.V. All rights reserved.}, |
| 747 |
> |
equations and introduce a family of mixed methods from combinations |
| 748 |
> |
of explicit Runge-Kutta methods. These methods have better stability |
| 749 |
> |
behavior than traditional Runge-Kutta methods and generally extend |
| 750 |
> |
the range of validity of the calculated solutions. These methods |
| 751 |
> |
also give a way of determining if the numerical solutions are real |
| 752 |
> |
or spurious. Emphasis is put on examples coming from mathematical |
| 753 |
> |
models in ecology. (C) 2002 IMACS. Published by Elsevier Science |
| 754 |
> |
B.V. All rights reserved.}, |
| 755 |
|
annote = {633ZD Times Cited:0 Cited References Count:9}, |
| 756 |
|
issn = {0168-9274}, |
| 757 |
|
uri = {<Go to ISI>://000180314200002}, |
| 760 |
|
@ARTICLE{Cheung2004, |
| 761 |
|
author = {D. L. Cheung and S. J. Clark and M. R. Wilson}, |
| 762 |
|
title = {Calculation of flexoelectric coefficients for a nematic liquid crystal |
| 763 |
< |
by atomistic simulation}, |
| 763 |
> |
by atomistic simulation}, |
| 764 |
|
journal = {Journal of Chemical Physics}, |
| 765 |
|
year = {2004}, |
| 766 |
|
volume = {121}, |
| 768 |
|
number = {18}, |
| 769 |
|
month = {Nov 8}, |
| 770 |
|
abstract = {Equilibrium molecular dynamics calculations have been performed for |
| 771 |
< |
the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile |
| 772 |
< |
(PCH5) using a fully atomistic model. Simulation data have been |
| 773 |
< |
obtained for a series of temperatures in the nematic phase. The |
| 774 |
< |
simulation data have been used to calculate the flexoelectric coefficients |
| 775 |
< |
e(s) and e(b) using the linear response formalism of Osipov and |
| 776 |
< |
Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr. |
| 777 |
< |
31, 125 (1986)]. The temperature and order parameter dependence |
| 778 |
< |
of e(s) and e(b) are examined, as are separate contributions from |
| 779 |
< |
different intermolecular interactions. Values of e(s) and e(b) calculated |
| 780 |
< |
from simulation are consistent with those found from experiment. |
| 781 |
< |
(C) 2004 American Institute of Physics.}, |
| 771 |
> |
the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile |
| 772 |
> |
(PCH5) using a fully atomistic model. Simulation data have been |
| 773 |
> |
obtained for a series of temperatures in the nematic phase. The |
| 774 |
> |
simulation data have been used to calculate the flexoelectric coefficients |
| 775 |
> |
e(s) and e(b) using the linear response formalism of Osipov and |
| 776 |
> |
Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr. |
| 777 |
> |
31, 125 (1986)]. The temperature and order parameter dependence |
| 778 |
> |
of e(s) and e(b) are examined, as are separate contributions from |
| 779 |
> |
different intermolecular interactions. Values of e(s) and e(b) calculated |
| 780 |
> |
from simulation are consistent with those found from experiment. |
| 781 |
> |
(C) 2004 American Institute of Physics.}, |
| 782 |
|
annote = {866UM Times Cited:4 Cited References Count:61}, |
| 783 |
|
issn = {0021-9606}, |
| 784 |
|
uri = {<Go to ISI>://000224798900053}, |
| 794 |
|
number = {1-2}, |
| 795 |
|
month = {Apr 15}, |
| 796 |
|
abstract = {Equilibrium molecular dynamics calculations have been performed for |
| 797 |
< |
the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile |
| 798 |
< |
(PCH5) using a fully atomistic model. Simulation data has been obtained |
| 799 |
< |
for a series of temperatures in the nematic phase. The rotational |
| 800 |
< |
viscosity co-efficient gamma(1), has been calculated using the angular |
| 801 |
< |
velocity correlation function of the nematic director, n, the mean |
| 802 |
< |
squared diffusion of n and statistical mechanical methods based |
| 803 |
< |
on the rotational diffusion co-efficient. We find good agreement |
| 804 |
< |
between the first two methods and experimental values. (C) 2002 |
| 805 |
< |
Published by Elsevier Science B.V.}, |
| 797 |
> |
the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile |
| 798 |
> |
(PCH5) using a fully atomistic model. Simulation data has been obtained |
| 799 |
> |
for a series of temperatures in the nematic phase. The rotational |
| 800 |
> |
viscosity co-efficient gamma(1), has been calculated using the angular |
| 801 |
> |
velocity correlation function of the nematic director, n, the mean |
| 802 |
> |
squared diffusion of n and statistical mechanical methods based |
| 803 |
> |
on the rotational diffusion co-efficient. We find good agreement |
| 804 |
> |
between the first two methods and experimental values. (C) 2002 |
| 805 |
> |
Published by Elsevier Science B.V.}, |
| 806 |
|
annote = {547KF Times Cited:8 Cited References Count:31}, |
| 807 |
|
issn = {0009-2614}, |
| 808 |
|
uri = {<Go to ISI>://000175331000020}, |
| 811 |
|
@ARTICLE{Chin2004, |
| 812 |
|
author = {S. A. Chin}, |
| 813 |
|
title = {Dynamical multiple-time stepping methods for overcoming resonance |
| 814 |
< |
instabilities}, |
| 814 |
> |
instabilities}, |
| 815 |
|
journal = {Journal of Chemical Physics}, |
| 816 |
|
year = {2004}, |
| 817 |
|
volume = {120}, |
| 819 |
|
number = {1}, |
| 820 |
|
month = {Jan 1}, |
| 821 |
|
abstract = {Current molecular dynamics simulations of biomolecules using multiple |
| 822 |
< |
time steps to update the slowly changing force are hampered by instabilities |
| 823 |
< |
beginning at time steps near the half period of the fastest vibrating |
| 824 |
< |
mode. These #resonance# instabilities have became a critical barrier |
| 825 |
< |
preventing the long time simulation of biomolecular dynamics. Attempts |
| 826 |
< |
to tame these instabilities by altering the slowly changing force |
| 827 |
< |
and efforts to damp them out by Langevin dynamics do not address |
| 828 |
< |
the fundamental cause of these instabilities. In this work, we trace |
| 829 |
< |
the instability to the nonanalytic character of the underlying spectrum |
| 830 |
< |
and show that a correct splitting of the Hamiltonian, which renders |
| 831 |
< |
the spectrum analytic, restores stability. The resulting Hamiltonian |
| 832 |
< |
dictates that in addition to updating the momentum due to the slowly |
| 833 |
< |
changing force, one must also update the position with a modified |
| 834 |
< |
mass. Thus multiple-time stepping must be done dynamically. (C) |
| 835 |
< |
2004 American Institute of Physics.}, |
| 822 |
> |
time steps to update the slowly changing force are hampered by instabilities |
| 823 |
> |
beginning at time steps near the half period of the fastest vibrating |
| 824 |
> |
mode. These #resonance# instabilities have became a critical barrier |
| 825 |
> |
preventing the long time simulation of biomolecular dynamics. Attempts |
| 826 |
> |
to tame these instabilities by altering the slowly changing force |
| 827 |
> |
and efforts to damp them out by Langevin dynamics do not address |
| 828 |
> |
the fundamental cause of these instabilities. In this work, we trace |
| 829 |
> |
the instability to the nonanalytic character of the underlying spectrum |
| 830 |
> |
and show that a correct splitting of the Hamiltonian, which renders |
| 831 |
> |
the spectrum analytic, restores stability. The resulting Hamiltonian |
| 832 |
> |
dictates that in addition to updating the momentum due to the slowly |
| 833 |
> |
changing force, one must also update the position with a modified |
| 834 |
> |
mass. Thus multiple-time stepping must be done dynamically. (C) |
| 835 |
> |
2004 American Institute of Physics.}, |
| 836 |
|
annote = {757TK Times Cited:1 Cited References Count:22}, |
| 837 |
|
issn = {0021-9606}, |
| 838 |
|
uri = {<Go to ISI>://000187577400003}, |
| 841 |
|
@ARTICLE{Cook2000, |
| 842 |
|
author = {M. J. Cook and M. R. Wilson}, |
| 843 |
|
title = {Simulation studies of dipole correlation in the isotropic liquid |
| 844 |
< |
phase}, |
| 844 |
> |
phase}, |
| 845 |
|
journal = {Liquid Crystals}, |
| 846 |
|
year = {2000}, |
| 847 |
|
volume = {27}, |
| 849 |
|
number = {12}, |
| 850 |
|
month = {Dec}, |
| 851 |
|
abstract = {The Kirkwood correlation factor g(1) determines the preference for |
| 852 |
< |
local parallel or antiparallel dipole association in the isotropic |
| 853 |
< |
phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood |
| 854 |
< |
factors greater than 1 have an enhanced effective dipole moment |
| 855 |
< |
along the molecular long axis. This leads to higher values of Delta |
| 856 |
< |
epsilon in the nematic phase. This paper describes state-of-the-art |
| 857 |
< |
molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile |
| 858 |
< |
(PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl) |
| 859 |
< |
in the isotropic liquid phase using an all-atom force field and |
| 860 |
< |
taking long range electrostatics into account using an Ewald summation. |
| 861 |
< |
Using this methodology, PCH5 is seen to prefer antiparallel dipole |
| 862 |
< |
alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel |
| 863 |
< |
dipole alignment with a positive g(1); this is in accordance with |
| 864 |
< |
experimental dielectric measurements. Analysis of the molecular |
| 865 |
< |
dynamics trajectories allows an assessment of why these molecules |
| 866 |
< |
behave differently.}, |
| 852 |
> |
local parallel or antiparallel dipole association in the isotropic |
| 853 |
> |
phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood |
| 854 |
> |
factors greater than 1 have an enhanced effective dipole moment |
| 855 |
> |
along the molecular long axis. This leads to higher values of Delta |
| 856 |
> |
epsilon in the nematic phase. This paper describes state-of-the-art |
| 857 |
> |
molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile |
| 858 |
> |
(PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl) |
| 859 |
> |
in the isotropic liquid phase using an all-atom force field and |
| 860 |
> |
taking long range electrostatics into account using an Ewald summation. |
| 861 |
> |
Using this methodology, PCH5 is seen to prefer antiparallel dipole |
| 862 |
> |
alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel |
| 863 |
> |
dipole alignment with a positive g(1); this is in accordance with |
| 864 |
> |
experimental dielectric measurements. Analysis of the molecular |
| 865 |
> |
dynamics trajectories allows an assessment of why these molecules |
| 866 |
> |
behave differently.}, |
| 867 |
|
annote = {376BF Times Cited:10 Cited References Count:16}, |
| 868 |
|
issn = {0267-8292}, |
| 869 |
|
uri = {<Go to ISI>://000165437800002}, |
| 872 |
|
@ARTICLE{Cui2003, |
| 873 |
|
author = {B. X. Cui and M. Y. Shen and K. F. Freed}, |
| 874 |
|
title = {Folding and misfolding of the papillomavirus E6 interacting peptide |
| 875 |
< |
E6ap}, |
| 875 |
> |
E6ap}, |
| 876 |
|
journal = {Proceedings of the National Academy of Sciences of the United States |
| 877 |
< |
of America}, |
| 877 |
> |
of America}, |
| 878 |
|
year = {2003}, |
| 879 |
|
volume = {100}, |
| 880 |
|
pages = {7087-7092}, |
| 881 |
|
number = {12}, |
| 882 |
|
month = {Jun 10}, |
| 883 |
|
abstract = {All-atom Langevin dynamics simulations have been performed to study |
| 884 |
< |
the folding pathways of the 18-residue binding domain fragment E6ap |
| 885 |
< |
of the human papillomavirus E6 interacting peptide. Six independent |
| 886 |
< |
folding trajectories, with a total duration of nearly 2 mus, all |
| 887 |
< |
lead to the same native state in which the E6ap adopts a fluctuating |
| 888 |
< |
a-helix structure in the central portion (Ser-4-Leu-13) but with |
| 889 |
< |
very flexible N and C termini. Simulations starting from different |
| 890 |
< |
core configurations exhibit the E6ap folding dynamics as either |
| 891 |
< |
a two- or three-state folder with an intermediate misfolded state. |
| 892 |
< |
The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13) |
| 893 |
< |
is well conserved in the native-state structure but absent in the |
| 894 |
< |
intermediate structure, suggesting that the leucine core is not |
| 895 |
< |
only essential for the binding activity of E6ap but also important |
| 896 |
< |
for the stability of the native structure. The free energy landscape |
| 897 |
< |
reveals a significant barrier between the basins separating the |
| 898 |
< |
native and misfolded states. We also discuss the various underlying |
| 899 |
< |
forces that drive the peptide into its native state.}, |
| 884 |
> |
the folding pathways of the 18-residue binding domain fragment E6ap |
| 885 |
> |
of the human papillomavirus E6 interacting peptide. Six independent |
| 886 |
> |
folding trajectories, with a total duration of nearly 2 mus, all |
| 887 |
> |
lead to the same native state in which the E6ap adopts a fluctuating |
| 888 |
> |
a-helix structure in the central portion (Ser-4-Leu-13) but with |
| 889 |
> |
very flexible N and C termini. Simulations starting from different |
| 890 |
> |
core configurations exhibit the E6ap folding dynamics as either |
| 891 |
> |
a two- or three-state folder with an intermediate misfolded state. |
| 892 |
> |
The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13) |
| 893 |
> |
is well conserved in the native-state structure but absent in the |
| 894 |
> |
intermediate structure, suggesting that the leucine core is not |
| 895 |
> |
only essential for the binding activity of E6ap but also important |
| 896 |
> |
for the stability of the native structure. The free energy landscape |
| 897 |
> |
reveals a significant barrier between the basins separating the |
| 898 |
> |
native and misfolded states. We also discuss the various underlying |
| 899 |
> |
forces that drive the peptide into its native state.}, |
| 900 |
|
annote = {689LC Times Cited:3 Cited References Count:48}, |
| 901 |
|
issn = {0027-8424}, |
| 902 |
|
uri = {<Go to ISI>://000183493500037}, |
| 912 |
|
number = {1}, |
| 913 |
|
month = {Jan 1}, |
| 914 |
|
abstract = {We study the slow phase of thermally activated magnetic relaxation |
| 915 |
< |
in finite two-dimensional ensembles of dipolar interacting ferromagnetic |
| 916 |
< |
nanoparticles whose easy axes of magnetization are perpendicular |
| 917 |
< |
to the distribution plane. We develop a method to numerically simulate |
| 918 |
< |
the magnetic relaxation for the case that the smallest heights of |
| 919 |
< |
the potential barriers between the equilibrium directions of the |
| 920 |
< |
nanoparticle magnetic moments are much larger than the thermal energy. |
| 921 |
< |
Within this framework, we analyze in detail the role that the correlations |
| 922 |
< |
of the nanoparticle magnetic moments and the finite size of the |
| 923 |
< |
nanoparticle ensemble play in magnetic relaxation.}, |
| 915 |
> |
in finite two-dimensional ensembles of dipolar interacting ferromagnetic |
| 916 |
> |
nanoparticles whose easy axes of magnetization are perpendicular |
| 917 |
> |
to the distribution plane. We develop a method to numerically simulate |
| 918 |
> |
the magnetic relaxation for the case that the smallest heights of |
| 919 |
> |
the potential barriers between the equilibrium directions of the |
| 920 |
> |
nanoparticle magnetic moments are much larger than the thermal energy. |
| 921 |
> |
Within this framework, we analyze in detail the role that the correlations |
| 922 |
> |
of the nanoparticle magnetic moments and the finite size of the |
| 923 |
> |
nanoparticle ensemble play in magnetic relaxation.}, |
| 924 |
|
annote = {642XH Times Cited:11 Cited References Count:31}, |
| 925 |
|
issn = {1098-0121}, |
| 926 |
|
uri = {<Go to ISI>://000180830400056}, |
| 936 |
|
number = {1}, |
| 937 |
|
month = {Jan}, |
| 938 |
|
abstract = {To explore the origin of the large-scale motion of triosephosphate |
| 939 |
< |
isomerase's flexible loop (residues 166 to 176) at the active site, |
| 940 |
< |
several simulation protocols are employed both for the free enzyme |
| 941 |
< |
in vacuo and for the free enzyme with some solvent modeling: high-temperature |
| 942 |
< |
Langevin dynamics simulations, sampling by a #dynamics##driver# |
| 943 |
< |
approach, and potential-energy surface calculations. Our focus is |
| 944 |
< |
on obtaining the energy barrier to the enzyme's motion and establishing |
| 945 |
< |
the nature of the loop movement. Previous calculations did not determine |
| 946 |
< |
this energy barrier and the effect of solvent on the barrier. High-temperature |
| 947 |
< |
molecular dynamics simulations and crystallographic studies have |
| 948 |
< |
suggested a rigid-body motion with two hinges located at both ends |
| 949 |
< |
of the loop; Brownian dynamics simulations at room temperature pointed |
| 950 |
< |
to a very flexible behavior. The present simulations and analyses |
| 951 |
< |
reveal that although solute/solvent hydrogen bonds play a crucial |
| 952 |
< |
role in lowering the energy along the pathway, there still remains |
| 953 |
< |
a high activation barrier, This finding clearly indicates that, |
| 954 |
< |
if the loop opens and closes in the absence of a substrate at standard |
| 955 |
< |
conditions (e.g., room temperature, appropriate concentration of |
| 956 |
< |
isomerase), the time scale for transition is not in the nanosecond |
| 957 |
< |
but rather the microsecond range. Our results also indicate that |
| 958 |
< |
in the context of spontaneous opening in the free enzyme, the motion |
| 959 |
< |
is of rigid-body type and that the specific interaction between |
| 960 |
< |
residues Ala(176) and Tyr(208) plays a crucial role in the loop |
| 961 |
< |
opening/closing mechanism.}, |
| 939 |
> |
isomerase's flexible loop (residues 166 to 176) at the active site, |
| 940 |
> |
several simulation protocols are employed both for the free enzyme |
| 941 |
> |
in vacuo and for the free enzyme with some solvent modeling: high-temperature |
| 942 |
> |
Langevin dynamics simulations, sampling by a #dynamics##driver# |
| 943 |
> |
approach, and potential-energy surface calculations. Our focus is |
| 944 |
> |
on obtaining the energy barrier to the enzyme's motion and establishing |
| 945 |
> |
the nature of the loop movement. Previous calculations did not determine |
| 946 |
> |
this energy barrier and the effect of solvent on the barrier. High-temperature |
| 947 |
> |
molecular dynamics simulations and crystallographic studies have |
| 948 |
> |
suggested a rigid-body motion with two hinges located at both ends |
| 949 |
> |
of the loop; Brownian dynamics simulations at room temperature pointed |
| 950 |
> |
to a very flexible behavior. The present simulations and analyses |
| 951 |
> |
reveal that although solute/solvent hydrogen bonds play a crucial |
| 952 |
> |
role in lowering the energy along the pathway, there still remains |
| 953 |
> |
a high activation barrier, This finding clearly indicates that, |
| 954 |
> |
if the loop opens and closes in the absence of a substrate at standard |
| 955 |
> |
conditions (e.g., room temperature, appropriate concentration of |
| 956 |
> |
isomerase), the time scale for transition is not in the nanosecond |
| 957 |
> |
but rather the microsecond range. Our results also indicate that |
| 958 |
> |
in the context of spontaneous opening in the free enzyme, the motion |
| 959 |
> |
is of rigid-body type and that the specific interaction between |
| 960 |
> |
residues Ala(176) and Tyr(208) plays a crucial role in the loop |
| 961 |
> |
opening/closing mechanism.}, |
| 962 |
|
annote = {Zl046 Times Cited:30 Cited References Count:29}, |
| 963 |
|
issn = {0006-3495}, |
| 964 |
|
uri = {<Go to ISI>://000073393400009}, |
| 974 |
|
number = {15}, |
| 975 |
|
month = {Oct 15}, |
| 976 |
|
abstract = {Rigid body molecular models possess symplectic structure and time-reversal |
| 977 |
< |
symmetry. Standard numerical integration methods destroy both properties, |
| 978 |
< |
introducing nonphysical dynamical behavior such as numerically induced |
| 979 |
< |
dissipative states and drift in the energy during long term simulations. |
| 980 |
< |
This article describes the construction, implementation, and practical |
| 981 |
< |
application of fast explicit symplectic-reversible integrators for |
| 982 |
< |
multiple rigid body molecular simulations, These methods use a reduction |
| 983 |
< |
to Euler equations for the free rigid body, together with a symplectic |
| 984 |
< |
splitting technique. In every time step, the orientational dynamics |
| 985 |
< |
of each rigid body is integrated by a sequence of planar rotations. |
| 986 |
< |
Besides preserving the symplectic and reversible structures of the |
| 987 |
< |
flow, this scheme accurately conserves the total angular momentum |
| 988 |
< |
of a system of interacting rigid bodies. Excellent energy conservation |
| 989 |
< |
fan be obtained relative to traditional methods, especially in long-time |
| 990 |
< |
simulations. The method is implemented in a research code, ORIENT |
| 991 |
< |
and compared with a quaternion/extrapolation scheme for the TIP4P |
| 992 |
< |
model of water. Our experiments show that the symplectic-reversible |
| 993 |
< |
scheme is far superior to the more traditional quaternion method. |
| 994 |
< |
(C) 1997 American Institute of Physics.}, |
| 977 |
> |
symmetry. Standard numerical integration methods destroy both properties, |
| 978 |
> |
introducing nonphysical dynamical behavior such as numerically induced |
| 979 |
> |
dissipative states and drift in the energy during long term simulations. |
| 980 |
> |
This article describes the construction, implementation, and practical |
| 981 |
> |
application of fast explicit symplectic-reversible integrators for |
| 982 |
> |
multiple rigid body molecular simulations, These methods use a reduction |
| 983 |
> |
to Euler equations for the free rigid body, together with a symplectic |
| 984 |
> |
splitting technique. In every time step, the orientational dynamics |
| 985 |
> |
of each rigid body is integrated by a sequence of planar rotations. |
| 986 |
> |
Besides preserving the symplectic and reversible structures of the |
| 987 |
> |
flow, this scheme accurately conserves the total angular momentum |
| 988 |
> |
of a system of interacting rigid bodies. Excellent energy conservation |
| 989 |
> |
fan be obtained relative to traditional methods, especially in long-time |
| 990 |
> |
simulations. The method is implemented in a research code, ORIENT |
| 991 |
> |
and compared with a quaternion/extrapolation scheme for the TIP4P |
| 992 |
> |
model of water. Our experiments show that the symplectic-reversible |
| 993 |
> |
scheme is far superior to the more traditional quaternion method. |
| 994 |
> |
(C) 1997 American Institute of Physics.}, |
| 995 |
|
annote = {Ya587 Times Cited:35 Cited References Count:32}, |
| 996 |
|
issn = {0021-9606}, |
| 997 |
|
uri = {<Go to ISI>://A1997YA58700024}, |
| 998 |
|
} |
| 999 |
|
|
| 1000 |
+ |
@BOOK{Gamma1994, |
| 1001 |
+ |
title = {Design Patterns: Elements of Reusable Object-Oriented Software}, |
| 1002 |
+ |
publisher = {Perason Education}, |
| 1003 |
+ |
year = {1994}, |
| 1004 |
+ |
author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides}, |
| 1005 |
+ |
address = {London}, |
| 1006 |
+ |
chapter = {7}, |
| 1007 |
+ |
} |
| 1008 |
+ |
|
| 1009 |
|
@ARTICLE{Edwards2005, |
| 1010 |
|
author = {S. A. Edwards and D. R. M. Williams}, |
| 1011 |
|
title = {Stretching a single diblock copolymer in a selective solvent: Langevin |
| 1012 |
< |
dynamics simulations}, |
| 1012 |
> |
dynamics simulations}, |
| 1013 |
|
journal = {Macromolecules}, |
| 1014 |
|
year = {2005}, |
| 1015 |
|
volume = {38}, |
| 1017 |
|
number = {25}, |
| 1018 |
|
month = {Dec 13}, |
| 1019 |
|
abstract = {Using the Langevin dynamics technique, we have carried out simulations |
| 1020 |
< |
of a single-chain flexible diblock copolymer. The polymer consists |
| 1021 |
< |
of two blocks of equal length, one very poorly solvated and the |
| 1022 |
< |
other close to theta-conditions. We study what happens when such |
| 1023 |
< |
a polymer is stretched, for a range of different stretching speeds, |
| 1024 |
< |
and correlate our observations with features in the plot of force |
| 1025 |
< |
vs extension. We find that at slow speeds this force profile does |
| 1026 |
< |
not increase monotonically, in disagreement with earlier predictions, |
| 1027 |
< |
and that at high speeds there is a strong dependence on which end |
| 1028 |
< |
of the polymer is pulled, as well as a high level of hysteresis.}, |
| 1020 |
> |
of a single-chain flexible diblock copolymer. The polymer consists |
| 1021 |
> |
of two blocks of equal length, one very poorly solvated and the |
| 1022 |
> |
other close to theta-conditions. We study what happens when such |
| 1023 |
> |
a polymer is stretched, for a range of different stretching speeds, |
| 1024 |
> |
and correlate our observations with features in the plot of force |
| 1025 |
> |
vs extension. We find that at slow speeds this force profile does |
| 1026 |
> |
not increase monotonically, in disagreement with earlier predictions, |
| 1027 |
> |
and that at high speeds there is a strong dependence on which end |
| 1028 |
> |
of the polymer is pulled, as well as a high level of hysteresis.}, |
| 1029 |
|
annote = {992EC Times Cited:0 Cited References Count:13}, |
| 1030 |
|
issn = {0024-9297}, |
| 1031 |
|
uri = {<Go to ISI>://000233866200035}, |
| 1034 |
|
@ARTICLE{Egberts1988, |
| 1035 |
|
author = {E. Egberts and H. J. C. Berendsen}, |
| 1036 |
|
title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic |
| 1037 |
< |
Detail}, |
| 1037 |
> |
Detail}, |
| 1038 |
|
journal = {Journal of Chemical Physics}, |
| 1039 |
|
year = {1988}, |
| 1040 |
|
volume = {89}, |
| 1059 |
|
uri = {<Go to ISI>://A1978FP21600004}, |
| 1060 |
|
} |
| 1061 |
|
|
| 1062 |
+ |
@ARTICLE{Evans1977, |
| 1063 |
+ |
author = {D. J. Evans}, |
| 1064 |
+ |
title = {Representation of Orientation Space}, |
| 1065 |
+ |
journal = {Molecular Physics}, |
| 1066 |
+ |
year = {1977}, |
| 1067 |
+ |
volume = {34}, |
| 1068 |
+ |
pages = {317-325}, |
| 1069 |
+ |
number = {2}, |
| 1070 |
+ |
annote = {Ds757 Times Cited:271 Cited References Count:18}, |
| 1071 |
+ |
issn = {0026-8976}, |
| 1072 |
+ |
uri = {<Go to ISI>://A1977DS75700002}, |
| 1073 |
+ |
} |
| 1074 |
+ |
|
| 1075 |
|
@ARTICLE{Fennell2004, |
| 1076 |
|
author = {C. J. Fennell and J. D. Gezelter}, |
| 1077 |
|
title = {On the structural and transport properties of the soft sticky dipole |
| 1078 |
< |
and related single-point water models}, |
| 1078 |
> |
and related single-point water models}, |
| 1079 |
|
journal = {Journal of Chemical Physics}, |
| 1080 |
|
year = {2004}, |
| 1081 |
|
volume = {120}, |
| 1083 |
|
number = {19}, |
| 1084 |
|
month = {May 15}, |
| 1085 |
|
abstract = {The density maximum and temperature dependence of the self-diffusion |
| 1086 |
< |
constant were investigated for the soft sticky dipole (SSD) water |
| 1087 |
< |
model and two related reparametrizations of this single-point model. |
| 1088 |
< |
A combination of microcanonical and isobaric-isothermal molecular |
| 1089 |
< |
dynamics simulations was used to calculate these properties, both |
| 1090 |
< |
with and without the use of reaction field to handle long-range |
| 1091 |
< |
electrostatics. The isobaric-isothermal simulations of the melting |
| 1092 |
< |
of both ice-I-h and ice-I-c showed a density maximum near 260 K. |
| 1093 |
< |
In most cases, the use of the reaction field resulted in calculated |
| 1094 |
< |
densities which were significantly lower than experimental densities. |
| 1095 |
< |
Analysis of self-diffusion constants shows that the original SSD |
| 1096 |
< |
model captures the transport properties of experimental water very |
| 1097 |
< |
well in both the normal and supercooled liquid regimes. We also |
| 1098 |
< |
present our reparametrized versions of SSD for use both with the |
| 1099 |
< |
reaction field or without any long-range electrostatic corrections. |
| 1100 |
< |
These are called the SSD/RF and SSD/E models, respectively. These |
| 1101 |
< |
modified models were shown to maintain or improve upon the experimental |
| 1102 |
< |
agreement with the structural and transport properties that can |
| 1103 |
< |
be obtained with either the original SSD or the density-corrected |
| 1104 |
< |
version of the original model (SSD1). Additionally, a novel low-density |
| 1105 |
< |
ice structure is presented which appears to be the most stable ice |
| 1106 |
< |
structure for the entire SSD family. (C) 2004 American Institute |
| 1107 |
< |
of Physics.}, |
| 1086 |
> |
constant were investigated for the soft sticky dipole (SSD) water |
| 1087 |
> |
model and two related reparametrizations of this single-point model. |
| 1088 |
> |
A combination of microcanonical and isobaric-isothermal molecular |
| 1089 |
> |
dynamics simulations was used to calculate these properties, both |
| 1090 |
> |
with and without the use of reaction field to handle long-range |
| 1091 |
> |
electrostatics. The isobaric-isothermal simulations of the melting |
| 1092 |
> |
of both ice-I-h and ice-I-c showed a density maximum near 260 K. |
| 1093 |
> |
In most cases, the use of the reaction field resulted in calculated |
| 1094 |
> |
densities which were significantly lower than experimental densities. |
| 1095 |
> |
Analysis of self-diffusion constants shows that the original SSD |
| 1096 |
> |
model captures the transport properties of experimental water very |
| 1097 |
> |
well in both the normal and supercooled liquid regimes. We also |
| 1098 |
> |
present our reparametrized versions of SSD for use both with the |
| 1099 |
> |
reaction field or without any long-range electrostatic corrections. |
| 1100 |
> |
These are called the SSD/RF and SSD/E models, respectively. These |
| 1101 |
> |
modified models were shown to maintain or improve upon the experimental |
| 1102 |
> |
agreement with the structural and transport properties that can |
| 1103 |
> |
be obtained with either the original SSD or the density-corrected |
| 1104 |
> |
version of the original model (SSD1). Additionally, a novel low-density |
| 1105 |
> |
ice structure is presented which appears to be the most stable ice |
| 1106 |
> |
structure for the entire SSD family. (C) 2004 American Institute |
| 1107 |
> |
of Physics.}, |
| 1108 |
|
annote = {816YY Times Cited:5 Cited References Count:39}, |
| 1109 |
|
issn = {0021-9606}, |
| 1110 |
|
uri = {<Go to ISI>://000221146400032}, |
| 1113 |
|
@ARTICLE{Fernandes2002, |
| 1114 |
|
author = {M. X. Fernandes and J. G. {de la Torre}}, |
| 1115 |
|
title = {Brownian dynamics simulation of rigid particles of arbitrary shape |
| 1116 |
< |
in external fields}, |
| 1116 |
> |
in external fields}, |
| 1117 |
|
journal = {Biophysical Journal}, |
| 1118 |
|
year = {2002}, |
| 1119 |
|
volume = {83}, |
| 1121 |
|
number = {6}, |
| 1122 |
|
month = {Dec}, |
| 1123 |
|
abstract = {We have developed a Brownian dynamics simulation algorithm to generate |
| 1124 |
< |
Brownian trajectories of an isolated, rigid particle of arbitrary |
| 1125 |
< |
shape in the presence of electric fields or any other external agents. |
| 1126 |
< |
Starting from the generalized diffusion tensor, which can be calculated |
| 1127 |
< |
with the existing HYDRO software, the new program BROWNRIG (including |
| 1128 |
< |
a case-specific subprogram for the external agent) carries out a |
| 1129 |
< |
simulation that is analyzed later to extract the observable dynamic |
| 1130 |
< |
properties. We provide a variety of examples of utilization of this |
| 1131 |
< |
method, which serve as tests of its performance, and also illustrate |
| 1132 |
< |
its applicability. Examples include free diffusion, transport in |
| 1133 |
< |
an electric field, and diffusion in a restricting environment.}, |
| 1124 |
> |
Brownian trajectories of an isolated, rigid particle of arbitrary |
| 1125 |
> |
shape in the presence of electric fields or any other external agents. |
| 1126 |
> |
Starting from the generalized diffusion tensor, which can be calculated |
| 1127 |
> |
with the existing HYDRO software, the new program BROWNRIG (including |
| 1128 |
> |
a case-specific subprogram for the external agent) carries out a |
| 1129 |
> |
simulation that is analyzed later to extract the observable dynamic |
| 1130 |
> |
properties. We provide a variety of examples of utilization of this |
| 1131 |
> |
method, which serve as tests of its performance, and also illustrate |
| 1132 |
> |
its applicability. Examples include free diffusion, transport in |
| 1133 |
> |
an electric field, and diffusion in a restricting environment.}, |
| 1134 |
|
annote = {633AD Times Cited:2 Cited References Count:43}, |
| 1135 |
|
issn = {0006-3495}, |
| 1136 |
|
uri = {<Go to ISI>://000180256300012}, |
| 1137 |
|
} |
| 1138 |
|
|
| 1139 |
+ |
@BOOK{Frenkel1996, |
| 1140 |
+ |
title = {Understanding Molecular Simulation : From Algorithms to Applications}, |
| 1141 |
+ |
publisher = {Academic Press}, |
| 1142 |
+ |
year = {1996}, |
| 1143 |
+ |
author = {D. Frenkel and B. Smit}, |
| 1144 |
+ |
address = {New York}, |
| 1145 |
+ |
} |
| 1146 |
+ |
|
| 1147 |
|
@ARTICLE{Gay1981, |
| 1148 |
|
author = {J. G. Gay and B. J. Berne}, |
| 1149 |
|
title = {Modification of the Overlap Potential to Mimic a Linear Site-Site |
| 1150 |
< |
Potential}, |
| 1150 |
> |
Potential}, |
| 1151 |
|
journal = {Journal of Chemical Physics}, |
| 1152 |
|
year = {1981}, |
| 1153 |
|
volume = {74}, |
| 1168 |
|
number = {6}, |
| 1169 |
|
month = {Nov}, |
| 1170 |
|
abstract = {To investigate the influence of inertial effects on the dynamics of |
| 1171 |
< |
an assembly of beads subjected to rigid constraints and placed in |
| 1172 |
< |
a buffer medium, a convenient method to introduce suitable generalized |
| 1173 |
< |
coordinates is presented. Without any restriction on the nature |
| 1174 |
< |
of the soft forces involved (both stochastic and deterministic), |
| 1175 |
< |
pertinent Langevin equations are derived. Provided that the Brownian |
| 1176 |
< |
forces are Gaussian and Markovian, the corresponding Fokker-Planck |
| 1177 |
< |
equation (FPE) is obtained in the complete phase space of generalized |
| 1178 |
< |
coordinates and momenta. The correct short time behavior for correlation |
| 1179 |
< |
functions (CFs) of generalized coordinates is established, and the |
| 1180 |
< |
diffusion equation with memory (DEM) is deduced from the FPE in |
| 1181 |
< |
the high friction Limit. The DEM is invoked to perform illustrative |
| 1182 |
< |
calculations in two dimensions of the orientational CFs for once |
| 1183 |
< |
broken nonrigid rods immobilized on a surface. These calculations |
| 1184 |
< |
reveal that the CFs under certain conditions exhibit an oscillatory |
| 1185 |
< |
behavior, which is irreproducible within the standard diffusion |
| 1186 |
< |
equation. Several methods are considered for the approximate solution |
| 1187 |
< |
of the DEM, and their application to three dimensional DEMs is discussed.}, |
| 1171 |
> |
an assembly of beads subjected to rigid constraints and placed in |
| 1172 |
> |
a buffer medium, a convenient method to introduce suitable generalized |
| 1173 |
> |
coordinates is presented. Without any restriction on the nature |
| 1174 |
> |
of the soft forces involved (both stochastic and deterministic), |
| 1175 |
> |
pertinent Langevin equations are derived. Provided that the Brownian |
| 1176 |
> |
forces are Gaussian and Markovian, the corresponding Fokker-Planck |
| 1177 |
> |
equation (FPE) is obtained in the complete phase space of generalized |
| 1178 |
> |
coordinates and momenta. The correct short time behavior for correlation |
| 1179 |
> |
functions (CFs) of generalized coordinates is established, and the |
| 1180 |
> |
diffusion equation with memory (DEM) is deduced from the FPE in |
| 1181 |
> |
the high friction Limit. The DEM is invoked to perform illustrative |
| 1182 |
> |
calculations in two dimensions of the orientational CFs for once |
| 1183 |
> |
broken nonrigid rods immobilized on a surface. These calculations |
| 1184 |
> |
reveal that the CFs under certain conditions exhibit an oscillatory |
| 1185 |
> |
behavior, which is irreproducible within the standard diffusion |
| 1186 |
> |
equation. Several methods are considered for the approximate solution |
| 1187 |
> |
of the DEM, and their application to three dimensional DEMs is discussed.}, |
| 1188 |
|
annote = {257MM Times Cited:2 Cited References Count:82}, |
| 1189 |
|
issn = {1022-1344}, |
| 1190 |
|
uri = {<Go to ISI>://000083785700002}, |
| 1201 |
|
|
| 1202 |
|
@ARTICLE{Gray2003, |
| 1203 |
|
author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and |
| 1204 |
< |
B. Kuhlman and C. A. Rohl and D. Baker}, |
| 1204 |
> |
B. Kuhlman and C. A. Rohl and D. Baker}, |
| 1205 |
|
title = {Protein-protein docking with simultaneous optimization of rigid-body |
| 1206 |
< |
displacement and side-chain conformations}, |
| 1206 |
> |
displacement and side-chain conformations}, |
| 1207 |
|
journal = {Journal of Molecular Biology}, |
| 1208 |
|
year = {2003}, |
| 1209 |
|
volume = {331}, |
| 1211 |
|
number = {1}, |
| 1212 |
|
month = {Aug 1}, |
| 1213 |
|
abstract = {Protein-protein docking algorithms provide a means to elucidate structural |
| 1214 |
< |
details for presently unknown complexes. Here, we present and evaluate |
| 1215 |
< |
a new method to predict protein-protein complexes from the coordinates |
| 1216 |
< |
of the unbound monomer components. The method employs a low-resolution, |
| 1217 |
< |
rigid-body, Monte Carlo search followed by simultaneous optimization |
| 1218 |
< |
of backbone displacement and side-chain conformations using Monte |
| 1219 |
< |
Carlo minimization. Up to 10(5) independent simulations are carried |
| 1220 |
< |
out, and the resulting #decoys# are ranked using an energy function |
| 1221 |
< |
dominated by van der Waals interactions, an implicit solvation model, |
| 1222 |
< |
and an orientation-dependent hydrogen bonding potential. Top-ranking |
| 1223 |
< |
decoys are clustered to select the final predictions. Small-perturbation |
| 1224 |
< |
studies reveal the formation of binding funnels in 42 of 54 cases |
| 1225 |
< |
using coordinates derived from the bound complexes and in 32 of |
| 1226 |
< |
54 cases using independently determined coordinates of one or both |
| 1227 |
< |
monomers. Experimental binding affinities correlate with the calculated |
| 1228 |
< |
score function and explain the predictive success or failure of |
| 1229 |
< |
many targets. Global searches using one or both unbound components |
| 1230 |
< |
predict at least 25% of the native residue-residue contacts in 28 |
| 1231 |
< |
of the 32 cases where binding funnels exist. The results suggest |
| 1232 |
< |
that the method may soon be useful for generating models of biologically |
| 1233 |
< |
important complexes from the structures of the isolated components, |
| 1234 |
< |
but they also highlight the challenges that must be met to achieve |
| 1235 |
< |
consistent and accurate prediction of protein-protein interactions. |
| 1236 |
< |
(C) 2003 Elsevier Ltd. All rights reserved.}, |
| 1214 |
> |
details for presently unknown complexes. Here, we present and evaluate |
| 1215 |
> |
a new method to predict protein-protein complexes from the coordinates |
| 1216 |
> |
of the unbound monomer components. The method employs a low-resolution, |
| 1217 |
> |
rigid-body, Monte Carlo search followed by simultaneous optimization |
| 1218 |
> |
of backbone displacement and side-chain conformations using Monte |
| 1219 |
> |
Carlo minimization. Up to 10(5) independent simulations are carried |
| 1220 |
> |
out, and the resulting #decoys# are ranked using an energy function |
| 1221 |
> |
dominated by van der Waals interactions, an implicit solvation model, |
| 1222 |
> |
and an orientation-dependent hydrogen bonding potential. Top-ranking |
| 1223 |
> |
decoys are clustered to select the final predictions. Small-perturbation |
| 1224 |
> |
studies reveal the formation of binding funnels in 42 of 54 cases |
| 1225 |
> |
using coordinates derived from the bound complexes and in 32 of |
| 1226 |
> |
54 cases using independently determined coordinates of one or both |
| 1227 |
> |
monomers. Experimental binding affinities correlate with the calculated |
| 1228 |
> |
score function and explain the predictive success or failure of |
| 1229 |
> |
many targets. Global searches using one or both unbound components |
| 1230 |
> |
predict at least 25% of the native residue-residue contacts in 28 |
| 1231 |
> |
of the 32 cases where binding funnels exist. The results suggest |
| 1232 |
> |
that the method may soon be useful for generating models of biologically |
| 1233 |
> |
important complexes from the structures of the isolated components, |
| 1234 |
> |
but they also highlight the challenges that must be met to achieve |
| 1235 |
> |
consistent and accurate prediction of protein-protein interactions. |
| 1236 |
> |
(C) 2003 Elsevier Ltd. All rights reserved.}, |
| 1237 |
|
annote = {704QL Times Cited:48 Cited References Count:60}, |
| 1238 |
|
issn = {0022-2836}, |
| 1239 |
|
uri = {<Go to ISI>://000184351300022}, |
| 1249 |
|
number = {5174}, |
| 1250 |
|
month = {Aug 12}, |
| 1251 |
|
abstract = {Some of the recently developed fast summation methods that have arisen |
| 1252 |
< |
in scientific computing are described. These methods require an |
| 1253 |
< |
amount of work proportional to N or N log N to evaluate all pairwise |
| 1254 |
< |
interactions in an ensemble of N particles. Traditional methods, |
| 1255 |
< |
by contrast, require an amount of work proportional to N-2. AS a |
| 1256 |
< |
result, large-scale simulations can be carried out using only modest |
| 1257 |
< |
computer resources. In combination with supercomputers, it is possible |
| 1258 |
< |
to address questions that were previously out of reach. Problems |
| 1259 |
< |
from diffusion, gravitation, and wave propagation are considered.}, |
| 1252 |
> |
in scientific computing are described. These methods require an |
| 1253 |
> |
amount of work proportional to N or N log N to evaluate all pairwise |
| 1254 |
> |
interactions in an ensemble of N particles. Traditional methods, |
| 1255 |
> |
by contrast, require an amount of work proportional to N-2. AS a |
| 1256 |
> |
result, large-scale simulations can be carried out using only modest |
| 1257 |
> |
computer resources. In combination with supercomputers, it is possible |
| 1258 |
> |
to address questions that were previously out of reach. Problems |
| 1259 |
> |
from diffusion, gravitation, and wave propagation are considered.}, |
| 1260 |
|
annote = {Pb499 Times Cited:99 Cited References Count:44}, |
| 1261 |
|
issn = {0036-8075}, |
| 1262 |
|
uri = {<Go to ISI>://A1994PB49900031}, |
| 1286 |
|
number = {4}, |
| 1287 |
|
month = {Jun}, |
| 1288 |
|
abstract = {Backward error analysis is a useful tool for the study of numerical |
| 1289 |
< |
approximations to ordinary differential equations. The numerical |
| 1290 |
< |
solution is formally interpreted as the exact solution of a perturbed |
| 1291 |
< |
differential equation, given as a formal and usually divergent series |
| 1292 |
< |
in powers of the step size. For a rigorous analysis, this series |
| 1293 |
< |
has to be truncated. In this article we study the influence of this |
| 1294 |
< |
truncation to the difference between the numerical solution and |
| 1295 |
< |
the exact solution of the perturbed differential equation. Results |
| 1296 |
< |
on the long-time behaviour of numerical solutions are obtained in |
| 1297 |
< |
this way. We present applications to the numerical phase portrait |
| 1298 |
< |
near hyperbolic equilibrium points, to asymptotically stable periodic |
| 1299 |
< |
orbits and Hopf bifurcation, and to energy conservation and approximation |
| 1300 |
< |
of invariant tori in Hamiltonian systems.}, |
| 1289 |
> |
approximations to ordinary differential equations. The numerical |
| 1290 |
> |
solution is formally interpreted as the exact solution of a perturbed |
| 1291 |
> |
differential equation, given as a formal and usually divergent series |
| 1292 |
> |
in powers of the step size. For a rigorous analysis, this series |
| 1293 |
> |
has to be truncated. In this article we study the influence of this |
| 1294 |
> |
truncation to the difference between the numerical solution and |
| 1295 |
> |
the exact solution of the perturbed differential equation. Results |
| 1296 |
> |
on the long-time behaviour of numerical solutions are obtained in |
| 1297 |
> |
this way. We present applications to the numerical phase portrait |
| 1298 |
> |
near hyperbolic equilibrium points, to asymptotically stable periodic |
| 1299 |
> |
orbits and Hopf bifurcation, and to energy conservation and approximation |
| 1300 |
> |
of invariant tori in Hamiltonian systems.}, |
| 1301 |
|
annote = {Xj488 Times Cited:50 Cited References Count:19}, |
| 1302 |
|
issn = {0029-599X}, |
| 1303 |
|
uri = {<Go to ISI>://A1997XJ48800002}, |
| 1306 |
|
@ARTICLE{Hao1993, |
| 1307 |
|
author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga}, |
| 1308 |
|
title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic |
| 1309 |
< |
Trypsin-Inhibitor Studied by Computer-Simulations}, |
| 1309 |
> |
Trypsin-Inhibitor Studied by Computer-Simulations}, |
| 1310 |
|
journal = {Biochemistry}, |
| 1311 |
|
year = {1993}, |
| 1312 |
|
volume = {32}, |
| 1314 |
|
number = {37}, |
| 1315 |
|
month = {Sep 21}, |
| 1316 |
|
abstract = {A new procedure for studying the folding and unfolding of proteins, |
| 1317 |
< |
with an application to bovine pancreatic trypsin inhibitor (BPTI), |
| 1318 |
< |
is reported. The unfolding and refolding of the native structure |
| 1319 |
< |
of the protein are characterized by the dimensions of the protein, |
| 1320 |
< |
expressed in terms of the three principal radii of the structure |
| 1321 |
< |
considered as an ellipsoid. A dynamic equation, describing the variations |
| 1322 |
< |
of the principal radii on the unfolding path, and a numerical procedure |
| 1323 |
< |
to solve this equation are proposed. Expanded and distorted conformations |
| 1324 |
< |
are refolded to the native structure by a dimensional-constraint |
| 1325 |
< |
energy minimization procedure. A unique and reproducible unfolding |
| 1326 |
< |
pathway for an intermediate of BPTI lacking the [30,51] disulfide |
| 1327 |
< |
bond is obtained. The resulting unfolded conformations are extended; |
| 1328 |
< |
they contain near-native local structure, but their longest principal |
| 1329 |
< |
radii are more than 2.5 times greater than that of the native structure. |
| 1330 |
< |
The most interesting finding is that the majority of expanded conformations, |
| 1331 |
< |
generated under various conditions, can be refolded closely to the |
| 1332 |
< |
native structure, as measured by the correct overall chain fold, |
| 1333 |
< |
by the rms deviations from the native structure of only 1.9-3.1 |
| 1334 |
< |
angstrom, and by the energy differences of about 10 kcal/mol from |
| 1335 |
< |
the native structure. Introduction of the [30,51] disulfide bond |
| 1336 |
< |
at this stage, followed by minimization, improves the closeness |
| 1337 |
< |
of the refolded structures to the native structure, reducing the |
| 1338 |
< |
rms deviations to 0.9-2.0 angstrom. The unique refolding of these |
| 1339 |
< |
expanded structures over such a large conformational space implies |
| 1340 |
< |
that the folding is strongly dictated by the interactions in the |
| 1341 |
< |
amino acid sequence of BPTI. The simulations indicate that, under |
| 1342 |
< |
conditions that favor a compact structure as mimicked by the volume |
| 1343 |
< |
constraints in our algorithm; the expanded conformations have a |
| 1344 |
< |
strong tendency to move toward the native structure; therefore, |
| 1345 |
< |
they probably would be favorable folding intermediates. The results |
| 1346 |
< |
presented here support a general model for protein folding, i.e., |
| 1347 |
< |
progressive formation of partially folded structural units, followed |
| 1348 |
< |
by collapse to the compact native structure. The general applicability |
| 1349 |
< |
of the procedure is also discussed.}, |
| 1317 |
> |
with an application to bovine pancreatic trypsin inhibitor (BPTI), |
| 1318 |
> |
is reported. The unfolding and refolding of the native structure |
| 1319 |
> |
of the protein are characterized by the dimensions of the protein, |
| 1320 |
> |
expressed in terms of the three principal radii of the structure |
| 1321 |
> |
considered as an ellipsoid. A dynamic equation, describing the variations |
| 1322 |
> |
of the principal radii on the unfolding path, and a numerical procedure |
| 1323 |
> |
to solve this equation are proposed. Expanded and distorted conformations |
| 1324 |
> |
are refolded to the native structure by a dimensional-constraint |
| 1325 |
> |
energy minimization procedure. A unique and reproducible unfolding |
| 1326 |
> |
pathway for an intermediate of BPTI lacking the [30,51] disulfide |
| 1327 |
> |
bond is obtained. The resulting unfolded conformations are extended; |
| 1328 |
> |
they contain near-native local structure, but their longest principal |
| 1329 |
> |
radii are more than 2.5 times greater than that of the native structure. |
| 1330 |
> |
The most interesting finding is that the majority of expanded conformations, |
| 1331 |
> |
generated under various conditions, can be refolded closely to the |
| 1332 |
> |
native structure, as measured by the correct overall chain fold, |
| 1333 |
> |
by the rms deviations from the native structure of only 1.9-3.1 |
| 1334 |
> |
angstrom, and by the energy differences of about 10 kcal/mol from |
| 1335 |
> |
the native structure. Introduction of the [30,51] disulfide bond |
| 1336 |
> |
at this stage, followed by minimization, improves the closeness |
| 1337 |
> |
of the refolded structures to the native structure, reducing the |
| 1338 |
> |
rms deviations to 0.9-2.0 angstrom. The unique refolding of these |
| 1339 |
> |
expanded structures over such a large conformational space implies |
| 1340 |
> |
that the folding is strongly dictated by the interactions in the |
| 1341 |
> |
amino acid sequence of BPTI. The simulations indicate that, under |
| 1342 |
> |
conditions that favor a compact structure as mimicked by the volume |
| 1343 |
> |
constraints in our algorithm; the expanded conformations have a |
| 1344 |
> |
strong tendency to move toward the native structure; therefore, |
| 1345 |
> |
they probably would be favorable folding intermediates. The results |
| 1346 |
> |
presented here support a general model for protein folding, i.e., |
| 1347 |
> |
progressive formation of partially folded structural units, followed |
| 1348 |
> |
by collapse to the compact native structure. The general applicability |
| 1349 |
> |
of the procedure is also discussed.}, |
| 1350 |
|
annote = {Ly294 Times Cited:27 Cited References Count:57}, |
| 1351 |
|
issn = {0006-2960}, |
| 1352 |
|
uri = {<Go to ISI>://A1993LY29400014}, |
| 1354 |
|
|
| 1355 |
|
@ARTICLE{Hinsen2000, |
| 1356 |
|
author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel |
| 1357 |
< |
and G. R. Kneller}, |
| 1357 |
> |
and G. R. Kneller}, |
| 1358 |
|
title = {Harmonicity in slow protein dynamics}, |
| 1359 |
|
journal = {Chemical Physics}, |
| 1360 |
|
year = {2000}, |
| 1363 |
|
number = {1-2}, |
| 1364 |
|
month = {Nov 1}, |
| 1365 |
|
abstract = {The slow dynamics of proteins around its native folded state is usually |
| 1366 |
< |
described by diffusion in a strongly anharmonic potential. In this |
| 1367 |
< |
paper, we try to understand the form and origin of the anharmonicities, |
| 1368 |
< |
with the principal aim of gaining a better understanding of the |
| 1369 |
< |
principal motion types, but also in order to develop more efficient |
| 1370 |
< |
numerical methods for simulating neutron scattering spectra of large |
| 1371 |
< |
proteins. First, we decompose a molecular dynamics (MD) trajectory |
| 1372 |
< |
of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water |
| 1373 |
< |
into three contributions that we expect to be independent: the global |
| 1374 |
< |
motion of the residues, the rigid-body motion of the sidechains |
| 1375 |
< |
relative to the backbone, and the internal deformations of the sidechains. |
| 1376 |
< |
We show that they are indeed almost independent by verifying the |
| 1377 |
< |
factorization of the incoherent intermediate scattering function. |
| 1378 |
< |
Then, we show that the global residue motions, which include all |
| 1379 |
< |
large-scale backbone motions, can be reproduced by a simple harmonic |
| 1380 |
< |
model which contains two contributions: a short-time vibrational |
| 1381 |
< |
term, described by a standard normal mode calculation in a local |
| 1382 |
< |
minimum, and a long-time diffusive term, described by Brownian motion |
| 1383 |
< |
in an effective harmonic potential. The potential and the friction |
| 1384 |
< |
constants were fitted to the MD data. The major anharmonic contribution |
| 1385 |
< |
to the incoherent intermediate scattering function comes from the |
| 1386 |
< |
rigid-body diffusion of the sidechains. This model can be used to |
| 1387 |
< |
calculate scattering functions for large proteins and for long-time |
| 1388 |
< |
scales very efficiently, and thus provides a useful complement to |
| 1389 |
< |
MD simulations, which are best suited for detailed studies on smaller |
| 1390 |
< |
systems or for shorter time scales. (C) 2000 Elsevier Science B.V. |
| 1391 |
< |
All rights reserved.}, |
| 1366 |
> |
described by diffusion in a strongly anharmonic potential. In this |
| 1367 |
> |
paper, we try to understand the form and origin of the anharmonicities, |
| 1368 |
> |
with the principal aim of gaining a better understanding of the |
| 1369 |
> |
principal motion types, but also in order to develop more efficient |
| 1370 |
> |
numerical methods for simulating neutron scattering spectra of large |
| 1371 |
> |
proteins. First, we decompose a molecular dynamics (MD) trajectory |
| 1372 |
> |
of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water |
| 1373 |
> |
into three contributions that we expect to be independent: the global |
| 1374 |
> |
motion of the residues, the rigid-body motion of the sidechains |
| 1375 |
> |
relative to the backbone, and the internal deformations of the sidechains. |
| 1376 |
> |
We show that they are indeed almost independent by verifying the |
| 1377 |
> |
factorization of the incoherent intermediate scattering function. |
| 1378 |
> |
Then, we show that the global residue motions, which include all |
| 1379 |
> |
large-scale backbone motions, can be reproduced by a simple harmonic |
| 1380 |
> |
model which contains two contributions: a short-time vibrational |
| 1381 |
> |
term, described by a standard normal mode calculation in a local |
| 1382 |
> |
minimum, and a long-time diffusive term, described by Brownian motion |
| 1383 |
> |
in an effective harmonic potential. The potential and the friction |
| 1384 |
> |
constants were fitted to the MD data. The major anharmonic contribution |
| 1385 |
> |
to the incoherent intermediate scattering function comes from the |
| 1386 |
> |
rigid-body diffusion of the sidechains. This model can be used to |
| 1387 |
> |
calculate scattering functions for large proteins and for long-time |
| 1388 |
> |
scales very efficiently, and thus provides a useful complement to |
| 1389 |
> |
MD simulations, which are best suited for detailed studies on smaller |
| 1390 |
> |
systems or for shorter time scales. (C) 2000 Elsevier Science B.V. |
| 1391 |
> |
All rights reserved.}, |
| 1392 |
|
annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31}, |
| 1393 |
|
issn = {0301-0104}, |
| 1394 |
|
uri = {<Go to ISI>://000090121700003}, |
| 1404 |
|
number = {4}, |
| 1405 |
|
month = {Oct}, |
| 1406 |
|
abstract = {Evidence has been found for the existence water at the protein-lipid |
| 1407 |
< |
hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome |
| 1408 |
< |
C, using two related fluorescence spectroscopic approaches. The |
| 1409 |
< |
first approach exploited the fact that the presence of water in |
| 1410 |
< |
the excited state solvent cage of a fluorophore increases the rate |
| 1411 |
< |
of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl) |
| 1412 |
< |
phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores |
| 1413 |
< |
are located in the hydrophobic core of the lipid bilayer, the introduction |
| 1414 |
< |
of gramicidin reduced the fluorescence lifetime, indicative of an |
| 1415 |
< |
increased presence of water in the bilayer. Since a high protein:lipid |
| 1416 |
< |
ratio was used, the fluorophores were forced to be adjacent to the |
| 1417 |
< |
protein hydrophobic surface, hence the presence of water in this |
| 1418 |
< |
region could be inferred. Cholesterol is known to reduce the water |
| 1419 |
< |
content of lipid bilayers and this effect was maintained at the |
| 1420 |
< |
protein-lipid interface with both gramicidin and apocytochrome C, |
| 1421 |
< |
again suggesting hydration in this region. The second approach was |
| 1422 |
< |
to use the fluorescence enhancement induced by exchanging deuterium |
| 1423 |
< |
oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH, |
| 1424 |
< |
located in the lipid head group region, and of the gramicidin intrinsic |
| 1425 |
< |
tryptophans were greater in a D2O buffer compared with H2O, showing |
| 1426 |
< |
that the fluorophores were exposed to water in the bilayer at the |
| 1427 |
< |
protein-lipid interface. In the presence of cholesterol the fluorescence |
| 1428 |
< |
intensity ratio of D2O to H2O decreased, indicating a removal of |
| 1429 |
< |
water by the cholesterol, in keeping with the lifetime data. Altered |
| 1430 |
< |
hydration at the protein-lipid interface could affect conformation, |
| 1431 |
< |
thereby offering a new route by which membrane protein functioning |
| 1432 |
< |
may be modified.}, |
| 1407 |
> |
hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome |
| 1408 |
> |
C, using two related fluorescence spectroscopic approaches. The |
| 1409 |
> |
first approach exploited the fact that the presence of water in |
| 1410 |
> |
the excited state solvent cage of a fluorophore increases the rate |
| 1411 |
> |
of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl) |
| 1412 |
> |
phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores |
| 1413 |
> |
are located in the hydrophobic core of the lipid bilayer, the introduction |
| 1414 |
> |
of gramicidin reduced the fluorescence lifetime, indicative of an |
| 1415 |
> |
increased presence of water in the bilayer. Since a high protein:lipid |
| 1416 |
> |
ratio was used, the fluorophores were forced to be adjacent to the |
| 1417 |
> |
protein hydrophobic surface, hence the presence of water in this |
| 1418 |
> |
region could be inferred. Cholesterol is known to reduce the water |
| 1419 |
> |
content of lipid bilayers and this effect was maintained at the |
| 1420 |
> |
protein-lipid interface with both gramicidin and apocytochrome C, |
| 1421 |
> |
again suggesting hydration in this region. The second approach was |
| 1422 |
> |
to use the fluorescence enhancement induced by exchanging deuterium |
| 1423 |
> |
oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH, |
| 1424 |
> |
located in the lipid head group region, and of the gramicidin intrinsic |
| 1425 |
> |
tryptophans were greater in a D2O buffer compared with H2O, showing |
| 1426 |
> |
that the fluorophores were exposed to water in the bilayer at the |
| 1427 |
> |
protein-lipid interface. In the presence of cholesterol the fluorescence |
| 1428 |
> |
intensity ratio of D2O to H2O decreased, indicating a removal of |
| 1429 |
> |
water by the cholesterol, in keeping with the lifetime data. Altered |
| 1430 |
> |
hydration at the protein-lipid interface could affect conformation, |
| 1431 |
> |
thereby offering a new route by which membrane protein functioning |
| 1432 |
> |
may be modified.}, |
| 1433 |
|
annote = {Ju251 Times Cited:55 Cited References Count:44}, |
| 1434 |
|
issn = {0006-3495}, |
| 1435 |
|
uri = {<Go to ISI>://A1992JU25100002}, |
| 1443 |
|
address = {New York}, |
| 1444 |
|
} |
| 1445 |
|
|
| 1446 |
+ |
@ARTICLE{Hoover1985, |
| 1447 |
+ |
author = {W. G. Hoover}, |
| 1448 |
+ |
title = {Canonical Dynamics - Equilibrium Phase-Space Distributions}, |
| 1449 |
+ |
journal = {Physical Review A}, |
| 1450 |
+ |
year = {1985}, |
| 1451 |
+ |
volume = {31}, |
| 1452 |
+ |
pages = {1695-1697}, |
| 1453 |
+ |
number = {3}, |
| 1454 |
+ |
annote = {Acr30 Times Cited:1809 Cited References Count:11}, |
| 1455 |
+ |
issn = {1050-2947}, |
| 1456 |
+ |
uri = {<Go to ISI>://A1985ACR3000056}, |
| 1457 |
+ |
} |
| 1458 |
+ |
|
| 1459 |
|
@ARTICLE{Huh2004, |
| 1460 |
|
author = {Y. Huh and N. M. Cann}, |
| 1461 |
|
title = {Discrimination in isotropic, nematic, and smectic phases of chiral |
| 1462 |
< |
calamitic molecules: A computer simulation study}, |
| 1462 |
> |
calamitic molecules: A computer simulation study}, |
| 1463 |
|
journal = {Journal of Chemical Physics}, |
| 1464 |
|
year = {2004}, |
| 1465 |
|
volume = {121}, |
| 1467 |
|
number = {20}, |
| 1468 |
|
month = {Nov 22}, |
| 1469 |
|
abstract = {Racemic fluids of chiral calamitic molecules are investigated with |
| 1470 |
< |
molecular dynamics simulations. In particular, the phase behavior |
| 1471 |
< |
as a function of density is examined for eight racemates. The relationship |
| 1472 |
< |
between chiral discrimination and orientational order in the phase |
| 1473 |
< |
is explored. We find that the transition from the isotropic phase |
| 1474 |
< |
to a liquid crystal phase is accompanied by an increase in chiral |
| 1475 |
< |
discrimination, as measured by differences in radial distributions. |
| 1476 |
< |
Among ordered phases, discrimination is largest for smectic phases |
| 1477 |
< |
with a significant preference for heterochiral contact within the |
| 1478 |
< |
layers. (C) 2004 American Institute of Physics.}, |
| 1470 |
> |
molecular dynamics simulations. In particular, the phase behavior |
| 1471 |
> |
as a function of density is examined for eight racemates. The relationship |
| 1472 |
> |
between chiral discrimination and orientational order in the phase |
| 1473 |
> |
is explored. We find that the transition from the isotropic phase |
| 1474 |
> |
to a liquid crystal phase is accompanied by an increase in chiral |
| 1475 |
> |
discrimination, as measured by differences in radial distributions. |
| 1476 |
> |
Among ordered phases, discrimination is largest for smectic phases |
| 1477 |
> |
with a significant preference for heterochiral contact within the |
| 1478 |
> |
layers. (C) 2004 American Institute of Physics.}, |
| 1479 |
|
annote = {870FJ Times Cited:0 Cited References Count:63}, |
| 1480 |
|
issn = {0021-9606}, |
| 1481 |
|
uri = {<Go to ISI>://000225042700059}, |
| 1482 |
|
} |
| 1483 |
|
|
| 1484 |
+ |
@ARTICLE{Humphrey1996, |
| 1485 |
+ |
author = {W. Humphrey and A. Dalke and K. Schulten}, |
| 1486 |
+ |
title = {VMD: Visual molecular dynamics}, |
| 1487 |
+ |
journal = {Journal of Molecular Graphics}, |
| 1488 |
+ |
year = {1996}, |
| 1489 |
+ |
volume = {14}, |
| 1490 |
+ |
pages = {33-\&}, |
| 1491 |
+ |
number = {1}, |
| 1492 |
+ |
month = {Feb}, |
| 1493 |
+ |
abstract = {VMD is a molecular graphics program designed for the display and analysis |
| 1494 |
+ |
of molecular assemblies, in particular biopolymers such as proteins |
| 1495 |
+ |
and nucleic acids. VMD can simultaneously display any number of |
| 1496 |
+ |
structures using a wide variety of rendering styles and coloring |
| 1497 |
+ |
methods. Molecules are displayed as one or more ''representations,'' |
| 1498 |
+ |
in which each representation embodies a particular rendering method |
| 1499 |
+ |
and coloring scheme for a selected subset of atoms. The atoms displayed |
| 1500 |
+ |
in each representation are chosen using an extensive atom selection |
| 1501 |
+ |
syntax, which includes Boolean operators and regular expressions. |
| 1502 |
+ |
VMD provides a complete graphical user interface for program control, |
| 1503 |
+ |
as well as a text interface using the Tcl embeddable parser to allow |
| 1504 |
+ |
for complex scripts with variable substitution, control loops, and |
| 1505 |
+ |
function calls. Full session logging is supported, which produces |
| 1506 |
+ |
a VMD command script for later playback. High-resolution raster |
| 1507 |
+ |
images of displayed molecules may be produced by generating input |
| 1508 |
+ |
scripts for use by a number of photorealistic image-rendering applications. |
| 1509 |
+ |
VMD has also been expressly designed with the ability to animate |
| 1510 |
+ |
molecular dynamics (MD) simulation trajectories, imported either |
| 1511 |
+ |
from files or from a direct connection to a running MD simulation. |
| 1512 |
+ |
VMD is the visualization component of MDScope, a set of tools for |
| 1513 |
+ |
interactive problem solving in structural biology, which also includes |
| 1514 |
+ |
the parallel MD program NAMD, and the MDCOMM software used to connect |
| 1515 |
+ |
the visualization and simulation programs. VMD is written in C++, |
| 1516 |
+ |
using an object-oriented design; the program, including source code |
| 1517 |
+ |
and extensive documentation, is freely available via anonymous ftp |
| 1518 |
+ |
and through the World Wide Web.}, |
| 1519 |
+ |
annote = {Uh515 Times Cited:1418 Cited References Count:19}, |
| 1520 |
+ |
issn = {0263-7855}, |
| 1521 |
+ |
uri = {<Go to ISI>://A1996UH51500005}, |
| 1522 |
+ |
} |
| 1523 |
+ |
|
| 1524 |
|
@ARTICLE{Izaguirre2001, |
| 1525 |
|
author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel}, |
| 1526 |
|
title = {Langevin stabilization of molecular dynamics}, |
| 1531 |
|
number = {5}, |
| 1532 |
|
month = {Feb 1}, |
| 1533 |
|
abstract = {In this paper we show the possibility of using very mild stochastic |
| 1534 |
< |
damping to stabilize long time step integrators for Newtonian molecular |
| 1535 |
< |
dynamics. More specifically, stable and accurate integrations are |
| 1536 |
< |
obtained for damping coefficients that are only a few percent of |
| 1537 |
< |
the natural decay rate of processes of interest, such as the velocity |
| 1538 |
< |
autocorrelation function. Two new multiple time stepping integrators, |
| 1539 |
< |
Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are |
| 1540 |
< |
introduced in this paper. Both use the mollified impulse method |
| 1541 |
< |
for the Newtonian term. LM uses a discretization of the Langevin |
| 1542 |
< |
equation that is exact for the constant force, and BBK-M uses the |
| 1543 |
< |
popular Brunger-Brooks-Karplus integrator (BBK). These integrators, |
| 1544 |
< |
along with an extrapolative method called LN, are evaluated across |
| 1545 |
< |
a wide range of damping coefficient values. When large damping coefficients |
| 1546 |
< |
are used, as one would for the implicit modeling of solvent molecules, |
| 1547 |
< |
the method LN is superior, with LM closely following. However, with |
| 1548 |
< |
mild damping of 0.2 ps(-1), LM produces the best results, allowing |
| 1549 |
< |
long time steps of 14 fs in simulations containing explicitly modeled |
| 1550 |
< |
flexible water. With BBK-M and the same damping coefficient, time |
| 1551 |
< |
steps of 12 fs are possible for the same system. Similar results |
| 1552 |
< |
are obtained for a solvated protein-DNA simulation of estrogen receptor |
| 1553 |
< |
ER with estrogen response element ERE. A parallel version of BBK-M |
| 1554 |
< |
runs nearly three times faster than the Verlet-I/r-RESPA (reversible |
| 1555 |
< |
reference system propagator algorithm) when using the largest stable |
| 1556 |
< |
time step on each one, and it also parallelizes well. The computation |
| 1557 |
< |
of diffusion coefficients for flexible water and ER/ERE shows that |
| 1558 |
< |
when mild damping of up to 0.2 ps-1 is used the dynamics are not |
| 1559 |
< |
significantly distorted. (C) 2001 American Institute of Physics.}, |
| 1534 |
> |
damping to stabilize long time step integrators for Newtonian molecular |
| 1535 |
> |
dynamics. More specifically, stable and accurate integrations are |
| 1536 |
> |
obtained for damping coefficients that are only a few percent of |
| 1537 |
> |
the natural decay rate of processes of interest, such as the velocity |
| 1538 |
> |
autocorrelation function. Two new multiple time stepping integrators, |
| 1539 |
> |
Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are |
| 1540 |
> |
introduced in this paper. Both use the mollified impulse method |
| 1541 |
> |
for the Newtonian term. LM uses a discretization of the Langevin |
| 1542 |
> |
equation that is exact for the constant force, and BBK-M uses the |
| 1543 |
> |
popular Brunger-Brooks-Karplus integrator (BBK). These integrators, |
| 1544 |
> |
along with an extrapolative method called LN, are evaluated across |
| 1545 |
> |
a wide range of damping coefficient values. When large damping coefficients |
| 1546 |
> |
are used, as one would for the implicit modeling of solvent molecules, |
| 1547 |
> |
the method LN is superior, with LM closely following. However, with |
| 1548 |
> |
mild damping of 0.2 ps(-1), LM produces the best results, allowing |
| 1549 |
> |
long time steps of 14 fs in simulations containing explicitly modeled |
| 1550 |
> |
flexible water. With BBK-M and the same damping coefficient, time |
| 1551 |
> |
steps of 12 fs are possible for the same system. Similar results |
| 1552 |
> |
are obtained for a solvated protein-DNA simulation of estrogen receptor |
| 1553 |
> |
ER with estrogen response element ERE. A parallel version of BBK-M |
| 1554 |
> |
runs nearly three times faster than the Verlet-I/r-RESPA (reversible |
| 1555 |
> |
reference system propagator algorithm) when using the largest stable |
| 1556 |
> |
time step on each one, and it also parallelizes well. The computation |
| 1557 |
> |
of diffusion coefficients for flexible water and ER/ERE shows that |
| 1558 |
> |
when mild damping of up to 0.2 ps-1 is used the dynamics are not |
| 1559 |
> |
significantly distorted. (C) 2001 American Institute of Physics.}, |
| 1560 |
|
annote = {397CQ Times Cited:14 Cited References Count:36}, |
| 1561 |
|
issn = {0021-9606}, |
| 1562 |
|
uri = {<Go to ISI>://000166676100020}, |
| 1571 |
|
pages = {1747-1763}, |
| 1572 |
|
} |
| 1573 |
|
|
| 1574 |
+ |
@ARTICLE{Kale1999, |
| 1575 |
+ |
author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy |
| 1576 |
+ |
and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan |
| 1577 |
+ |
and K. Schulten}, |
| 1578 |
+ |
title = {NAMD2: Greater scalability for parallel molecular dynamics}, |
| 1579 |
+ |
journal = {Journal of Computational Physics}, |
| 1580 |
+ |
year = {1999}, |
| 1581 |
+ |
volume = {151}, |
| 1582 |
+ |
pages = {283-312}, |
| 1583 |
+ |
number = {1}, |
| 1584 |
+ |
month = {May 1}, |
| 1585 |
+ |
abstract = {Molecular dynamics programs simulate the behavior of biomolecular |
| 1586 |
+ |
systems, leading to understanding of their functions. However, the |
| 1587 |
+ |
computational complexity of such simulations is enormous. Parallel |
| 1588 |
+ |
machines provide the potential to meet this computational challenge. |
| 1589 |
+ |
To harness this potential, it is necessary to develop a scalable |
| 1590 |
+ |
program. It is also necessary that the program be easily modified |
| 1591 |
+ |
by application-domain programmers. The NAMD2 program presented in |
| 1592 |
+ |
this paper seeks to provide these desirable features. It uses spatial |
| 1593 |
+ |
decomposition combined with force decomposition to enhance scalability. |
| 1594 |
+ |
It uses intelligent periodic load balancing, so as to maximally |
| 1595 |
+ |
utilize the available compute power. It is modularly organized, |
| 1596 |
+ |
and implemented using Charm++, a parallel C++ dialect, so as to |
| 1597 |
+ |
enhance its modifiability. It uses a combination of numerical techniques |
| 1598 |
+ |
and algorithms to ensure that energy drifts are minimized, ensuring |
| 1599 |
+ |
accuracy in long running calculations. NAMD2 uses a portable run-time |
| 1600 |
+ |
framework called Converse that also supports interoperability among |
| 1601 |
+ |
multiple parallel paradigms. As a result, different components of |
| 1602 |
+ |
applications can be written in the most appropriate parallel paradigms. |
| 1603 |
+ |
NAMD2 runs on most parallel machines including workstation clusters |
| 1604 |
+ |
and has yielded speedups in excess of 180 on 220 processors. This |
| 1605 |
+ |
paper also describes the performance obtained on some benchmark |
| 1606 |
+ |
applications. (C) 1999 Academic Press.}, |
| 1607 |
+ |
annote = {194FM Times Cited:373 Cited References Count:51}, |
| 1608 |
+ |
issn = {0021-9991}, |
| 1609 |
+ |
uri = {<Go to ISI>://000080181500013}, |
| 1610 |
+ |
} |
| 1611 |
+ |
|
| 1612 |
|
@ARTICLE{Kane2000, |
| 1613 |
|
author = {C. Kane and J. E. Marsden and M. Ortiz and M. West}, |
| 1614 |
|
title = {Variational integrators and the Newmark algorithm for conservative |
| 1615 |
< |
and dissipative mechanical systems}, |
| 1615 |
> |
and dissipative mechanical systems}, |
| 1616 |
|
journal = {International Journal for Numerical Methods in Engineering}, |
| 1617 |
|
year = {2000}, |
| 1618 |
|
volume = {49}, |
| 1620 |
|
number = {10}, |
| 1621 |
|
month = {Dec 10}, |
| 1622 |
|
abstract = {The purpose of this work is twofold. First, we demonstrate analytically |
| 1623 |
< |
that the classical Newmark family as well as related integration |
| 1624 |
< |
algorithms are variational in the sense of the Veselov formulation |
| 1625 |
< |
of discrete mechanics. Such variational algorithms are well known |
| 1626 |
< |
to be symplectic and momentum preserving and to often have excellent |
| 1627 |
< |
global energy behaviour. This analytical result is verified through |
| 1628 |
< |
numerical examples and is believed to be one of the primary reasons |
| 1629 |
< |
that this class of algorithms performs so well. Second, we develop |
| 1630 |
< |
algorithms for mechanical systems with forcing, and in particular, |
| 1631 |
< |
for dissipative systems. In this case, we develop integrators that |
| 1632 |
< |
are based on a discretization of the Lagrange d'Alembert principle |
| 1633 |
< |
as well as on a variational formulation of dissipation. It is demonstrated |
| 1634 |
< |
that these types of structured integrators have good numerical behaviour |
| 1635 |
< |
in terms of obtaining the correct amounts by which the energy changes |
| 1636 |
< |
over the integration run. Copyright (C) 2000 John Wiley & Sons, |
| 1637 |
< |
Ltd.}, |
| 1623 |
> |
that the classical Newmark family as well as related integration |
| 1624 |
> |
algorithms are variational in the sense of the Veselov formulation |
| 1625 |
> |
of discrete mechanics. Such variational algorithms are well known |
| 1626 |
> |
to be symplectic and momentum preserving and to often have excellent |
| 1627 |
> |
global energy behaviour. This analytical result is verified through |
| 1628 |
> |
numerical examples and is believed to be one of the primary reasons |
| 1629 |
> |
that this class of algorithms performs so well. Second, we develop |
| 1630 |
> |
algorithms for mechanical systems with forcing, and in particular, |
| 1631 |
> |
for dissipative systems. In this case, we develop integrators that |
| 1632 |
> |
are based on a discretization of the Lagrange d'Alembert principle |
| 1633 |
> |
as well as on a variational formulation of dissipation. It is demonstrated |
| 1634 |
> |
that these types of structured integrators have good numerical behaviour |
| 1635 |
> |
in terms of obtaining the correct amounts by which the energy changes |
| 1636 |
> |
over the integration run. Copyright (C) 2000 John Wiley & Sons, |
| 1637 |
> |
Ltd.}, |
| 1638 |
|
annote = {373CJ Times Cited:30 Cited References Count:41}, |
| 1639 |
|
issn = {0029-5981}, |
| 1640 |
|
uri = {<Go to ISI>://000165270600004}, |
| 1650 |
|
number = {2}, |
| 1651 |
|
month = {Jul 14}, |
| 1652 |
|
abstract = {The viscosity (eta) dependence of the folding rates for four sequences |
| 1653 |
< |
(the native state of three sequences is a beta sheet, while the |
| 1654 |
< |
fourth forms an alpha helix) is calculated for off-lattice models |
| 1655 |
< |
of proteins. Assuming that the dynamics is given by the Langevin |
| 1656 |
< |
equation, we show that the folding rates increase linearly at low |
| 1657 |
< |
viscosities eta, decrease as 1/eta at large eta, and have a maximum |
| 1658 |
< |
at intermediate values. The Kramers' theory of barrier crossing |
| 1659 |
< |
provides a quantitative fit of the numerical results. By mapping |
| 1660 |
< |
the simulation results to real proteins we estimate that for optimized |
| 1661 |
< |
sequences the time scale for forming a four turn alpha-helix topology |
| 1662 |
< |
is about 500 ns, whereas for beta sheet it is about 10 mu s.}, |
| 1653 |
> |
(the native state of three sequences is a beta sheet, while the |
| 1654 |
> |
fourth forms an alpha helix) is calculated for off-lattice models |
| 1655 |
> |
of proteins. Assuming that the dynamics is given by the Langevin |
| 1656 |
> |
equation, we show that the folding rates increase linearly at low |
| 1657 |
> |
viscosities eta, decrease as 1/eta at large eta, and have a maximum |
| 1658 |
> |
at intermediate values. The Kramers' theory of barrier crossing |
| 1659 |
> |
provides a quantitative fit of the numerical results. By mapping |
| 1660 |
> |
the simulation results to real proteins we estimate that for optimized |
| 1661 |
> |
sequences the time scale for forming a four turn alpha-helix topology |
| 1662 |
> |
is about 500 ns, whereas for beta sheet it is about 10 mu s.}, |
| 1663 |
|
annote = {Xk293 Times Cited:77 Cited References Count:17}, |
| 1664 |
|
issn = {0031-9007}, |
| 1665 |
|
uri = {<Go to ISI>://A1997XK29300035}, |
| 1675 |
|
number = {7}, |
| 1676 |
|
month = {Aug 15}, |
| 1677 |
|
abstract = {Rigid-body molecular dynamics simulations typically are performed |
| 1678 |
< |
in a quaternion representation. The nonseparable form of the Hamiltonian |
| 1679 |
< |
in quaternions prevents the use of a standard leapfrog (Verlet) |
| 1680 |
< |
integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation |
| 1681 |
< |
methods are generally used, This is unfortunate since symplectic |
| 1682 |
< |
methods like Verlet exhibit superior energy conservation in long-time |
| 1683 |
< |
integrations. In this article, we describe an alternative method, |
| 1684 |
< |
which we call RSHAKE (for rotation-SHAKE), in which the entire rotation |
| 1685 |
< |
matrix is evolved (using the scheme of McLachlan and Scovel [J. |
| 1686 |
< |
Nonlin. Sci, 16 233 (1995)]) in tandem with the particle positions. |
| 1687 |
< |
We employ a fast approximate Newton solver to preserve the orthogonality |
| 1688 |
< |
of the rotation matrix. We test our method on a system of soft-sphere |
| 1689 |
< |
dipoles and compare with quaternion evolution using a 4th-order |
| 1690 |
< |
predictor-corrector integrator, Although the short-time error of |
| 1691 |
< |
the quaternion algorithm is smaller for fixed time step than that |
| 1692 |
< |
for RSHAKE, the quaternion scheme exhibits an energy drift which |
| 1693 |
< |
is not observed in simulations with RSHAKE, hence a fixed energy |
| 1694 |
< |
tolerance can be achieved by using a larger time step, The superiority |
| 1695 |
< |
of RSHAKE increases with system size. (C) 1997 American Institute |
| 1696 |
< |
of Physics.}, |
| 1678 |
> |
in a quaternion representation. The nonseparable form of the Hamiltonian |
| 1679 |
> |
in quaternions prevents the use of a standard leapfrog (Verlet) |
| 1680 |
> |
integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation |
| 1681 |
> |
methods are generally used, This is unfortunate since symplectic |
| 1682 |
> |
methods like Verlet exhibit superior energy conservation in long-time |
| 1683 |
> |
integrations. In this article, we describe an alternative method, |
| 1684 |
> |
which we call RSHAKE (for rotation-SHAKE), in which the entire rotation |
| 1685 |
> |
matrix is evolved (using the scheme of McLachlan and Scovel [J. |
| 1686 |
> |
Nonlin. Sci, 16 233 (1995)]) in tandem with the particle positions. |
| 1687 |
> |
We employ a fast approximate Newton solver to preserve the orthogonality |
| 1688 |
> |
of the rotation matrix. We test our method on a system of soft-sphere |
| 1689 |
> |
dipoles and compare with quaternion evolution using a 4th-order |
| 1690 |
> |
predictor-corrector integrator, Although the short-time error of |
| 1691 |
> |
the quaternion algorithm is smaller for fixed time step than that |
| 1692 |
> |
for RSHAKE, the quaternion scheme exhibits an energy drift which |
| 1693 |
> |
is not observed in simulations with RSHAKE, hence a fixed energy |
| 1694 |
> |
tolerance can be achieved by using a larger time step, The superiority |
| 1695 |
> |
of RSHAKE increases with system size. (C) 1997 American Institute |
| 1696 |
> |
of Physics.}, |
| 1697 |
|
annote = {Xq332 Times Cited:11 Cited References Count:18}, |
| 1698 |
|
issn = {0021-9606}, |
| 1699 |
|
uri = {<Go to ISI>://A1997XQ33200046}, |
| 1702 |
|
@ARTICLE{Lansac2001, |
| 1703 |
|
author = {Y. Lansac and M. A. Glaser and N. A. Clark}, |
| 1704 |
|
title = {Microscopic structure and dynamics of a partial bilayer smectic liquid |
| 1705 |
< |
crystal}, |
| 1705 |
> |
crystal}, |
| 1706 |
|
journal = {Physical Review E}, |
| 1707 |
|
year = {2001}, |
| 1708 |
|
volume = {6405}, |
| 1710 |
|
number = {5}, |
| 1711 |
|
month = {Nov}, |
| 1712 |
|
abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied |
| 1713 |
< |
class of mesogens. Many of the peculiar properties of nCB's (e.g., |
| 1714 |
< |
the occurence of the partial bilayer smectic-A(d) phase) are thought |
| 1715 |
< |
to be a manifestation of short-range antiparallel association of |
| 1716 |
< |
neighboring molecules, resulting from strong dipole-dipole interactions |
| 1717 |
< |
between cyano groups. To test and extend existing models of microscopic |
| 1718 |
< |
ordering in nCB's, we carry out large-scale atomistic simulation |
| 1719 |
< |
studies of the microscopic structure and dynamics of the Sm-A(d) |
| 1720 |
< |
phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of |
| 1721 |
< |
thermodynamic, structural, and dynamical properties for this material, |
| 1722 |
< |
and make a detailed comparison of our results with experimental |
| 1723 |
< |
measurements in order to validate our molecular model. Semiquantitative |
| 1724 |
< |
agreement with experiment is found: the smectic layer spacing and |
| 1725 |
< |
mass density are well reproduced, translational diffusion constants |
| 1726 |
< |
are similar to experiment, but the orientational ordering of alkyl |
| 1727 |
< |
chains is overestimated. This simulation provides a detailed picture |
| 1728 |
< |
of molecular conformation, smectic layer structure, and intermolecular |
| 1729 |
< |
correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range |
| 1730 |
< |
antiparallel association of molecules arising from dipole-dipole |
| 1731 |
< |
interactions plays a dominant role in determining the molecular-scale |
| 1732 |
< |
structure of 8CB.}, |
| 1713 |
> |
class of mesogens. Many of the peculiar properties of nCB's (e.g., |
| 1714 |
> |
the occurence of the partial bilayer smectic-A(d) phase) are thought |
| 1715 |
> |
to be a manifestation of short-range antiparallel association of |
| 1716 |
> |
neighboring molecules, resulting from strong dipole-dipole interactions |
| 1717 |
> |
between cyano groups. To test and extend existing models of microscopic |
| 1718 |
> |
ordering in nCB's, we carry out large-scale atomistic simulation |
| 1719 |
> |
studies of the microscopic structure and dynamics of the Sm-A(d) |
| 1720 |
> |
phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of |
| 1721 |
> |
thermodynamic, structural, and dynamical properties for this material, |
| 1722 |
> |
and make a detailed comparison of our results with experimental |
| 1723 |
> |
measurements in order to validate our molecular model. Semiquantitative |
| 1724 |
> |
agreement with experiment is found: the smectic layer spacing and |
| 1725 |
> |
mass density are well reproduced, translational diffusion constants |
| 1726 |
> |
are similar to experiment, but the orientational ordering of alkyl |
| 1727 |
> |
chains is overestimated. This simulation provides a detailed picture |
| 1728 |
> |
of molecular conformation, smectic layer structure, and intermolecular |
| 1729 |
> |
correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range |
| 1730 |
> |
antiparallel association of molecules arising from dipole-dipole |
| 1731 |
> |
interactions plays a dominant role in determining the molecular-scale |
| 1732 |
> |
structure of 8CB.}, |
| 1733 |
|
annote = {Part 1 496QF Times Cited:10 Cited References Count:60}, |
| 1734 |
|
issn = {1063-651X}, |
| 1735 |
|
uri = {<Go to ISI>://000172406900063}, |
| 1745 |
|
number = {1}, |
| 1746 |
|
month = {Jan}, |
| 1747 |
|
abstract = {Recently, a new class of smectic liquid crystal phases characterized |
| 1748 |
< |
by the spontaneous formation of macroscopic chiral domains from |
| 1749 |
< |
achiral bent-core molecules has been discovered. We have carried |
| 1750 |
< |
out Monte Carlo simulations of a minimal hard spherocylinder dimer |
| 1751 |
< |
model to investigate the role of excluded volume interactions in |
| 1752 |
< |
determining the phase behavior of bent-core materials and to probe |
| 1753 |
< |
the molecular origins of polar and chiral symmetry breaking. We |
| 1754 |
< |
present the phase diagram of hard spherocylinder dimers of length-diameter |
| 1755 |
< |
ratio of 5 as a function of pressure or density and dimer opening |
| 1756 |
< |
angle psi. With decreasing psi, a transition from a nonpolar to |
| 1757 |
< |
a polar smectic A phase is observed near psi=167degrees, and the |
| 1758 |
< |
nematic phase becomes thermodynamically unstable for psi<135degrees. |
| 1759 |
< |
Free energy calculations indicate that the antipolar smectic A (SmAP(A)) |
| 1760 |
< |
phase is more stable than the polar smectic A phase (SmAP(F)). No |
| 1761 |
< |
chiral smectic or biaxial nematic phases were found.}, |
| 1748 |
> |
by the spontaneous formation of macroscopic chiral domains from |
| 1749 |
> |
achiral bent-core molecules has been discovered. We have carried |
| 1750 |
> |
out Monte Carlo simulations of a minimal hard spherocylinder dimer |
| 1751 |
> |
model to investigate the role of excluded volume interactions in |
| 1752 |
> |
determining the phase behavior of bent-core materials and to probe |
| 1753 |
> |
the molecular origins of polar and chiral symmetry breaking. We |
| 1754 |
> |
present the phase diagram of hard spherocylinder dimers of length-diameter |
| 1755 |
> |
ratio of 5 as a function of pressure or density and dimer opening |
| 1756 |
> |
angle psi. With decreasing psi, a transition from a nonpolar to |
| 1757 |
> |
a polar smectic A phase is observed near psi=167degrees, and the |
| 1758 |
> |
nematic phase becomes thermodynamically unstable for psi<135degrees. |
| 1759 |
> |
Free energy calculations indicate that the antipolar smectic A (SmAP(A)) |
| 1760 |
> |
phase is more stable than the polar smectic A phase (SmAP(F)). No |
| 1761 |
> |
chiral smectic or biaxial nematic phases were found.}, |
| 1762 |
|
annote = {Part 1 646CM Times Cited:15 Cited References Count:38}, |
| 1763 |
|
issn = {1063-651X}, |
| 1764 |
|
uri = {<Go to ISI>://000181017300042}, |
| 1776 |
|
@ARTICLE{Leimkuhler1999, |
| 1777 |
|
author = {B. Leimkuhler}, |
| 1778 |
|
title = {Reversible adaptive regularization: perturbed Kepler motion and classical |
| 1779 |
< |
atomic trajectories}, |
| 1779 |
> |
atomic trajectories}, |
| 1780 |
|
journal = {Philosophical Transactions of the Royal Society of London Series |
| 1781 |
< |
a-Mathematical Physical and Engineering Sciences}, |
| 1781 |
> |
a-Mathematical Physical and Engineering Sciences}, |
| 1782 |
|
year = {1999}, |
| 1783 |
|
volume = {357}, |
| 1784 |
|
pages = {1101-1133}, |
| 1785 |
|
number = {1754}, |
| 1786 |
|
month = {Apr 15}, |
| 1787 |
|
abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel |
| 1788 |
< |
regularization and modified Sundman transformations are applied |
| 1789 |
< |
to simulate general perturbed Kepler motion and to compute classical |
| 1790 |
< |
trajectories of atomic systems (e.g. Rydberg atoms). The new family |
| 1791 |
< |
of reversible adaptive regularization methods also conserves angular |
| 1792 |
< |
momentum and exhibits superior energy conservation and numerical |
| 1793 |
< |
stability in long-time integrations. The schemes are appropriate |
| 1794 |
< |
for scattering, for astronomical calculations of escape time and |
| 1795 |
< |
long-term stability, and for classical and semiclassical studies |
| 1796 |
< |
of atomic dynamics. The components of an algorithm for trajectory |
| 1797 |
< |
calculations are described. Numerical experiments illustrate the |
| 1798 |
< |
effectiveness of the reversible approach.}, |
| 1788 |
> |
regularization and modified Sundman transformations are applied |
| 1789 |
> |
to simulate general perturbed Kepler motion and to compute classical |
| 1790 |
> |
trajectories of atomic systems (e.g. Rydberg atoms). The new family |
| 1791 |
> |
of reversible adaptive regularization methods also conserves angular |
| 1792 |
> |
momentum and exhibits superior energy conservation and numerical |
| 1793 |
> |
stability in long-time integrations. The schemes are appropriate |
| 1794 |
> |
for scattering, for astronomical calculations of escape time and |
| 1795 |
> |
long-term stability, and for classical and semiclassical studies |
| 1796 |
> |
of atomic dynamics. The components of an algorithm for trajectory |
| 1797 |
> |
calculations are described. Numerical experiments illustrate the |
| 1798 |
> |
effectiveness of the reversible approach.}, |
| 1799 |
|
annote = {199EE Times Cited:11 Cited References Count:48}, |
| 1800 |
|
issn = {1364-503X}, |
| 1801 |
|
uri = {<Go to ISI>://000080466800007}, |
| 1811 |
|
|
| 1812 |
|
@ARTICLE{Levelut1981, |
| 1813 |
|
author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard |
| 1814 |
< |
and G. Sigaud}, |
| 1814 |
> |
and G. Sigaud}, |
| 1815 |
|
title = {Number of Sa Phases}, |
| 1816 |
|
journal = {Physical Review A}, |
| 1817 |
|
year = {1981}, |
| 1826 |
|
@ARTICLE{Lieb1982, |
| 1827 |
|
author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn}, |
| 1828 |
|
title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - |
| 1829 |
< |
Evidence from Raman-Scattering}, |
| 1829 |
> |
Evidence from Raman-Scattering}, |
| 1830 |
|
journal = {Biochimica Et Biophysica Acta}, |
| 1831 |
|
year = {1982}, |
| 1832 |
|
volume = {688}, |
| 1839 |
|
|
| 1840 |
|
@ARTICLE{Link1997, |
| 1841 |
|
author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A. |
| 1842 |
< |
Clark and E. Korblova and D. M. Walba}, |
| 1842 |
> |
Clark and E. Korblova and D. M. Walba}, |
| 1843 |
|
title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic |
| 1844 |
< |
phase of achiral molecules}, |
| 1844 |
> |
phase of achiral molecules}, |
| 1845 |
|
journal = {Science}, |
| 1846 |
|
year = {1997}, |
| 1847 |
|
volume = {278}, |
| 1849 |
|
number = {5345}, |
| 1850 |
|
month = {Dec 12}, |
| 1851 |
|
abstract = {A smectic liquid-crystal phase made from achiral molecules with bent |
| 1852 |
< |
cores was found to have fluid layers that exhibit two spontaneous |
| 1853 |
< |
symmetry-breaking instabilities: polar molecular orientational ordering |
| 1854 |
< |
about the layer normal and molecular tilt. These instabilities combine |
| 1855 |
< |
to form a chiral layer structure with a handedness that depends |
| 1856 |
< |
on the sign of the tilt. The bulk states are either antiferroelectric-racemic, |
| 1857 |
< |
with the layer polar direction and handedness alternating in sign |
| 1858 |
< |
from layer to layer, or antiferroelectric-chiral, which is of uniform |
| 1859 |
< |
layer handedness. Both states exhibit an electric field-induced |
| 1860 |
< |
transition from antiferroelectric to ferroelectric.}, |
| 1852 |
> |
cores was found to have fluid layers that exhibit two spontaneous |
| 1853 |
> |
symmetry-breaking instabilities: polar molecular orientational ordering |
| 1854 |
> |
about the layer normal and molecular tilt. These instabilities combine |
| 1855 |
> |
to form a chiral layer structure with a handedness that depends |
| 1856 |
> |
on the sign of the tilt. The bulk states are either antiferroelectric-racemic, |
| 1857 |
> |
with the layer polar direction and handedness alternating in sign |
| 1858 |
> |
from layer to layer, or antiferroelectric-chiral, which is of uniform |
| 1859 |
> |
layer handedness. Both states exhibit an electric field-induced |
| 1860 |
> |
transition from antiferroelectric to ferroelectric.}, |
| 1861 |
|
annote = {Yl002 Times Cited:407 Cited References Count:25}, |
| 1862 |
|
issn = {0036-8075}, |
| 1863 |
|
uri = {<Go to ISI>://A1997YL00200028}, |
| 1866 |
|
@ARTICLE{Liwo2005, |
| 1867 |
|
author = {A. Liwo and M. Khalili and H. A. Scheraga}, |
| 1868 |
|
title = {Ab initio simulations of protein folding pathways by molecular dynamics |
| 1869 |
< |
with the united-residue (UNRES) model of polypeptide chains}, |
| 1869 |
> |
with the united-residue (UNRES) model of polypeptide chains}, |
| 1870 |
|
journal = {Febs Journal}, |
| 1871 |
|
year = {2005}, |
| 1872 |
|
volume = {272}, |
| 1880 |
|
@ARTICLE{Luty1994, |
| 1881 |
|
author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren}, |
| 1882 |
|
title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods |
| 1883 |
< |
for Calculating Electrostatic Interactions in Periodic Molecular-Systems}, |
| 1883 |
> |
for Calculating Electrostatic Interactions in Periodic Molecular-Systems}, |
| 1884 |
|
journal = {Molecular Simulation}, |
| 1885 |
|
year = {1994}, |
| 1886 |
|
volume = {14}, |
| 1887 |
|
pages = {11-20}, |
| 1888 |
|
number = {1}, |
| 1889 |
|
abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods |
| 1890 |
< |
for calculating electrostatic interactions in periodic molecular |
| 1891 |
< |
systems. A brief comparison of the theories shows that the methods |
| 1892 |
< |
are very similar differing mainly in the technique which is used |
| 1893 |
< |
to perform the ''k-space'' or mesh calculation. Because the PPPM |
| 1894 |
< |
utilizes the highly efficient numerical Fast Fourier Transform (FFT) |
| 1895 |
< |
method it requires significantly less computational effort than |
| 1896 |
< |
the Ewald method and scale's almost linearly with system size.}, |
| 1890 |
> |
for calculating electrostatic interactions in periodic molecular |
| 1891 |
> |
systems. A brief comparison of the theories shows that the methods |
| 1892 |
> |
are very similar differing mainly in the technique which is used |
| 1893 |
> |
to perform the ''k-space'' or mesh calculation. Because the PPPM |
| 1894 |
> |
utilizes the highly efficient numerical Fast Fourier Transform (FFT) |
| 1895 |
> |
method it requires significantly less computational effort than |
| 1896 |
> |
the Ewald method and scale's almost linearly with system size.}, |
| 1897 |
|
annote = {Qf464 Times Cited:50 Cited References Count:20}, |
| 1898 |
|
issn = {0892-7022}, |
| 1899 |
|
uri = {<Go to ISI>://A1994QF46400002}, |
| 1908 |
|
edition = {2rd}, |
| 1909 |
|
} |
| 1910 |
|
|
| 1911 |
+ |
@ARTICLE{Marrink1994, |
| 1912 |
+ |
author = {S. J. Marrink and H. J. C. Berendsen}, |
| 1913 |
+ |
title = {Simulation of Water Transport through a Lipid-Membrane}, |
| 1914 |
+ |
journal = {Journal of Physical Chemistry}, |
| 1915 |
+ |
year = {1994}, |
| 1916 |
+ |
volume = {98}, |
| 1917 |
+ |
pages = {4155-4168}, |
| 1918 |
+ |
number = {15}, |
| 1919 |
+ |
month = {Apr 14}, |
| 1920 |
+ |
abstract = {To obtain insight in the process of water permeation through a lipid |
| 1921 |
+ |
membrane, we performed molecular dynamics simulations on a phospholipid |
| 1922 |
+ |
(DPPC)/water system with atomic detail. Since the actual process |
| 1923 |
+ |
of permeation is too slow to be studied directly, we deduced the |
| 1924 |
+ |
permeation rate indirectly via computation of the free energy and |
| 1925 |
+ |
diffusion rate profiles of a water molecule across the bilayer. |
| 1926 |
+ |
We conclude that the permeation of water through a lipid membrane |
| 1927 |
+ |
cannot be described adequately by a simple homogeneous solubility-diffusion |
| 1928 |
+ |
model. Both the excess free energy and the diffusion rate strongly |
| 1929 |
+ |
depend on the position in the membrane, as a result from the inhomogeneous |
| 1930 |
+ |
nature of the membrane. The calculated excess free energy profile |
| 1931 |
+ |
has a shallow slope and a maximum height of 26 kJ/mol. The diffusion |
| 1932 |
+ |
rate is highest in the middle of the membrane where the lipid density |
| 1933 |
+ |
is low. In the interfacial region almost all water molecules are |
| 1934 |
+ |
bound by the lipid headgroups, and the diffusion turns out to be |
| 1935 |
+ |
1 order of magnitude smaller. The total transport process is essentially |
| 1936 |
+ |
determined by the free energy barrier. The rate-limiting step is |
| 1937 |
+ |
the permeation through the dense part of the lipid tails, where |
| 1938 |
+ |
the resistance is highest. We found a permeation rate of 7(+/-3) |
| 1939 |
+ |
x 10(-2) cm/s at 350 K, comparable to experimental values for DPPC |
| 1940 |
+ |
membranes, if corrected for the temperature of the simulation. Taking |
| 1941 |
+ |
the inhomogeneity of the membrane into account, we define a new |
| 1942 |
+ |
''four-region'' model which seems to be more realistic than the |
| 1943 |
+ |
''two-phase'' solubility-diffusion model.}, |
| 1944 |
+ |
annote = {Ng219 Times Cited:187 Cited References Count:25}, |
| 1945 |
+ |
issn = {0022-3654}, |
| 1946 |
+ |
uri = {<Go to ISI>://A1994NG21900040}, |
| 1947 |
+ |
} |
| 1948 |
+ |
|
| 1949 |
|
@ARTICLE{Marsden1998, |
| 1950 |
|
author = {J. E. Marsden and G. W. Patrick and S. Shkoller}, |
| 1951 |
|
title = {Multisymplectic geometry, variational integrators, and nonlinear |
| 1952 |
< |
PDEs}, |
| 1952 |
> |
PDEs}, |
| 1953 |
|
journal = {Communications in Mathematical Physics}, |
| 1954 |
|
year = {1998}, |
| 1955 |
|
volume = {199}, |
| 1957 |
|
number = {2}, |
| 1958 |
|
month = {Dec}, |
| 1959 |
|
abstract = {This paper presents a geometric-variational approach to continuous |
| 1960 |
< |
and discrete mechanics and field theories. Using multisymplectic |
| 1961 |
< |
geometry, we show that the existence of the fundamental geometric |
| 1962 |
< |
structures as well as their preservation along solutions can be |
| 1963 |
< |
obtained directly from the variational principle. In particular, |
| 1964 |
< |
we prove that a unique multisymplectic structure is obtained by |
| 1965 |
< |
taking the derivative of an action function, and use this structure |
| 1966 |
< |
to prove covariant generalizations of conservation of symplecticity |
| 1967 |
< |
and Noether's theorem. Natural discretization schemes for PDEs, |
| 1968 |
< |
which have these important preservation properties, then follow |
| 1969 |
< |
by choosing a discrete action functional. In the case of mechanics, |
| 1970 |
< |
we recover the variational symplectic integrators of Veselov type, |
| 1971 |
< |
while for PDEs we obtain covariant spacetime integrators which conserve |
| 1972 |
< |
the corresponding discrete multisymplectic form as well as the discrete |
| 1973 |
< |
momentum mappings corresponding to symmetries. We show that the |
| 1974 |
< |
usual notion of symplecticity along an infinite-dimensional space |
| 1975 |
< |
of fields can be naturally obtained by making a spacetime split. |
| 1976 |
< |
All of the aspects of our method are demonstrated with a nonlinear |
| 1977 |
< |
sine-Gordon equation, including computational results and a comparison |
| 1978 |
< |
with other discretization schemes.}, |
| 1960 |
> |
and discrete mechanics and field theories. Using multisymplectic |
| 1961 |
> |
geometry, we show that the existence of the fundamental geometric |
| 1962 |
> |
structures as well as their preservation along solutions can be |
| 1963 |
> |
obtained directly from the variational principle. In particular, |
| 1964 |
> |
we prove that a unique multisymplectic structure is obtained by |
| 1965 |
> |
taking the derivative of an action function, and use this structure |
| 1966 |
> |
to prove covariant generalizations of conservation of symplecticity |
| 1967 |
> |
and Noether's theorem. Natural discretization schemes for PDEs, |
| 1968 |
> |
which have these important preservation properties, then follow |
| 1969 |
> |
by choosing a discrete action functional. In the case of mechanics, |
| 1970 |
> |
we recover the variational symplectic integrators of Veselov type, |
| 1971 |
> |
while for PDEs we obtain covariant spacetime integrators which conserve |
| 1972 |
> |
the corresponding discrete multisymplectic form as well as the discrete |
| 1973 |
> |
momentum mappings corresponding to symmetries. We show that the |
| 1974 |
> |
usual notion of symplecticity along an infinite-dimensional space |
| 1975 |
> |
of fields can be naturally obtained by making a spacetime split. |
| 1976 |
> |
All of the aspects of our method are demonstrated with a nonlinear |
| 1977 |
> |
sine-Gordon equation, including computational results and a comparison |
| 1978 |
> |
with other discretization schemes.}, |
| 1979 |
|
annote = {154RH Times Cited:88 Cited References Count:36}, |
| 1980 |
|
issn = {0010-3616}, |
| 1981 |
|
uri = {<Go to ISI>://000077902200006}, |
| 1982 |
|
} |
| 1983 |
|
|
| 1984 |
+ |
@ARTICLE{Matthey2004, |
| 1985 |
+ |
author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and |
| 1986 |
+ |
M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre}, |
| 1987 |
+ |
title = {ProtoMol, an object-oriented framework for prototyping novel algorithms |
| 1988 |
+ |
for molecular dynamics}, |
| 1989 |
+ |
journal = {Acm Transactions on Mathematical Software}, |
| 1990 |
+ |
year = {2004}, |
| 1991 |
+ |
volume = {30}, |
| 1992 |
+ |
pages = {237-265}, |
| 1993 |
+ |
number = {3}, |
| 1994 |
+ |
month = {Sep}, |
| 1995 |
+ |
abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping |
| 1996 |
+ |
of novel algorithms for molecular dynamics and related applications. |
| 1997 |
+ |
Its flexibility is achieved primarily through the use of inheritance |
| 1998 |
+ |
and design patterns (object-oriented programming): Performance is |
| 1999 |
+ |
obtained by using templates that enable generation of efficient |
| 2000 |
+ |
code for sections critical to performance (generic programming). |
| 2001 |
+ |
The framework encapsulates important optimizations that can be used |
| 2002 |
+ |
by developers, such as parallelism in the force computation. Its |
| 2003 |
+ |
design is based on domain analysis of numerical integrators for |
| 2004 |
+ |
molecular dynamics (MD) and of fast solvers for the force computation, |
| 2005 |
+ |
particularly due to electrostatic interactions. Several new and |
| 2006 |
+ |
efficient algorithms are implemented in PROTOMOL. Finally, it is |
| 2007 |
+ |
shown that PROTOMOL'S sequential performance is excellent when compared |
| 2008 |
+ |
to a leading MD program, and that it scales well for moderate number |
| 2009 |
+ |
of processors. Binaries and source codes for Windows, Linux, Solaris, |
| 2010 |
+ |
IRIX, HP-UX, and AIX platforms are available under open source license |
| 2011 |
+ |
at http://protomol.sourceforge.net.}, |
| 2012 |
+ |
annote = {860EP Times Cited:2 Cited References Count:52}, |
| 2013 |
+ |
issn = {0098-3500}, |
| 2014 |
+ |
uri = {<Go to ISI>://000224325600001}, |
| 2015 |
+ |
} |
| 2016 |
+ |
|
| 2017 |
|
@ARTICLE{McLachlan1993, |
| 2018 |
|
author = {R.~I McLachlan}, |
| 2019 |
|
title = {Explicit Lie-Poisson integration and the Euler equations}, |
| 2023 |
|
pages = {3043-3046}, |
| 2024 |
|
} |
| 2025 |
|
|
| 2026 |
< |
@ARTICLE{McLachlan1998a, |
| 2026 |
> |
@ARTICLE{McLachlan1998, |
| 2027 |
|
author = {R. I. McLachlan and G. R. W. Quispel}, |
| 2028 |
|
title = {Generating functions for dynamical systems with symmetries, integrals, |
| 2029 |
< |
and differential invariants}, |
| 2029 |
> |
and differential invariants}, |
| 2030 |
|
journal = {Physica D}, |
| 2031 |
|
year = {1998}, |
| 2032 |
|
volume = {112}, |
| 2034 |
|
number = {1-2}, |
| 2035 |
|
month = {Jan 15}, |
| 2036 |
|
abstract = {We give a survey and some new examples of generating functions for |
| 2037 |
< |
systems with symplectic structure, systems with a first integral, |
| 2038 |
< |
systems that preserve volume, and systems with symmetries and/or |
| 2039 |
< |
time-reversing symmetries. Both ODEs and maps are treated, and we |
| 2040 |
< |
discuss how generating functions may be used in the structure-preserving |
| 2041 |
< |
numerical integration of ODEs with the above properties.}, |
| 2037 |
> |
systems with symplectic structure, systems with a first integral, |
| 2038 |
> |
systems that preserve volume, and systems with symmetries and/or |
| 2039 |
> |
time-reversing symmetries. Both ODEs and maps are treated, and we |
| 2040 |
> |
discuss how generating functions may be used in the structure-preserving |
| 2041 |
> |
numerical integration of ODEs with the above properties.}, |
| 2042 |
|
annote = {Yt049 Times Cited:7 Cited References Count:26}, |
| 2043 |
|
issn = {0167-2789}, |
| 2044 |
|
uri = {<Go to ISI>://000071558900021}, |
| 2045 |
|
} |
| 2046 |
|
|
| 2047 |
< |
@ARTICLE{McLachlan1998, |
| 2047 |
> |
@ARTICLE{McLachlan1998a, |
| 2048 |
|
author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner}, |
| 2049 |
|
title = {Numerical integrators that preserve symmetries and reversing symmetries}, |
| 2050 |
|
journal = {Siam Journal on Numerical Analysis}, |
| 2054 |
|
number = {2}, |
| 2055 |
|
month = {Apr}, |
| 2056 |
|
abstract = {We consider properties of flows, the relationships between them, and |
| 2057 |
< |
whether numerical integrators can be made to preserve these properties. |
| 2058 |
< |
This is done in the context of automorphisms and antiautomorphisms |
| 2059 |
< |
of a certain group generated by maps associated to vector fields. |
| 2060 |
< |
This new framework unifies several known constructions. We also |
| 2061 |
< |
use the concept of #covariance# of a numerical method with respect |
| 2062 |
< |
to a group of coordinate transformations. The main application is |
| 2063 |
< |
to explore the relationship between spatial symmetries, reversing |
| 2064 |
< |
symmetries, and time symmetry of flows and numerical integrators.}, |
| 2057 |
> |
whether numerical integrators can be made to preserve these properties. |
| 2058 |
> |
This is done in the context of automorphisms and antiautomorphisms |
| 2059 |
> |
of a certain group generated by maps associated to vector fields. |
| 2060 |
> |
This new framework unifies several known constructions. We also |
| 2061 |
> |
use the concept of #covariance# of a numerical method with respect |
| 2062 |
> |
to a group of coordinate transformations. The main application is |
| 2063 |
> |
to explore the relationship between spatial symmetries, reversing |
| 2064 |
> |
symmetries, and time symmetry of flows and numerical integrators.}, |
| 2065 |
|
annote = {Zc449 Times Cited:14 Cited References Count:33}, |
| 2066 |
|
issn = {0036-1429}, |
| 2067 |
|
uri = {<Go to ISI>://000072580500010}, |
| 2077 |
|
number = {1}, |
| 2078 |
|
month = {Feb}, |
| 2079 |
|
abstract = {In this paper we revisit the Moser-Veselov description of the free |
| 2080 |
< |
rigid body in body coordinates, which, in the 3 x 3 case, can be |
| 2081 |
< |
implemented as an explicit, second-order, integrable approximation |
| 2082 |
< |
of the continuous solution. By backward error analysis, we study |
| 2083 |
< |
the modified vector field which is integrated exactly by the discrete |
| 2084 |
< |
algorithm. We deduce that the discrete Moser-Veselov (DMV) is well |
| 2085 |
< |
approximated to higher order by time reparametrizations of the continuous |
| 2086 |
< |
equations (modified vector field). We use the modified vector field |
| 2087 |
< |
to scale the initial data of the DMV to improve the order of the |
| 2088 |
< |
approximation and show the equivalence of the DMV and the RATTLE |
| 2089 |
< |
algorithm. Numerical integration with these preprocessed initial |
| 2090 |
< |
data is several orders of magnitude more accurate than the original |
| 2091 |
< |
DMV and RATTLE approach.}, |
| 2080 |
> |
rigid body in body coordinates, which, in the 3 x 3 case, can be |
| 2081 |
> |
implemented as an explicit, second-order, integrable approximation |
| 2082 |
> |
of the continuous solution. By backward error analysis, we study |
| 2083 |
> |
the modified vector field which is integrated exactly by the discrete |
| 2084 |
> |
algorithm. We deduce that the discrete Moser-Veselov (DMV) is well |
| 2085 |
> |
approximated to higher order by time reparametrizations of the continuous |
| 2086 |
> |
equations (modified vector field). We use the modified vector field |
| 2087 |
> |
to scale the initial data of the DMV to improve the order of the |
| 2088 |
> |
approximation and show the equivalence of the DMV and the RATTLE |
| 2089 |
> |
algorithm. Numerical integration with these preprocessed initial |
| 2090 |
> |
data is several orders of magnitude more accurate than the original |
| 2091 |
> |
DMV and RATTLE approach.}, |
| 2092 |
|
annote = {911NS Times Cited:0 Cited References Count:14}, |
| 2093 |
|
issn = {1615-3375}, |
| 2094 |
|
uri = {<Go to ISI>://000228011900003}, |
| 2095 |
|
} |
| 2096 |
|
|
| 2097 |
+ |
@ARTICLE{Meineke2005, |
| 2098 |
+ |
author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and |
| 2099 |
+ |
J. D. Gezelter}, |
| 2100 |
+ |
title = {OOPSE: An object-oriented parallel simulation engine for molecular |
| 2101 |
+ |
dynamics}, |
| 2102 |
+ |
journal = {Journal of Computational Chemistry}, |
| 2103 |
+ |
year = {2005}, |
| 2104 |
+ |
volume = {26}, |
| 2105 |
+ |
pages = {252-271}, |
| 2106 |
+ |
number = {3}, |
| 2107 |
+ |
month = {Feb}, |
| 2108 |
+ |
abstract = {OOPSE is a new molecular dynamics simulation program that is capable |
| 2109 |
+ |
of efficiently integrating equations of motion for atom types with |
| 2110 |
+ |
orientational degrees of freedom (e.g. #sticky# atoms and point |
| 2111 |
+ |
dipoles). Transition metals can also be simulated using the embedded |
| 2112 |
+ |
atom method (EAM) potential included in the code. Parallel simulations |
| 2113 |
+ |
are carried out using the force-based decomposition method. Simulations |
| 2114 |
+ |
are specified using a very simple C-based meta-data language. A |
| 2115 |
+ |
number of advanced integrators are included, and the basic integrator |
| 2116 |
+ |
for orientational dynamics provides substantial improvements over |
| 2117 |
+ |
older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.}, |
| 2118 |
+ |
annote = {891CF Times Cited:1 Cited References Count:56}, |
| 2119 |
+ |
issn = {0192-8651}, |
| 2120 |
+ |
uri = {<Go to ISI>://000226558200006}, |
| 2121 |
+ |
} |
| 2122 |
+ |
|
| 2123 |
+ |
@ARTICLE{Melchionna1993, |
| 2124 |
+ |
author = {S. Melchionna and G. Ciccotti and B. L. Holian}, |
| 2125 |
+ |
title = {Hoover Npt Dynamics for Systems Varying in Shape and Size}, |
| 2126 |
+ |
journal = {Molecular Physics}, |
| 2127 |
+ |
year = {1993}, |
| 2128 |
+ |
volume = {78}, |
| 2129 |
+ |
pages = {533-544}, |
| 2130 |
+ |
number = {3}, |
| 2131 |
+ |
month = {Feb 20}, |
| 2132 |
+ |
abstract = {In this paper we write down equations of motion (following the approach |
| 2133 |
+ |
pioneered by Hoover) for an exact isothermal-isobaric molecular |
| 2134 |
+ |
dynamics simulation, and we extend them to multiple thermostating |
| 2135 |
+ |
rates, to a shape-varying cell and to molecular systems, coherently |
| 2136 |
+ |
with the previous 'extended system method'. An integration scheme |
| 2137 |
+ |
is proposed together with a numerical illustration of the method.}, |
| 2138 |
+ |
annote = {Kq355 Times Cited:172 Cited References Count:17}, |
| 2139 |
+ |
issn = {0026-8976}, |
| 2140 |
+ |
uri = {<Go to ISI>://A1993KQ35500002}, |
| 2141 |
+ |
} |
| 2142 |
+ |
|
| 2143 |
|
@ARTICLE{Memmer2002, |
| 2144 |
|
author = {R. Memmer}, |
| 2145 |
|
title = {Liquid crystal phases of achiral banana-shaped molecules: a computer |
| 2146 |
< |
simulation study}, |
| 2146 |
> |
simulation study}, |
| 2147 |
|
journal = {Liquid Crystals}, |
| 2148 |
|
year = {2002}, |
| 2149 |
|
volume = {29}, |
| 2151 |
|
number = {4}, |
| 2152 |
|
month = {Apr}, |
| 2153 |
|
abstract = {The phase behaviour of achiral banana-shaped molecules was studied |
| 2154 |
< |
by computer simulation. The banana-shaped molecules were described |
| 2155 |
< |
by model intermolecular interactions based on the Gay-Berne potential. |
| 2156 |
< |
The characteristic molecular structure was considered by joining |
| 2157 |
< |
two calamitic Gay-Berne particles through a bond to form a biaxial |
| 2158 |
< |
molecule of point symmetry group C-2v with a suitable bending angle. |
| 2159 |
< |
The dependence on temperature of systems of N=1024 rigid banana-shaped |
| 2160 |
< |
molecules with bending angle phi=140degrees has been studied by |
| 2161 |
< |
means of Monte Carlo simulations in the isobaric-isothermal ensemble |
| 2162 |
< |
(NpT). On cooling an isotropic system, two phase transitions characterized |
| 2163 |
< |
by phase transition enthalpy, entropy and relative volume change |
| 2164 |
< |
have been observed. For the first time by computer simulation of |
| 2165 |
< |
a many-particle system of banana-shaped molecules, at low temperature |
| 2166 |
< |
an untilted smectic phase showing a global phase biaxiality and |
| 2167 |
< |
a spontaneous local polarization in the layers, i.e. a local polar |
| 2168 |
< |
arrangement of the steric dipoles, with an antiferroelectric-like |
| 2169 |
< |
superstructure could be proven, a phase structure which recently |
| 2170 |
< |
has been discovered experimentally. Additionally, at intermediate |
| 2171 |
< |
temperature a nematic-like phase has been proved, whereas close |
| 2172 |
< |
to the transition to the smectic phase hints of a spontaneous achiral |
| 2173 |
< |
symmetry breaking have been determined. Here, in the absence of |
| 2174 |
< |
a layered structure a helical superstructure has been formed. All |
| 2175 |
< |
phases have been characterized by visual representations of selected |
| 2176 |
< |
configurations, scalar and pseudoscalar correlation functions, and |
| 2177 |
< |
order parameters.}, |
| 2154 |
> |
by computer simulation. The banana-shaped molecules were described |
| 2155 |
> |
by model intermolecular interactions based on the Gay-Berne potential. |
| 2156 |
> |
The characteristic molecular structure was considered by joining |
| 2157 |
> |
two calamitic Gay-Berne particles through a bond to form a biaxial |
| 2158 |
> |
molecule of point symmetry group C-2v with a suitable bending angle. |
| 2159 |
> |
The dependence on temperature of systems of N=1024 rigid banana-shaped |
| 2160 |
> |
molecules with bending angle phi=140degrees has been studied by |
| 2161 |
> |
means of Monte Carlo simulations in the isobaric-isothermal ensemble |
| 2162 |
> |
(NpT). On cooling an isotropic system, two phase transitions characterized |
| 2163 |
> |
by phase transition enthalpy, entropy and relative volume change |
| 2164 |
> |
have been observed. For the first time by computer simulation of |
| 2165 |
> |
a many-particle system of banana-shaped molecules, at low temperature |
| 2166 |
> |
an untilted smectic phase showing a global phase biaxiality and |
| 2167 |
> |
a spontaneous local polarization in the layers, i.e. a local polar |
| 2168 |
> |
arrangement of the steric dipoles, with an antiferroelectric-like |
| 2169 |
> |
superstructure could be proven, a phase structure which recently |
| 2170 |
> |
has been discovered experimentally. Additionally, at intermediate |
| 2171 |
> |
temperature a nematic-like phase has been proved, whereas close |
| 2172 |
> |
to the transition to the smectic phase hints of a spontaneous achiral |
| 2173 |
> |
symmetry breaking have been determined. Here, in the absence of |
| 2174 |
> |
a layered structure a helical superstructure has been formed. All |
| 2175 |
> |
phases have been characterized by visual representations of selected |
| 2176 |
> |
configurations, scalar and pseudoscalar correlation functions, and |
| 2177 |
> |
order parameters.}, |
| 2178 |
|
annote = {531HT Times Cited:12 Cited References Count:37}, |
| 2179 |
|
issn = {0267-8292}, |
| 2180 |
|
uri = {<Go to ISI>://000174410500001}, |
| 2191 |
|
|
| 2192 |
|
@ARTICLE{Mielke2004, |
| 2193 |
|
author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen |
| 2194 |
< |
and C. J. Benham}, |
| 2194 |
> |
and C. J. Benham}, |
| 2195 |
|
title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian |
| 2196 |
< |
dynamics study}, |
| 2196 |
> |
dynamics study}, |
| 2197 |
|
journal = {Journal of Chemical Physics}, |
| 2198 |
|
year = {2004}, |
| 2199 |
|
volume = {121}, |
| 2201 |
|
number = {16}, |
| 2202 |
|
month = {Oct 22}, |
| 2203 |
|
abstract = {The torque generated by RNA polymerase as it tracks along double-stranded |
| 2204 |
< |
DNA can potentially induce long-range structural deformations integral |
| 2205 |
< |
to mechanisms of biological significance in both prokaryotes and |
| 2206 |
< |
eukaryotes. In this paper, we introduce a dynamic computer model |
| 2207 |
< |
for investigating this phenomenon. Duplex DNA is represented as |
| 2208 |
< |
a chain of hydrodynamic beads interacting through potentials of |
| 2209 |
< |
linearly elastic stretching, bending, and twisting, as well as excluded |
| 2210 |
< |
volume. The chain, linear when relaxed, is looped to form two open |
| 2211 |
< |
but topologically constrained subdomains. This permits the dynamic |
| 2212 |
< |
introduction of torsional stress via a centrally applied torque. |
| 2213 |
< |
We simulate by Brownian dynamics the 100 mus response of a 477-base |
| 2214 |
< |
pair B-DNA template to the localized torque generated by the prokaryotic |
| 2215 |
< |
transcription ensemble. Following a sharp rise at early times, the |
| 2216 |
< |
distributed twist assumes a nearly constant value in both subdomains, |
| 2217 |
< |
and a succession of supercoiling deformations occurs as superhelical |
| 2218 |
< |
stress is increasingly partitioned to writhe. The magnitude of writhe |
| 2219 |
< |
surpasses that of twist before also leveling off when the structure |
| 2220 |
< |
reaches mechanical equilibrium with the torsional load. Superhelicity |
| 2221 |
< |
is simultaneously right handed in one subdomain and left handed |
| 2222 |
< |
in the other, as predicted by the #transcription-induced##twin-supercoiled-domain# |
| 2223 |
< |
model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, |
| 2224 |
< |
7024 (1987)]. The properties of the chain at the onset of writhing |
| 2225 |
< |
agree well with predictions from theory, and the generated stress |
| 2226 |
< |
is ample for driving secondary structural transitions in physiological |
| 2227 |
< |
DNA. (C) 2004 American Institute of Physics.}, |
| 2204 |
> |
DNA can potentially induce long-range structural deformations integral |
| 2205 |
> |
to mechanisms of biological significance in both prokaryotes and |
| 2206 |
> |
eukaryotes. In this paper, we introduce a dynamic computer model |
| 2207 |
> |
for investigating this phenomenon. Duplex DNA is represented as |
| 2208 |
> |
a chain of hydrodynamic beads interacting through potentials of |
| 2209 |
> |
linearly elastic stretching, bending, and twisting, as well as excluded |
| 2210 |
> |
volume. The chain, linear when relaxed, is looped to form two open |
| 2211 |
> |
but topologically constrained subdomains. This permits the dynamic |
| 2212 |
> |
introduction of torsional stress via a centrally applied torque. |
| 2213 |
> |
We simulate by Brownian dynamics the 100 mus response of a 477-base |
| 2214 |
> |
pair B-DNA template to the localized torque generated by the prokaryotic |
| 2215 |
> |
transcription ensemble. Following a sharp rise at early times, the |
| 2216 |
> |
distributed twist assumes a nearly constant value in both subdomains, |
| 2217 |
> |
and a succession of supercoiling deformations occurs as superhelical |
| 2218 |
> |
stress is increasingly partitioned to writhe. The magnitude of writhe |
| 2219 |
> |
surpasses that of twist before also leveling off when the structure |
| 2220 |
> |
reaches mechanical equilibrium with the torsional load. Superhelicity |
| 2221 |
> |
is simultaneously right handed in one subdomain and left handed |
| 2222 |
> |
in the other, as predicted by the #transcription-induced##twin-supercoiled-domain# |
| 2223 |
> |
model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, |
| 2224 |
> |
7024 (1987)]. The properties of the chain at the onset of writhing |
| 2225 |
> |
agree well with predictions from theory, and the generated stress |
| 2226 |
> |
is ample for driving secondary structural transitions in physiological |
| 2227 |
> |
DNA. (C) 2004 American Institute of Physics.}, |
| 2228 |
|
annote = {861ZF Times Cited:3 Cited References Count:34}, |
| 2229 |
|
issn = {0021-9606}, |
| 2230 |
|
uri = {<Go to ISI>://000224456500064}, |
| 2233 |
|
@ARTICLE{Naess2001, |
| 2234 |
|
author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter}, |
| 2235 |
|
title = {Brownian dynamics simulation of rigid bodies and segmented polymer |
| 2236 |
< |
chains. Use of Cartesian rotation vectors as the generalized coordinates |
| 2237 |
< |
describing angular orientations}, |
| 2236 |
> |
chains. Use of Cartesian rotation vectors as the generalized coordinates |
| 2237 |
> |
describing angular orientations}, |
| 2238 |
|
journal = {Physica A}, |
| 2239 |
|
year = {2001}, |
| 2240 |
|
volume = {294}, |
| 2242 |
|
number = {3-4}, |
| 2243 |
|
month = {May 15}, |
| 2244 |
|
abstract = {The three Eulerian angles constitute the classical choice of generalized |
| 2245 |
< |
coordinates used to describe the three degrees of rotational freedom |
| 2246 |
< |
of a rigid body, but it has long been known that this choice yields |
| 2247 |
< |
singular equations of motion. The latter is also true when Eulerian |
| 2248 |
< |
angles are used in Brownian dynamics analyses of the angular orientation |
| 2249 |
< |
of single rigid bodies and segmented polymer chains. Starting from |
| 2250 |
< |
kinetic theory we here show that by instead employing the three |
| 2251 |
< |
components of Cartesian rotation vectors as the generalized coordinates |
| 2252 |
< |
describing angular orientation, no singularity appears in the configuration |
| 2253 |
< |
space diffusion equation and the associated Brownian dynamics algorithm. |
| 2254 |
< |
The suitability of Cartesian rotation vectors in Brownian dynamics |
| 2255 |
< |
simulations of segmented polymer chains with spring-like or ball-socket |
| 2256 |
< |
joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.}, |
| 2245 |
> |
coordinates used to describe the three degrees of rotational freedom |
| 2246 |
> |
of a rigid body, but it has long been known that this choice yields |
| 2247 |
> |
singular equations of motion. The latter is also true when Eulerian |
| 2248 |
> |
angles are used in Brownian dynamics analyses of the angular orientation |
| 2249 |
> |
of single rigid bodies and segmented polymer chains. Starting from |
| 2250 |
> |
kinetic theory we here show that by instead employing the three |
| 2251 |
> |
components of Cartesian rotation vectors as the generalized coordinates |
| 2252 |
> |
describing angular orientation, no singularity appears in the configuration |
| 2253 |
> |
space diffusion equation and the associated Brownian dynamics algorithm. |
| 2254 |
> |
The suitability of Cartesian rotation vectors in Brownian dynamics |
| 2255 |
> |
simulations of segmented polymer chains with spring-like or ball-socket |
| 2256 |
> |
joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.}, |
| 2257 |
|
annote = {433TA Times Cited:7 Cited References Count:19}, |
| 2258 |
|
issn = {0378-4371}, |
| 2259 |
|
uri = {<Go to ISI>://000168774800005}, |
| 2262 |
|
@ARTICLE{Niori1996, |
| 2263 |
|
author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe}, |
| 2264 |
|
title = {Distinct ferroelectric smectic liquid crystals consisting of banana |
| 2265 |
< |
shaped achiral molecules}, |
| 2265 |
> |
shaped achiral molecules}, |
| 2266 |
|
journal = {Journal of Materials Chemistry}, |
| 2267 |
|
year = {1996}, |
| 2268 |
|
volume = {6}, |
| 2270 |
|
number = {7}, |
| 2271 |
|
month = {Jul}, |
| 2272 |
|
abstract = {The synthesis of a banana-shaped molecule is reported and it is found |
| 2273 |
< |
that the smectic phase which it forms is biaxial with the molecules |
| 2274 |
< |
packed in the best,direction into a layer. Because of this characteristic |
| 2275 |
< |
packing, spontaneous polarization appears parallel to the layer |
| 2276 |
< |
and switches on reversal of an applied electric field. This is the |
| 2277 |
< |
first obvious example of ferroelectricity in an achiral smectic |
| 2278 |
< |
phase and is ascribed to the C-2v symmetry of the molecular packing.}, |
| 2273 |
> |
that the smectic phase which it forms is biaxial with the molecules |
| 2274 |
> |
packed in the best,direction into a layer. Because of this characteristic |
| 2275 |
> |
packing, spontaneous polarization appears parallel to the layer |
| 2276 |
> |
and switches on reversal of an applied electric field. This is the |
| 2277 |
> |
first obvious example of ferroelectricity in an achiral smectic |
| 2278 |
> |
phase and is ascribed to the C-2v symmetry of the molecular packing.}, |
| 2279 |
|
annote = {Ux855 Times Cited:447 Cited References Count:18}, |
| 2280 |
|
issn = {0959-9428}, |
| 2281 |
|
uri = {<Go to ISI>://A1996UX85500025}, |
| 2291 |
|
number = {5}, |
| 2292 |
|
month = {may}, |
| 2293 |
|
abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical |
| 2294 |
< |
forces using a Brownian dynamics simulation. Two nanoparticles, |
| 2295 |
< |
which interact repulsively with amphiphilic molecules, are put inside |
| 2296 |
< |
a vesicle. The position of one nanoparticle is fixed, and the other |
| 2297 |
< |
is moved by a constant force as in optical-trapping experiments. |
| 2298 |
< |
First, the pulled vesicle stretches into a pear or tube shape. Then |
| 2299 |
< |
the inner monolayer in the tube-shaped region is deformed, and a |
| 2300 |
< |
cylindrical structure is formed between two vesicles. After stretching |
| 2301 |
< |
the cylindrical region, fission occurs near the moved vesicle. Soon |
| 2302 |
< |
after this the cylindrical region shrinks. The trapping force similar |
| 2303 |
< |
to 100 pN is needed to induce the formation of the cylindrical structure |
| 2304 |
< |
and fission.}, |
| 2294 |
> |
forces using a Brownian dynamics simulation. Two nanoparticles, |
| 2295 |
> |
which interact repulsively with amphiphilic molecules, are put inside |
| 2296 |
> |
a vesicle. The position of one nanoparticle is fixed, and the other |
| 2297 |
> |
is moved by a constant force as in optical-trapping experiments. |
| 2298 |
> |
First, the pulled vesicle stretches into a pear or tube shape. Then |
| 2299 |
> |
the inner monolayer in the tube-shaped region is deformed, and a |
| 2300 |
> |
cylindrical structure is formed between two vesicles. After stretching |
| 2301 |
> |
the cylindrical region, fission occurs near the moved vesicle. Soon |
| 2302 |
> |
after this the cylindrical region shrinks. The trapping force similar |
| 2303 |
> |
to 100 pN is needed to induce the formation of the cylindrical structure |
| 2304 |
> |
and fission.}, |
| 2305 |
|
annote = {Part 1 568PX Times Cited:5 Cited References Count:39}, |
| 2306 |
|
issn = {1063-651X}, |
| 2307 |
|
uri = {<Go to ISI>://000176552300084}, |
| 2317 |
|
number = {20}, |
| 2318 |
|
month = {Nov 22}, |
| 2319 |
|
abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics |
| 2320 |
< |
simulation. Amphiphilic molecules spontaneously form vesicles with |
| 2321 |
< |
a bilayer structure. Two vesicles come into contact and form a stalk |
| 2322 |
< |
intermediate, in which a necklike structure only connects the outer |
| 2323 |
< |
monolayers, as predicted by the stalk hypothesis. We have found |
| 2324 |
< |
a new pathway of pore opening from stalks at high temperature: the |
| 2325 |
< |
elliptic stalk bends and contact between the ends of the arc-shaped |
| 2326 |
< |
stalk leads to pore opening. On the other hand, we have clarified |
| 2327 |
< |
that the pore-opening process at low temperature agrees with the |
| 2328 |
< |
modified stalk model: a pore is induced by contact between the inner |
| 2329 |
< |
monolayers inside the stalk. (C) 2001 American Institute of Physics.}, |
| 2320 |
> |
simulation. Amphiphilic molecules spontaneously form vesicles with |
| 2321 |
> |
a bilayer structure. Two vesicles come into contact and form a stalk |
| 2322 |
> |
intermediate, in which a necklike structure only connects the outer |
| 2323 |
> |
monolayers, as predicted by the stalk hypothesis. We have found |
| 2324 |
> |
a new pathway of pore opening from stalks at high temperature: the |
| 2325 |
> |
elliptic stalk bends and contact between the ends of the arc-shaped |
| 2326 |
> |
stalk leads to pore opening. On the other hand, we have clarified |
| 2327 |
> |
that the pore-opening process at low temperature agrees with the |
| 2328 |
> |
modified stalk model: a pore is induced by contact between the inner |
| 2329 |
> |
monolayers inside the stalk. (C) 2001 American Institute of Physics.}, |
| 2330 |
|
annote = {491UW Times Cited:48 Cited References Count:25}, |
| 2331 |
|
issn = {0021-9606}, |
| 2332 |
|
uri = {<Go to ISI>://000172129300049}, |
| 2343 |
|
@ARTICLE{Omelyan1998, |
| 2344 |
|
author = {I. P. Omelyan}, |
| 2345 |
|
title = {On the numerical integration of motion for rigid polyatomics: The |
| 2346 |
< |
modified quaternion approach}, |
| 2346 |
> |
modified quaternion approach}, |
| 2347 |
|
journal = {Computers in Physics}, |
| 2348 |
|
year = {1998}, |
| 2349 |
|
volume = {12}, |
| 2351 |
|
number = {1}, |
| 2352 |
|
month = {Jan-Feb}, |
| 2353 |
|
abstract = {A revised version of the quaternion approach for numerical integration |
| 2354 |
< |
of the equations of motion for rigid polyatomic molecules is proposed. |
| 2355 |
< |
The modified approach is based on a formulation of the quaternion |
| 2356 |
< |
dynamics with constraints. This allows one to resolve the rigidity |
| 2357 |
< |
problem rigorously using constraint forces. It is shown that the |
| 2358 |
< |
procedure for preservation of molecular rigidity can be realized |
| 2359 |
< |
particularly simply within the Verlet algorithm in velocity form. |
| 2360 |
< |
We demonstrate that the method presented leads to an improved numerical |
| 2361 |
< |
stability with respect to the usual quaternion rescaling scheme |
| 2362 |
< |
and it is roughly as good as the cumbersome atomic-constraint technique. |
| 2363 |
< |
(C) 1998 American Institute of Physics.}, |
| 2354 |
> |
of the equations of motion for rigid polyatomic molecules is proposed. |
| 2355 |
> |
The modified approach is based on a formulation of the quaternion |
| 2356 |
> |
dynamics with constraints. This allows one to resolve the rigidity |
| 2357 |
> |
problem rigorously using constraint forces. It is shown that the |
| 2358 |
> |
procedure for preservation of molecular rigidity can be realized |
| 2359 |
> |
particularly simply within the Verlet algorithm in velocity form. |
| 2360 |
> |
We demonstrate that the method presented leads to an improved numerical |
| 2361 |
> |
stability with respect to the usual quaternion rescaling scheme |
| 2362 |
> |
and it is roughly as good as the cumbersome atomic-constraint technique. |
| 2363 |
> |
(C) 1998 American Institute of Physics.}, |
| 2364 |
|
annote = {Yx279 Times Cited:12 Cited References Count:28}, |
| 2365 |
|
issn = {0894-1866}, |
| 2366 |
|
uri = {<Go to ISI>://000072024300025}, |
| 2369 |
|
@ARTICLE{Omelyan1998a, |
| 2370 |
|
author = {I. P. Omelyan}, |
| 2371 |
|
title = {Algorithm for numerical integration of the rigid-body equations of |
| 2372 |
< |
motion}, |
| 2372 |
> |
motion}, |
| 2373 |
|
journal = {Physical Review E}, |
| 2374 |
|
year = {1998}, |
| 2375 |
|
volume = {58}, |
| 2377 |
|
number = {1}, |
| 2378 |
|
month = {Jul}, |
| 2379 |
|
abstract = {An algorithm for numerical integration of the rigid-body equations |
| 2380 |
< |
of motion is proposed. The algorithm uses the leapfrog scheme and |
| 2381 |
< |
the quantities involved are angular velocities and orientational |
| 2382 |
< |
variables that can be expressed in terms of either principal axes |
| 2383 |
< |
or quaternions. Due to specific features of the algorithm, orthonormality |
| 2384 |
< |
and unit norms of the orientational variables are integrals of motion, |
| 2385 |
< |
despite an approximate character of the produced trajectories. It |
| 2386 |
< |
is shown that the method presented appears to be the most efficient |
| 2387 |
< |
among all such algorithms known.}, |
| 2380 |
> |
of motion is proposed. The algorithm uses the leapfrog scheme and |
| 2381 |
> |
the quantities involved are angular velocities and orientational |
| 2382 |
> |
variables that can be expressed in terms of either principal axes |
| 2383 |
> |
or quaternions. Due to specific features of the algorithm, orthonormality |
| 2384 |
> |
and unit norms of the orientational variables are integrals of motion, |
| 2385 |
> |
despite an approximate character of the produced trajectories. It |
| 2386 |
> |
is shown that the method presented appears to be the most efficient |
| 2387 |
> |
among all such algorithms known.}, |
| 2388 |
|
annote = {101XL Times Cited:8 Cited References Count:22}, |
| 2389 |
|
issn = {1063-651X}, |
| 2390 |
|
uri = {<Go to ISI>://000074893400151}, |
| 2393 |
|
@ARTICLE{Orlandi2006, |
| 2394 |
|
author = {S. Orlandi and R. Berardi and J. Steltzer and C. Zannoni}, |
| 2395 |
|
title = {A Monte Carlo study of the mesophases formed by polar bent-shaped |
| 2396 |
< |
molecules}, |
| 2396 |
> |
molecules}, |
| 2397 |
|
journal = {Journal of Chemical Physics}, |
| 2398 |
|
year = {2006}, |
| 2399 |
|
volume = {124}, |
| 2401 |
|
number = {12}, |
| 2402 |
|
month = {Mar 28}, |
| 2403 |
|
abstract = {Liquid crystal phases formed by bent-shaped (or #banana#) molecules |
| 2404 |
< |
are currently of great interest. Here we investigate by Monte Carlo |
| 2405 |
< |
computer simulations the phases formed by rigid banana molecules |
| 2406 |
< |
modeled combining three Gay-Berne sites and containing either one |
| 2407 |
< |
central or two lateral and transversal dipoles. We show that changing |
| 2408 |
< |
the dipole position and orientation has a profound effect on the |
| 2409 |
< |
mesophase stability and molecular organization. In particular, we |
| 2410 |
< |
find a uniaxial nematic phase only for off-center dipolar models |
| 2411 |
< |
and tilted phases only for the one with terminal dipoles. (c) 2006 |
| 2412 |
< |
American Institute of Physics.}, |
| 2404 |
> |
are currently of great interest. Here we investigate by Monte Carlo |
| 2405 |
> |
computer simulations the phases formed by rigid banana molecules |
| 2406 |
> |
modeled combining three Gay-Berne sites and containing either one |
| 2407 |
> |
central or two lateral and transversal dipoles. We show that changing |
| 2408 |
> |
the dipole position and orientation has a profound effect on the |
| 2409 |
> |
mesophase stability and molecular organization. In particular, we |
| 2410 |
> |
find a uniaxial nematic phase only for off-center dipolar models |
| 2411 |
> |
and tilted phases only for the one with terminal dipoles. (c) 2006 |
| 2412 |
> |
American Institute of Physics.}, |
| 2413 |
|
annote = {028CP Times Cited:0 Cited References Count:42}, |
| 2414 |
|
issn = {0021-9606}, |
| 2415 |
|
uri = {<Go to ISI>://000236464000072}, |
| 2425 |
|
number = {6}, |
| 2426 |
|
month = {Nov}, |
| 2427 |
|
abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of |
| 2428 |
< |
stages are considered. These methods are continuously differentiable |
| 2429 |
< |
if and only if one of the stages is the FSAL evaluation. A characterization |
| 2430 |
< |
of a subclass of these methods is developed for orders 3, 4, and |
| 2431 |
< |
5. It is shown how the free parameters of these methods can be used |
| 2432 |
< |
either to minimize the continuous truncation error coefficients |
| 2433 |
< |
or to maximize the stability region. As a representative for these |
| 2434 |
< |
methods the fifth-order method with minimized error coefficients |
| 2435 |
< |
is chosen, supplied with an error estimation method, and analysed |
| 2436 |
< |
by using the DETEST software. The results are compared with a similar |
| 2437 |
< |
implementation of the Dormand-Prince 5(4) pair with interpolant, |
| 2438 |
< |
showing a significant advantage in the new method for the chosen |
| 2439 |
< |
problems.}, |
| 2428 |
> |
stages are considered. These methods are continuously differentiable |
| 2429 |
> |
if and only if one of the stages is the FSAL evaluation. A characterization |
| 2430 |
> |
of a subclass of these methods is developed for orders 3, 4, and |
| 2431 |
> |
5. It is shown how the free parameters of these methods can be used |
| 2432 |
> |
either to minimize the continuous truncation error coefficients |
| 2433 |
> |
or to maximize the stability region. As a representative for these |
| 2434 |
> |
methods the fifth-order method with minimized error coefficients |
| 2435 |
> |
is chosen, supplied with an error estimation method, and analysed |
| 2436 |
> |
by using the DETEST software. The results are compared with a similar |
| 2437 |
> |
implementation of the Dormand-Prince 5(4) pair with interpolant, |
| 2438 |
> |
showing a significant advantage in the new method for the chosen |
| 2439 |
> |
problems.}, |
| 2440 |
|
annote = {Ju936 Times Cited:25 Cited References Count:20}, |
| 2441 |
|
issn = {0196-5204}, |
| 2442 |
|
uri = {<Go to ISI>://A1992JU93600013}, |
| 2445 |
|
@ARTICLE{Palacios1998, |
| 2446 |
|
author = {J. L. Garcia-Palacios and F. J. Lazaro}, |
| 2447 |
|
title = {Langevin-dynamics study of the dynamical properties of small magnetic |
| 2448 |
< |
particles}, |
| 2448 |
> |
particles}, |
| 2449 |
|
journal = {Physical Review B}, |
| 2450 |
|
year = {1998}, |
| 2451 |
|
volume = {58}, |
| 2453 |
|
number = {22}, |
| 2454 |
|
month = {Dec 1}, |
| 2455 |
|
abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical |
| 2456 |
< |
magnetic moment is numerically solved (properly observing the customary |
| 2457 |
< |
interpretation of it as a Stratonovich stochastic differential equation), |
| 2458 |
< |
in order to study the dynamics of magnetic nanoparticles. The corresponding |
| 2459 |
< |
Langevin-dynamics approach allows for the study of the fluctuating |
| 2460 |
< |
trajectories of individual magnetic moments, where we have encountered |
| 2461 |
< |
remarkable phenomena in the overbarrier rotation process, such as |
| 2462 |
< |
crossing-back or multiple crossing of the potential barrier, rooted |
| 2463 |
< |
in the gyromagnetic nature of the system. Concerning averaged quantities, |
| 2464 |
< |
we study the linear dynamic response of the archetypal ensemble |
| 2465 |
< |
of noninteracting classical magnetic moments with axially symmetric |
| 2466 |
< |
magnetic anisotropy. The results are compared with different analytical |
| 2467 |
< |
expressions used to model the relaxation of nanoparticle ensembles, |
| 2468 |
< |
assessing their accuracy. It has been found that, among a number |
| 2469 |
< |
of heuristic expressions for the linear dynamic susceptibility, |
| 2470 |
< |
only the simple formula proposed by Shliomis and Stepanov matches |
| 2471 |
< |
the coarse features of the susceptibility reasonably. By comparing |
| 2472 |
< |
the numerical results with the asymptotic formula of Storonkin {Sov. |
| 2473 |
< |
Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]}, |
| 2474 |
< |
the effects of the intra-potential-well relaxation modes on the |
| 2475 |
< |
low-temperature longitudinal dynamic response have been assessed, |
| 2476 |
< |
showing their relatively small reflection in the susceptibility |
| 2477 |
< |
curves but their dramatic influence on the phase shifts. Comparison |
| 2478 |
< |
of the numerical results with the exact zero-damping expression |
| 2479 |
< |
for the transverse susceptibility by Garanin, Ishchenko, and Panina |
| 2480 |
< |
{Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242 |
| 2481 |
< |
(1990)]}, reveals a sizable contribution of the spread of the precession |
| 2482 |
< |
frequencies of the magnetic moment in the anisotropy field to the |
| 2483 |
< |
dynamic response at intermediate-to-high temperatures. [S0163-1829 |
| 2484 |
< |
(98)00446-9].}, |
| 2456 |
> |
magnetic moment is numerically solved (properly observing the customary |
| 2457 |
> |
interpretation of it as a Stratonovich stochastic differential equation), |
| 2458 |
> |
in order to study the dynamics of magnetic nanoparticles. The corresponding |
| 2459 |
> |
Langevin-dynamics approach allows for the study of the fluctuating |
| 2460 |
> |
trajectories of individual magnetic moments, where we have encountered |
| 2461 |
> |
remarkable phenomena in the overbarrier rotation process, such as |
| 2462 |
> |
crossing-back or multiple crossing of the potential barrier, rooted |
| 2463 |
> |
in the gyromagnetic nature of the system. Concerning averaged quantities, |
| 2464 |
> |
we study the linear dynamic response of the archetypal ensemble |
| 2465 |
> |
of noninteracting classical magnetic moments with axially symmetric |
| 2466 |
> |
magnetic anisotropy. The results are compared with different analytical |
| 2467 |
> |
expressions used to model the relaxation of nanoparticle ensembles, |
| 2468 |
> |
assessing their accuracy. It has been found that, among a number |
| 2469 |
> |
of heuristic expressions for the linear dynamic susceptibility, |
| 2470 |
> |
only the simple formula proposed by Shliomis and Stepanov matches |
| 2471 |
> |
the coarse features of the susceptibility reasonably. By comparing |
| 2472 |
> |
the numerical results with the asymptotic formula of Storonkin {Sov. |
| 2473 |
> |
Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]}, |
| 2474 |
> |
the effects of the intra-potential-well relaxation modes on the |
| 2475 |
> |
low-temperature longitudinal dynamic response have been assessed, |
| 2476 |
> |
showing their relatively small reflection in the susceptibility |
| 2477 |
> |
curves but their dramatic influence on the phase shifts. Comparison |
| 2478 |
> |
of the numerical results with the exact zero-damping expression |
| 2479 |
> |
for the transverse susceptibility by Garanin, Ishchenko, and Panina |
| 2480 |
> |
{Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242 |
| 2481 |
> |
(1990)]}, reveals a sizable contribution of the spread of the precession |
| 2482 |
> |
frequencies of the magnetic moment in the anisotropy field to the |
| 2483 |
> |
dynamic response at intermediate-to-high temperatures. [S0163-1829 |
| 2484 |
> |
(98)00446-9].}, |
| 2485 |
|
annote = {146XW Times Cited:66 Cited References Count:45}, |
| 2486 |
|
issn = {0163-1829}, |
| 2487 |
|
uri = {<Go to ISI>://000077460000052}, |
| 2488 |
+ |
} |
| 2489 |
+ |
|
| 2490 |
+ |
@ARTICLE{Parr1995, |
| 2491 |
+ |
author = {T. J. Parr and R. W. Quong}, |
| 2492 |
+ |
title = {Antlr - a Predicated-Ll(K) Parser Generator}, |
| 2493 |
+ |
journal = {Software-Practice \& Experience}, |
| 2494 |
+ |
year = {1995}, |
| 2495 |
+ |
volume = {25}, |
| 2496 |
+ |
pages = {789-810}, |
| 2497 |
+ |
number = {7}, |
| 2498 |
+ |
month = {Jul}, |
| 2499 |
+ |
abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers |
| 2500 |
+ |
often choose to write recursive-descent parsers by hand to obtain |
| 2501 |
+ |
increased flexibility, better error handling, and ease of debugging. |
| 2502 |
+ |
We introduce ANTLR, a public-domain parser generator that combines |
| 2503 |
+ |
the flexibility of hand-coded parsing with the convenience of a |
| 2504 |
+ |
parser generator, which is a component of PCCTS. ANTLR has many |
| 2505 |
+ |
features that make it easier to use than other language tools. Most |
| 2506 |
+ |
important, ANTLR provides predicates which let the programmer systematically |
| 2507 |
+ |
direct the parse via arbitrary expressions using semantic and syntactic |
| 2508 |
+ |
context; in practice, the use of predicates eliminates the need |
| 2509 |
+ |
to hand-tweak the ANTLR output, even for difficult parsing problems. |
| 2510 |
+ |
ANTLR also integrates the description of lexical and syntactic analysis, |
| 2511 |
+ |
accepts LL(k) grammars for k > 1 with extended BNF notation, and |
| 2512 |
+ |
can automatically generate abstract syntax trees. ANTLR is widely |
| 2513 |
+ |
used, with over 1000 registered industrial and academic users in |
| 2514 |
+ |
37 countries. It has been ported to many popular systems such as |
| 2515 |
+ |
the PC, Macintosh, and a variety of UNIX platforms; a commercial |
| 2516 |
+ |
C++ front-end has been developed as a result of one of our industrial |
| 2517 |
+ |
collaborations.}, |
| 2518 |
+ |
annote = {Rk104 Times Cited:19 Cited References Count:10}, |
| 2519 |
+ |
issn = {0038-0644}, |
| 2520 |
+ |
uri = {<Go to ISI>://A1995RK10400004}, |
| 2521 |
|
} |
| 2522 |
|
|
| 2523 |
|
@ARTICLE{Pastor1988, |
| 2551 |
|
@ARTICLE{Perram1985, |
| 2552 |
|
author = {J. W. Perram and M. S. Wertheim}, |
| 2553 |
|
title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and |
| 2554 |
< |
the Contact Function}, |
| 2554 |
> |
the Contact Function}, |
| 2555 |
|
journal = {Journal of Computational Physics}, |
| 2556 |
|
year = {1985}, |
| 2557 |
|
volume = {58}, |
| 2574 |
|
@ARTICLE{Perrin1936, |
| 2575 |
|
author = {F. Perrin}, |
| 2576 |
|
title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation |
| 2577 |
< |
des fluorescences. Translation et diffusion de moleculese ellipsoidales}, |
| 2577 |
> |
des fluorescences. Translation et diffusion de moleculese ellipsoidales}, |
| 2578 |
|
journal = {J. Phys. Radium}, |
| 2579 |
|
year = {1936}, |
| 2580 |
|
volume = {7}, |
| 2584 |
|
@ARTICLE{Perrin1934, |
| 2585 |
|
author = {F. Perrin}, |
| 2586 |
|
title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour |
| 2587 |
< |
des molecules ellipsoidales}, |
| 2587 |
> |
des molecules ellipsoidales}, |
| 2588 |
|
journal = {J. Phys. Radium}, |
| 2589 |
|
year = {1934}, |
| 2590 |
|
volume = {5}, |
| 2591 |
|
pages = {497-511}, |
| 2592 |
|
} |
| 2593 |
|
|
| 2594 |
+ |
@ARTICLE{Petrache2000, |
| 2595 |
+ |
author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown}, |
| 2596 |
+ |
title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines |
| 2597 |
+ |
Determined by $^2\text{H}$ {\sc nmr} Spectroscopy}, |
| 2598 |
+ |
journal = {Biophysical Journal}, |
| 2599 |
+ |
year = {2000}, |
| 2600 |
+ |
volume = {79}, |
| 2601 |
+ |
pages = {3172-3192}, |
| 2602 |
+ |
} |
| 2603 |
+ |
|
| 2604 |
|
@ARTICLE{Petrache1998, |
| 2605 |
|
author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle}, |
| 2606 |
|
title = {Fluid phase structure of EPC and DMPC bilayers}, |
| 2611 |
|
number = {1}, |
| 2612 |
|
month = {Sep}, |
| 2613 |
|
abstract = {X-ray diffraction data taken at high instrumental resolution were |
| 2614 |
< |
obtained for EPC and DMPC under various osmotic pressures, primarily |
| 2615 |
< |
at T = 30 degrees C. The headgroup thickness D-HH was obtained from |
| 2616 |
< |
relative electron density profiles. By using volumetric results |
| 2617 |
< |
and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4 |
| 2618 |
< |
+/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The |
| 2619 |
< |
analysis also gives estimates for the areal compressibility K-A. |
| 2620 |
< |
The A(F) results lead to other structural results regarding membrane |
| 2621 |
< |
thickness and associated waters. Using the recently determined absolute |
| 2622 |
< |
electrons density profile of DPPC, the AF results also lead to absolute |
| 2623 |
< |
electron density profiles and absolute continuous transforms \F(q)\ |
| 2624 |
< |
for EPC and DMPC, Limited measurements of temperature dependence |
| 2625 |
< |
show directly that fluctuations increase with increasing temperature |
| 2626 |
< |
and that a small decrease in bending modulus K-c accounts for the |
| 2627 |
< |
increased water spacing reported by Simon et al. (1995) Biophys. |
| 2628 |
< |
J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights |
| 2629 |
< |
reserved.}, |
| 2614 |
> |
obtained for EPC and DMPC under various osmotic pressures, primarily |
| 2615 |
> |
at T = 30 degrees C. The headgroup thickness D-HH was obtained from |
| 2616 |
> |
relative electron density profiles. By using volumetric results |
| 2617 |
> |
and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4 |
| 2618 |
> |
+/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The |
| 2619 |
> |
analysis also gives estimates for the areal compressibility K-A. |
| 2620 |
> |
The A(F) results lead to other structural results regarding membrane |
| 2621 |
> |
thickness and associated waters. Using the recently determined absolute |
| 2622 |
> |
electrons density profile of DPPC, the AF results also lead to absolute |
| 2623 |
> |
electron density profiles and absolute continuous transforms \F(q)\ |
| 2624 |
> |
for EPC and DMPC, Limited measurements of temperature dependence |
| 2625 |
> |
show directly that fluctuations increase with increasing temperature |
| 2626 |
> |
and that a small decrease in bending modulus K-c accounts for the |
| 2627 |
> |
increased water spacing reported by Simon et al. (1995) Biophys. |
| 2628 |
> |
J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights |
| 2629 |
> |
reserved.}, |
| 2630 |
|
annote = {130AT Times Cited:98 Cited References Count:39}, |
| 2631 |
|
issn = {0009-3084}, |
| 2632 |
|
uri = {<Go to ISI>://000076497600007}, |
| 2635 |
|
@ARTICLE{Powles1973, |
| 2636 |
|
author = {J.~G. Powles}, |
| 2637 |
|
title = {A general ellipsoid can not always serve as a modle for the rotational |
| 2638 |
< |
diffusion properties of arbitrary shaped rigid molecules}, |
| 2638 |
> |
diffusion properties of arbitrary shaped rigid molecules}, |
| 2639 |
|
journal = {Advan. Phys.}, |
| 2640 |
|
year = {1973}, |
| 2641 |
|
volume = {22}, |
| 2645 |
|
@ARTICLE{Recio2004, |
| 2646 |
|
author = {J. Fernandez-Recio and M. Totrov and R. Abagyan}, |
| 2647 |
|
title = {Identification of protein-protein interaction sites from docking |
| 2648 |
< |
energy landscapes}, |
| 2648 |
> |
energy landscapes}, |
| 2649 |
|
journal = {Journal of Molecular Biology}, |
| 2650 |
|
year = {2004}, |
| 2651 |
|
volume = {335}, |
| 2653 |
|
number = {3}, |
| 2654 |
|
month = {Jan 16}, |
| 2655 |
|
abstract = {Protein recognition is one of the most challenging and intriguing |
| 2656 |
< |
problems in structural biology. Despite all the available structural, |
| 2657 |
< |
sequence and biophysical information about protein-protein complexes, |
| 2658 |
< |
the physico-chemical patterns, if any, that make a protein surface |
| 2659 |
< |
likely to be involved in protein-protein interactions, remain elusive. |
| 2660 |
< |
Here, we apply protein docking simulations and analysis of the interaction |
| 2661 |
< |
energy landscapes to identify protein-protein interaction sites. |
| 2662 |
< |
The new protocol for global docking based on multi-start global |
| 2663 |
< |
energy optimization of an allatom model of the ligand, with detailed |
| 2664 |
< |
receptor potentials and atomic solvation parameters optimized in |
| 2665 |
< |
a training set of 24 complexes, explores the conformational space |
| 2666 |
< |
around the whole receptor without restrictions. The ensembles of |
| 2667 |
< |
the rigid-body docking solutions generated by the simulations were |
| 2668 |
< |
subsequently used to project the docking energy landscapes onto |
| 2669 |
< |
the protein surfaces. We found that highly populated low-energy |
| 2670 |
< |
regions consistently corresponded to actual binding sites. The procedure |
| 2671 |
< |
was validated on a test set of 21 known protein-protein complexes |
| 2672 |
< |
not used in the training set. As much as 81% of the predicted high-propensity |
| 2673 |
< |
patch residues were located correctly in the native interfaces. |
| 2674 |
< |
This approach can guide the design of mutations on the surfaces |
| 2675 |
< |
of proteins, provide geometrical details of a possible interaction, |
| 2676 |
< |
and help to annotate protein surfaces in structural proteomics. |
| 2677 |
< |
(C) 2003 Elsevier Ltd. All rights reserved.}, |
| 2656 |
> |
problems in structural biology. Despite all the available structural, |
| 2657 |
> |
sequence and biophysical information about protein-protein complexes, |
| 2658 |
> |
the physico-chemical patterns, if any, that make a protein surface |
| 2659 |
> |
likely to be involved in protein-protein interactions, remain elusive. |
| 2660 |
> |
Here, we apply protein docking simulations and analysis of the interaction |
| 2661 |
> |
energy landscapes to identify protein-protein interaction sites. |
| 2662 |
> |
The new protocol for global docking based on multi-start global |
| 2663 |
> |
energy optimization of an allatom model of the ligand, with detailed |
| 2664 |
> |
receptor potentials and atomic solvation parameters optimized in |
| 2665 |
> |
a training set of 24 complexes, explores the conformational space |
| 2666 |
> |
around the whole receptor without restrictions. The ensembles of |
| 2667 |
> |
the rigid-body docking solutions generated by the simulations were |
| 2668 |
> |
subsequently used to project the docking energy landscapes onto |
| 2669 |
> |
the protein surfaces. We found that highly populated low-energy |
| 2670 |
> |
regions consistently corresponded to actual binding sites. The procedure |
| 2671 |
> |
was validated on a test set of 21 known protein-protein complexes |
| 2672 |
> |
not used in the training set. As much as 81% of the predicted high-propensity |
| 2673 |
> |
patch residues were located correctly in the native interfaces. |
| 2674 |
> |
This approach can guide the design of mutations on the surfaces |
| 2675 |
> |
of proteins, provide geometrical details of a possible interaction, |
| 2676 |
> |
and help to annotate protein surfaces in structural proteomics. |
| 2677 |
> |
(C) 2003 Elsevier Ltd. All rights reserved.}, |
| 2678 |
|
annote = {763GQ Times Cited:21 Cited References Count:59}, |
| 2679 |
|
issn = {0022-2836}, |
| 2680 |
|
uri = {<Go to ISI>://000188066900016}, |
| 2683 |
|
@ARTICLE{Reddy2006, |
| 2684 |
|
author = {R. A. Reddy and C. Tschierske}, |
| 2685 |
|
title = {Bent-core liquid crystals: polar order, superstructural chirality |
| 2686 |
< |
and spontaneous desymmetrisation in soft matter systems}, |
| 2686 |
> |
and spontaneous desymmetrisation in soft matter systems}, |
| 2687 |
|
journal = {Journal of Materials Chemistry}, |
| 2688 |
|
year = {2006}, |
| 2689 |
|
volume = {16}, |
| 2690 |
|
pages = {907-961}, |
| 2691 |
|
number = {10}, |
| 2692 |
|
abstract = {An overview on the recent developments in the field of liquid crystalline |
| 2693 |
< |
bent-core molecules (so-called banana liquid crystals) is given. |
| 2694 |
< |
After some basic issues, dealing with general aspects of the systematisation |
| 2695 |
< |
of the mesophases, development of polar order and chirality in this |
| 2696 |
< |
class of LC systems and explaining some general structure-property |
| 2697 |
< |
relationships, we focus on fascinating new developments in this |
| 2698 |
< |
field, such as modulated, undulated and columnar phases, so-called |
| 2699 |
< |
B7 phases, phase biaxiality, ferroelectric and antiferroelectric |
| 2700 |
< |
polar order in smectic and columnar phases, amplification and switching |
| 2701 |
< |
of chirality and the spontaneous formation of superstructural and |
| 2702 |
< |
supramolecular chirality.}, |
| 2693 |
> |
bent-core molecules (so-called banana liquid crystals) is given. |
| 2694 |
> |
After some basic issues, dealing with general aspects of the systematisation |
| 2695 |
> |
of the mesophases, development of polar order and chirality in this |
| 2696 |
> |
class of LC systems and explaining some general structure-property |
| 2697 |
> |
relationships, we focus on fascinating new developments in this |
| 2698 |
> |
field, such as modulated, undulated and columnar phases, so-called |
| 2699 |
> |
B7 phases, phase biaxiality, ferroelectric and antiferroelectric |
| 2700 |
> |
polar order in smectic and columnar phases, amplification and switching |
| 2701 |
> |
of chirality and the spontaneous formation of superstructural and |
| 2702 |
> |
supramolecular chirality.}, |
| 2703 |
|
annote = {021NS Times Cited:2 Cited References Count:316}, |
| 2704 |
|
issn = {0959-9428}, |
| 2705 |
|
uri = {<Go to ISI>://000235990500001}, |
| 2715 |
|
number = {5}, |
| 2716 |
|
month = {Sep 8}, |
| 2717 |
|
abstract = {Backward error analysis has become an important tool for understanding |
| 2718 |
< |
the long time behavior of numerical integration methods. This is |
| 2719 |
< |
true in particular for the integration of Hamiltonian systems where |
| 2720 |
< |
backward error analysis can be used to show that a symplectic method |
| 2721 |
< |
will conserve energy over exponentially long periods of time. Such |
| 2722 |
< |
results are typically based on two aspects of backward error analysis: |
| 2723 |
< |
(i) It can be shown that the modified vector fields have some qualitative |
| 2724 |
< |
properties which they share with the given problem and (ii) an estimate |
| 2725 |
< |
is given for the difference between the best interpolating vector |
| 2726 |
< |
field and the numerical method. These aspects have been investigated |
| 2727 |
< |
recently, for example, by Benettin and Giorgilli in [J. Statist. |
| 2728 |
< |
Phys., 74 (1994), pp. 1117-1143], by Hairer in [Ann. Numer. Math., |
| 2729 |
< |
1 (1994), pp. 107-132], and by Hairer and Lubich in [Numer. Math., |
| 2730 |
< |
76 (1997), pp. 441-462]. In this paper we aim at providing a unifying |
| 2731 |
< |
framework and a simplification of the existing results and corresponding |
| 2732 |
< |
proofs. Our approach to backward error analysis is based on a simple |
| 2733 |
< |
recursive definition of the modified vector fields that does not |
| 2734 |
< |
require explicit Taylor series expansion of the numerical method |
| 2735 |
< |
and the corresponding flow maps as in the above-cited works. As |
| 2736 |
< |
an application we discuss the long time integration of chaotic Hamiltonian |
| 2737 |
< |
systems and the approximation of time averages along numerically |
| 2738 |
< |
computed trajectories.}, |
| 2718 |
> |
the long time behavior of numerical integration methods. This is |
| 2719 |
> |
true in particular for the integration of Hamiltonian systems where |
| 2720 |
> |
backward error analysis can be used to show that a symplectic method |
| 2721 |
> |
will conserve energy over exponentially long periods of time. Such |
| 2722 |
> |
results are typically based on two aspects of backward error analysis: |
| 2723 |
> |
(i) It can be shown that the modified vector fields have some qualitative |
| 2724 |
> |
properties which they share with the given problem and (ii) an estimate |
| 2725 |
> |
is given for the difference between the best interpolating vector |
| 2726 |
> |
field and the numerical method. These aspects have been investigated |
| 2727 |
> |
recently, for example, by Benettin and Giorgilli in [J. Statist. |
| 2728 |
> |
Phys., 74 (1994), pp. 1117-1143], by Hairer in [Ann. Numer. Math., |
| 2729 |
> |
1 (1994), pp. 107-132], and by Hairer and Lubich in [Numer. Math., |
| 2730 |
> |
76 (1997), pp. 441-462]. In this paper we aim at providing a unifying |
| 2731 |
> |
framework and a simplification of the existing results and corresponding |
| 2732 |
> |
proofs. Our approach to backward error analysis is based on a simple |
| 2733 |
> |
recursive definition of the modified vector fields that does not |
| 2734 |
> |
require explicit Taylor series expansion of the numerical method |
| 2735 |
> |
and the corresponding flow maps as in the above-cited works. As |
| 2736 |
> |
an application we discuss the long time integration of chaotic Hamiltonian |
| 2737 |
> |
systems and the approximation of time averages along numerically |
| 2738 |
> |
computed trajectories.}, |
| 2739 |
|
annote = {237HV Times Cited:43 Cited References Count:41}, |
| 2740 |
|
issn = {0036-1429}, |
| 2741 |
|
uri = {<Go to ISI>://000082650600010}, |
| 2750 |
|
pages = {5093-5098}, |
| 2751 |
|
number = {48}, |
| 2752 |
|
abstract = {The recent literature in the field of liquid crystals shows that banana-shaped |
| 2753 |
< |
mesogenic materials represent a bewitching and stimulating field |
| 2754 |
< |
of research that is interesting both academically and in terms of |
| 2755 |
< |
applications. Numerous topics are open to investigation in this |
| 2756 |
< |
area because of the rich phenomenology and new possibilities that |
| 2757 |
< |
these materials offer. The principal concepts in this area are reviewed |
| 2758 |
< |
along with recent results. In addition, new directions to stimulate |
| 2759 |
< |
further research activities are highlighted.}, |
| 2753 |
> |
mesogenic materials represent a bewitching and stimulating field |
| 2754 |
> |
of research that is interesting both academically and in terms of |
| 2755 |
> |
applications. Numerous topics are open to investigation in this |
| 2756 |
> |
area because of the rich phenomenology and new possibilities that |
| 2757 |
> |
these materials offer. The principal concepts in this area are reviewed |
| 2758 |
> |
along with recent results. In addition, new directions to stimulate |
| 2759 |
> |
further research activities are highlighted.}, |
| 2760 |
|
annote = {990XA Times Cited:3 Cited References Count:72}, |
| 2761 |
|
issn = {0959-9428}, |
| 2762 |
|
uri = {<Go to ISI>://000233775500001}, |
| 2763 |
|
} |
| 2764 |
|
|
| 2765 |
+ |
@ARTICLE{Roux1991, |
| 2766 |
+ |
author = {B. Roux and M. Karplus}, |
| 2767 |
+ |
title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility}, |
| 2768 |
+ |
journal = {Journal of Physical Chemistry}, |
| 2769 |
+ |
year = {1991}, |
| 2770 |
+ |
volume = {95}, |
| 2771 |
+ |
pages = {4856-4868}, |
| 2772 |
+ |
number = {12}, |
| 2773 |
+ |
month = {Jun 13}, |
| 2774 |
+ |
abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic |
| 2775 |
+ |
poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin |
| 2776 |
+ |
channel. Because of the different dynamical regimes for the three |
| 2777 |
+ |
species (high barrier for Na+, low barrier for K+, almost free diffusion |
| 2778 |
+ |
for water), different methods are used to calculate the mobilities. |
| 2779 |
+ |
By use of activated dynamics and a potential of mean force determined |
| 2780 |
+ |
previously (Roux, B.; Karplus, M. Biophys. J. 1991, 59, 961), the |
| 2781 |
+ |
barrier crossing rate of Na+ ion is determined. The motion of Na+ |
| 2782 |
+ |
at the transition state is controlled by local interactions and |
| 2783 |
+ |
collisions with the neighboring carbonyls and the two nearest water |
| 2784 |
+ |
molecules. There are significant deviations from transition-state |
| 2785 |
+ |
theory; the transmission coefficient is equal to 0.11. The water |
| 2786 |
+ |
and K+ motions are found to be well described by a diffusive model; |
| 2787 |
+ |
the motion of K+ appears to be controlled by the diffusion of water. |
| 2788 |
+ |
The time-dependent friction functions of Na+ and K+ ions in the |
| 2789 |
+ |
periodic beta-helix are calculated and analyzed by using a generalized |
| 2790 |
+ |
Langevin equation approach. Both Na+ and K+ suffer many rapid collisions, |
| 2791 |
+ |
and their dynamics is overdamped and noninertial. Thus, the selectivity |
| 2792 |
+ |
sequence of ions in the beta-helix is not influenced strongly by |
| 2793 |
+ |
their masses.}, |
| 2794 |
+ |
annote = {Fr756 Times Cited:97 Cited References Count:65}, |
| 2795 |
+ |
issn = {0022-3654}, |
| 2796 |
+ |
uri = {<Go to ISI>://A1991FR75600049}, |
| 2797 |
+ |
} |
| 2798 |
+ |
|
| 2799 |
|
@ARTICLE{Roy2005, |
| 2800 |
|
author = {A. Roy and N. V. Madhusudana}, |
| 2801 |
|
title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases |
| 2802 |
< |
in banana shaped molecules}, |
| 2802 |
> |
in banana shaped molecules}, |
| 2803 |
|
journal = {European Physical Journal E}, |
| 2804 |
|
year = {2005}, |
| 2805 |
|
volume = {18}, |
| 2807 |
|
number = {3}, |
| 2808 |
|
month = {Nov}, |
| 2809 |
|
abstract = {A vast majority of compounds with bent core or banana shaped molecules |
| 2810 |
< |
exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased |
| 2811 |
< |
in a homologous series. The B-6 phase has an intercalated fluid |
| 2812 |
< |
lamellar structure with a layer spacing of half the molecular length. |
| 2813 |
< |
The B-1 phase has a two dimensionally periodic rectangular columnar |
| 2814 |
< |
structure. The B-2 phase has a monolayer fluid lamellar structure |
| 2815 |
< |
with molecules tilted with respect to the layer normal. Neglecting |
| 2816 |
< |
the tilt order of the molecules in the B-2 phase, we have developed |
| 2817 |
< |
a frustrated packing model to describe this phase sequence qualitatively. |
| 2818 |
< |
The model has some analogy with that of the frustrated smectics |
| 2819 |
< |
exhibited by highly polar rod like molecules.}, |
| 2810 |
> |
exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased |
| 2811 |
> |
in a homologous series. The B-6 phase has an intercalated fluid |
| 2812 |
> |
lamellar structure with a layer spacing of half the molecular length. |
| 2813 |
> |
The B-1 phase has a two dimensionally periodic rectangular columnar |
| 2814 |
> |
structure. The B-2 phase has a monolayer fluid lamellar structure |
| 2815 |
> |
with molecules tilted with respect to the layer normal. Neglecting |
| 2816 |
> |
the tilt order of the molecules in the B-2 phase, we have developed |
| 2817 |
> |
a frustrated packing model to describe this phase sequence qualitatively. |
| 2818 |
> |
The model has some analogy with that of the frustrated smectics |
| 2819 |
> |
exhibited by highly polar rod like molecules.}, |
| 2820 |
|
annote = {985FW Times Cited:0 Cited References Count:30}, |
| 2821 |
|
issn = {1292-8941}, |
| 2822 |
|
uri = {<Go to ISI>://000233363300002}, |
| 2825 |
|
@ARTICLE{Ryckaert1977, |
| 2826 |
|
author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen}, |
| 2827 |
|
title = {Numerical-Integration of Cartesian Equations of Motion of a System |
| 2828 |
< |
with Constraints - Molecular-Dynamics of N-Alkanes}, |
| 2828 |
> |
with Constraints - Molecular-Dynamics of N-Alkanes}, |
| 2829 |
|
journal = {Journal of Computational Physics}, |
| 2830 |
|
year = {1977}, |
| 2831 |
|
volume = {23}, |
| 2839 |
|
@ARTICLE{Sagui1999, |
| 2840 |
|
author = {C. Sagui and T. A. Darden}, |
| 2841 |
|
title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic |
| 2842 |
< |
effects}, |
| 2842 |
> |
effects}, |
| 2843 |
|
journal = {Annual Review of Biophysics and Biomolecular Structure}, |
| 2844 |
|
year = {1999}, |
| 2845 |
|
volume = {28}, |
| 2846 |
|
pages = {155-179}, |
| 2847 |
|
abstract = {Current computer simulations of biomolecules typically make use of |
| 2848 |
< |
classical molecular dynamics methods, as a very large number (tens |
| 2849 |
< |
to hundreds of thousands) of atoms are involved over timescales |
| 2850 |
< |
of many nanoseconds. The methodology for treating short-range bonded |
| 2851 |
< |
and van der Waals interactions has matured. However, long-range |
| 2852 |
< |
electrostatic interactions still represent a bottleneck in simulations. |
| 2853 |
< |
In this article, we introduce the basic issues for an accurate representation |
| 2854 |
< |
of the relevant electrostatic interactions. In spite of the huge |
| 2855 |
< |
computational time demanded by most biomolecular systems, it is |
| 2856 |
< |
no longer necessary to resort to uncontrolled approximations such |
| 2857 |
< |
as the use of cutoffs. In particular, we discuss the Ewald summation |
| 2858 |
< |
methods, the fast particle mesh methods, and the fast multipole |
| 2859 |
< |
methods. We also review recent efforts to understand the role of |
| 2860 |
< |
boundary conditions in systems with long-range interactions, and |
| 2861 |
< |
conclude with a short perspective on future trends.}, |
| 2848 |
> |
classical molecular dynamics methods, as a very large number (tens |
| 2849 |
> |
to hundreds of thousands) of atoms are involved over timescales |
| 2850 |
> |
of many nanoseconds. The methodology for treating short-range bonded |
| 2851 |
> |
and van der Waals interactions has matured. However, long-range |
| 2852 |
> |
electrostatic interactions still represent a bottleneck in simulations. |
| 2853 |
> |
In this article, we introduce the basic issues for an accurate representation |
| 2854 |
> |
of the relevant electrostatic interactions. In spite of the huge |
| 2855 |
> |
computational time demanded by most biomolecular systems, it is |
| 2856 |
> |
no longer necessary to resort to uncontrolled approximations such |
| 2857 |
> |
as the use of cutoffs. In particular, we discuss the Ewald summation |
| 2858 |
> |
methods, the fast particle mesh methods, and the fast multipole |
| 2859 |
> |
methods. We also review recent efforts to understand the role of |
| 2860 |
> |
boundary conditions in systems with long-range interactions, and |
| 2861 |
> |
conclude with a short perspective on future trends.}, |
| 2862 |
|
annote = {213KJ Times Cited:126 Cited References Count:73}, |
| 2863 |
|
issn = {1056-8700}, |
| 2864 |
|
uri = {<Go to ISI>://000081271400008}, |
| 2867 |
|
@ARTICLE{Sandu1999, |
| 2868 |
|
author = {A. Sandu and T. Schlick}, |
| 2869 |
|
title = {Masking resonance artifacts in force-splitting methods for biomolecular |
| 2870 |
< |
simulations by extrapolative Langevin dynamics}, |
| 2870 |
> |
simulations by extrapolative Langevin dynamics}, |
| 2871 |
|
journal = {Journal of Computational Physics}, |
| 2872 |
|
year = {1999}, |
| 2873 |
|
volume = {151}, |
| 2875 |
|
number = {1}, |
| 2876 |
|
month = {May 1}, |
| 2877 |
|
abstract = {Numerical resonance artifacts have become recognized recently as a |
| 2878 |
< |
limiting factor to increasing the timestep in multiple-timestep |
| 2879 |
< |
(MTS) biomolecular dynamics simulations. At certain timesteps correlated |
| 2880 |
< |
to internal motions (e.g., 5 fs, around half the period of the fastest |
| 2881 |
< |
bond stretch, T-min), visible inaccuracies or instabilities can |
| 2882 |
< |
occur. Impulse-MTS schemes are vulnerable to these resonance errors |
| 2883 |
< |
since large energy pulses are introduced to the governing dynamics |
| 2884 |
< |
equations when the slow forces are evaluated. We recently showed |
| 2885 |
< |
that such resonance artifacts can be masked significantly by applying |
| 2886 |
< |
extrapolative splitting to stochastic dynamics. Theoretical and |
| 2887 |
< |
numerical analyses of force-splitting integrators based on the Verlet |
| 2888 |
< |
discretization are reported here for linear models to explain these |
| 2889 |
< |
observations and to suggest how to construct effective integrators |
| 2890 |
< |
for biomolecular dynamics that balance stability with accuracy. |
| 2891 |
< |
Analyses for Newtonian dynamics demonstrate the severe resonance |
| 2892 |
< |
patterns of the Impulse splitting, with this severity worsening |
| 2893 |
< |
with the outer timestep. Delta t: Constant Extrapolation is generally |
| 2894 |
< |
unstable, but the disturbances do not grow with Delta t. Thus. the |
| 2895 |
< |
stochastic extrapolative combination can counteract generic instabilities |
| 2896 |
< |
and largely alleviate resonances with a sufficiently strong Langevin |
| 2897 |
< |
heat-bath coupling (gamma), estimates for which are derived here |
| 2898 |
< |
based on the fastest and slowest motion periods. These resonance |
| 2899 |
< |
results generally hold for nonlinear test systems: a water tetramer |
| 2900 |
< |
and solvated protein. Proposed related approaches such as Extrapolation/Correction |
| 2901 |
< |
and Midpoint Extrapolation work better than Constant Extrapolation |
| 2902 |
< |
only for timesteps less than T-min/2. An effective extrapolative |
| 2903 |
< |
stochastic approach for biomolecules that balances long-timestep |
| 2904 |
< |
stability with good accuracy for the fast subsystem is then applied |
| 2905 |
< |
to a biomolecule using a three-class partitioning: the medium forces |
| 2906 |
< |
are treated by Midpoint Extrapolation via position Verlet, and the |
| 2907 |
< |
slow forces are incorporated by Constant Extrapolation. The resulting |
| 2908 |
< |
algorithm (LN) performs well on a solvated protein system in terms |
| 2909 |
< |
of thermodynamic properties and yields an order of magnitude speedup |
| 2910 |
< |
with respect to single-timestep Langevin trajectories. Computed |
| 2911 |
< |
spectral density functions also show how the Newtonian modes can |
| 2912 |
< |
be approximated by using a small gamma in the range Of 5-20 ps(-1). |
| 2913 |
< |
(C) 1999 Academic Press.}, |
| 2878 |
> |
limiting factor to increasing the timestep in multiple-timestep |
| 2879 |
> |
(MTS) biomolecular dynamics simulations. At certain timesteps correlated |
| 2880 |
> |
to internal motions (e.g., 5 fs, around half the period of the fastest |
| 2881 |
> |
bond stretch, T-min), visible inaccuracies or instabilities can |
| 2882 |
> |
occur. Impulse-MTS schemes are vulnerable to these resonance errors |
| 2883 |
> |
since large energy pulses are introduced to the governing dynamics |
| 2884 |
> |
equations when the slow forces are evaluated. We recently showed |
| 2885 |
> |
that such resonance artifacts can be masked significantly by applying |
| 2886 |
> |
extrapolative splitting to stochastic dynamics. Theoretical and |
| 2887 |
> |
numerical analyses of force-splitting integrators based on the Verlet |
| 2888 |
> |
discretization are reported here for linear models to explain these |
| 2889 |
> |
observations and to suggest how to construct effective integrators |
| 2890 |
> |
for biomolecular dynamics that balance stability with accuracy. |
| 2891 |
> |
Analyses for Newtonian dynamics demonstrate the severe resonance |
| 2892 |
> |
patterns of the Impulse splitting, with this severity worsening |
| 2893 |
> |
with the outer timestep. Delta t: Constant Extrapolation is generally |
| 2894 |
> |
unstable, but the disturbances do not grow with Delta t. Thus. the |
| 2895 |
> |
stochastic extrapolative combination can counteract generic instabilities |
| 2896 |
> |
and largely alleviate resonances with a sufficiently strong Langevin |
| 2897 |
> |
heat-bath coupling (gamma), estimates for which are derived here |
| 2898 |
> |
based on the fastest and slowest motion periods. These resonance |
| 2899 |
> |
results generally hold for nonlinear test systems: a water tetramer |
| 2900 |
> |
and solvated protein. Proposed related approaches such as Extrapolation/Correction |
| 2901 |
> |
and Midpoint Extrapolation work better than Constant Extrapolation |
| 2902 |
> |
only for timesteps less than T-min/2. An effective extrapolative |
| 2903 |
> |
stochastic approach for biomolecules that balances long-timestep |
| 2904 |
> |
stability with good accuracy for the fast subsystem is then applied |
| 2905 |
> |
to a biomolecule using a three-class partitioning: the medium forces |
| 2906 |
> |
are treated by Midpoint Extrapolation via position Verlet, and the |
| 2907 |
> |
slow forces are incorporated by Constant Extrapolation. The resulting |
| 2908 |
> |
algorithm (LN) performs well on a solvated protein system in terms |
| 2909 |
> |
of thermodynamic properties and yields an order of magnitude speedup |
| 2910 |
> |
with respect to single-timestep Langevin trajectories. Computed |
| 2911 |
> |
spectral density functions also show how the Newtonian modes can |
| 2912 |
> |
be approximated by using a small gamma in the range Of 5-20 ps(-1). |
| 2913 |
> |
(C) 1999 Academic Press.}, |
| 2914 |
|
annote = {194FM Times Cited:14 Cited References Count:32}, |
| 2915 |
|
issn = {0021-9991}, |
| 2916 |
|
uri = {<Go to ISI>://000080181500004}, |
| 2917 |
|
} |
| 2918 |
|
|
| 2919 |
+ |
@ARTICLE{Sasaki2004, |
| 2920 |
+ |
author = {Y. Sasaki and R. Shukla and B. D. Smith}, |
| 2921 |
+ |
title = {Facilitated phosphatidylserine flip-flop across vesicle and cell |
| 2922 |
+ |
membranes using urea-derived synthetic translocases}, |
| 2923 |
+ |
journal = {Organic \& Biomolecular Chemistry}, |
| 2924 |
+ |
year = {2004}, |
| 2925 |
+ |
volume = {2}, |
| 2926 |
+ |
pages = {214-219}, |
| 2927 |
+ |
number = {2}, |
| 2928 |
+ |
abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide |
| 2929 |
+ |
groups are shown to facilitate the translocation of fluorescent |
| 2930 |
+ |
phospholipid probes and endogenous phosphatidylserine across vesicle |
| 2931 |
+ |
and erythrocyte cell membranes. The synthetic translocases appear |
| 2932 |
+ |
to operate by binding to the phospholipid head groups and forming |
| 2933 |
+ |
lipophilic supramolecular complexes which diffuse through the non-polar |
| 2934 |
+ |
interior of the bilayer membrane.}, |
| 2935 |
+ |
annote = {760PX Times Cited:8 Cited References Count:25}, |
| 2936 |
+ |
issn = {1477-0520}, |
| 2937 |
+ |
uri = {<Go to ISI>://000187843800012}, |
| 2938 |
+ |
} |
| 2939 |
+ |
|
| 2940 |
|
@ARTICLE{Satoh1996, |
| 2941 |
|
author = {K. Satoh and S. Mita and S. Kondo}, |
| 2942 |
|
title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect |
| 2943 |
< |
of terminal dipole moment on mesophase formation}, |
| 2943 |
> |
of terminal dipole moment on mesophase formation}, |
| 2944 |
|
journal = {Chemical Physics Letters}, |
| 2945 |
|
year = {1996}, |
| 2946 |
|
volume = {255}, |
| 2948 |
|
number = {1-3}, |
| 2949 |
|
month = {Jun 7}, |
| 2950 |
|
abstract = {The effects of dipole-dipole interaction on mesophase formation are |
| 2951 |
< |
investigated with a Monte Carlo simulation using the dipolar Gay-Berne |
| 2952 |
< |
potential. It is shown that the dipole moment at the end of a molecule |
| 2953 |
< |
causes a shift in the nematic-isotropic transition toward higher |
| 2954 |
< |
temperature and a spread of the temperature range of the nematic |
| 2955 |
< |
phase and that layer structures with various interdigitations are |
| 2956 |
< |
formed in the smectic phase.}, |
| 2951 |
> |
investigated with a Monte Carlo simulation using the dipolar Gay-Berne |
| 2952 |
> |
potential. It is shown that the dipole moment at the end of a molecule |
| 2953 |
> |
causes a shift in the nematic-isotropic transition toward higher |
| 2954 |
> |
temperature and a spread of the temperature range of the nematic |
| 2955 |
> |
phase and that layer structures with various interdigitations are |
| 2956 |
> |
formed in the smectic phase.}, |
| 2957 |
|
annote = {Uq975 Times Cited:32 Cited References Count:33}, |
| 2958 |
|
issn = {0009-2614}, |
| 2959 |
|
uri = {<Go to ISI>://A1996UQ97500017}, |
| 2960 |
|
} |
| 2961 |
|
|
| 2962 |
+ |
@ARTICLE{Schaps1999, |
| 2963 |
+ |
author = {G. L. Schaps}, |
| 2964 |
+ |
title = {Compiler construction with ANTLR and Java - Tools for building tools}, |
| 2965 |
+ |
journal = {Dr Dobbs Journal}, |
| 2966 |
+ |
year = {1999}, |
| 2967 |
+ |
volume = {24}, |
| 2968 |
+ |
pages = {84-+}, |
| 2969 |
+ |
number = {3}, |
| 2970 |
+ |
month = {Mar}, |
| 2971 |
+ |
annote = {163EC Times Cited:0 Cited References Count:0}, |
| 2972 |
+ |
issn = {1044-789X}, |
| 2973 |
+ |
uri = {<Go to ISI>://000078389200023}, |
| 2974 |
+ |
} |
| 2975 |
+ |
|
| 2976 |
|
@ARTICLE{Shen2002, |
| 2977 |
|
author = {M. Y. Shen and K. F. Freed}, |
| 2978 |
|
title = {Long time dynamics of met-enkephalin: Comparison of explicit and |
| 2979 |
< |
implicit solvent models}, |
| 2979 |
> |
implicit solvent models}, |
| 2980 |
|
journal = {Biophysical Journal}, |
| 2981 |
|
year = {2002}, |
| 2982 |
|
volume = {82}, |
| 2984 |
|
number = {4}, |
| 2985 |
|
month = {Apr}, |
| 2986 |
|
abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical |
| 2987 |
< |
structure and receptor docking mechanism are still not well understood. |
| 2988 |
< |
The conformational dynamics of this neuron peptide in liquid water |
| 2989 |
< |
are studied here by using all-atom molecular dynamics (MID) and |
| 2990 |
< |
implicit water Langevin dynamics (LD) simulations with AMBER potential |
| 2991 |
< |
functions and the three-site transferable intermolecular potential |
| 2992 |
< |
(TIP3P) model for water. To achieve the same simulation length in |
| 2993 |
< |
physical time, the full MID simulations require 200 times as much |
| 2994 |
< |
CPU time as the implicit water LID simulations. The solvent hydrophobicity |
| 2995 |
< |
and dielectric behavior are treated in the implicit solvent LD simulations |
| 2996 |
< |
by using a macroscopic solvation potential, a single dielectric |
| 2997 |
< |
constant, and atomic friction coefficients computed using the accessible |
| 2998 |
< |
surface area method with the TIP3P model water viscosity as determined |
| 2999 |
< |
here from MID simulations for pure TIP3P water. Both the local and |
| 3000 |
< |
the global dynamics obtained from the implicit solvent LD simulations |
| 3001 |
< |
agree very well with those from the explicit solvent MD simulations. |
| 3002 |
< |
The simulations provide insights into the conformational restrictions |
| 3003 |
< |
that are associated with the bioactivity of the opiate peptide dermorphin |
| 3004 |
< |
for the delta-receptor.}, |
| 2987 |
> |
structure and receptor docking mechanism are still not well understood. |
| 2988 |
> |
The conformational dynamics of this neuron peptide in liquid water |
| 2989 |
> |
are studied here by using all-atom molecular dynamics (MID) and |
| 2990 |
> |
implicit water Langevin dynamics (LD) simulations with AMBER potential |
| 2991 |
> |
functions and the three-site transferable intermolecular potential |
| 2992 |
> |
(TIP3P) model for water. To achieve the same simulation length in |
| 2993 |
> |
physical time, the full MID simulations require 200 times as much |
| 2994 |
> |
CPU time as the implicit water LID simulations. The solvent hydrophobicity |
| 2995 |
> |
and dielectric behavior are treated in the implicit solvent LD simulations |
| 2996 |
> |
by using a macroscopic solvation potential, a single dielectric |
| 2997 |
> |
constant, and atomic friction coefficients computed using the accessible |
| 2998 |
> |
surface area method with the TIP3P model water viscosity as determined |
| 2999 |
> |
here from MID simulations for pure TIP3P water. Both the local and |
| 3000 |
> |
the global dynamics obtained from the implicit solvent LD simulations |
| 3001 |
> |
agree very well with those from the explicit solvent MD simulations. |
| 3002 |
> |
The simulations provide insights into the conformational restrictions |
| 3003 |
> |
that are associated with the bioactivity of the opiate peptide dermorphin |
| 3004 |
> |
for the delta-receptor.}, |
| 3005 |
|
annote = {540MH Times Cited:36 Cited References Count:45}, |
| 3006 |
|
issn = {0006-3495}, |
| 3007 |
|
uri = {<Go to ISI>://000174932400010}, |
| 3024 |
|
@ARTICLE{Shimada1993, |
| 3025 |
|
author = {J. Shimada and H. Kaneko and T. Takada}, |
| 3026 |
|
title = {Efficient Calculations of Coulombic Interactions in Biomolecular |
| 3027 |
< |
Simulations with Periodic Boundary-Conditions}, |
| 3027 |
> |
Simulations with Periodic Boundary-Conditions}, |
| 3028 |
|
journal = {Journal of Computational Chemistry}, |
| 3029 |
|
year = {1993}, |
| 3030 |
|
volume = {14}, |
| 3032 |
|
number = {7}, |
| 3033 |
|
month = {Jul}, |
| 3034 |
|
abstract = {To make improved treatments of electrostatic interactions in biomacromolecular |
| 3035 |
< |
simulations, two possibilities are considered. The first is the |
| 3036 |
< |
famous particle-particle and particle-mesh (PPPM) method developed |
| 3037 |
< |
by Hockney and Eastwood, and the second is a new one developed here |
| 3038 |
< |
in their spirit but by the use of the multipole expansion technique |
| 3039 |
< |
suggested by Ladd. It is then numerically found that the new PPPM |
| 3040 |
< |
method gives more accurate results for a two-particle system at |
| 3041 |
< |
small separation of particles. Preliminary numerical examination |
| 3042 |
< |
of the various computational methods for a single configuration |
| 3043 |
< |
of a model BPTI-water system containing about 24,000 particles indicates |
| 3044 |
< |
that both of the PPPM methods give far more accurate values with |
| 3045 |
< |
reasonable computational cost than do the conventional truncation |
| 3046 |
< |
methods. It is concluded the two PPPM methods are nearly comparable |
| 3047 |
< |
in overall performance for the many-particle systems, although the |
| 3048 |
< |
first method has the drawback that the accuracy in the total electrostatic |
| 3049 |
< |
energy is not high for configurations of charged particles randomly |
| 3050 |
< |
generated.}, |
| 3035 |
> |
simulations, two possibilities are considered. The first is the |
| 3036 |
> |
famous particle-particle and particle-mesh (PPPM) method developed |
| 3037 |
> |
by Hockney and Eastwood, and the second is a new one developed here |
| 3038 |
> |
in their spirit but by the use of the multipole expansion technique |
| 3039 |
> |
suggested by Ladd. It is then numerically found that the new PPPM |
| 3040 |
> |
method gives more accurate results for a two-particle system at |
| 3041 |
> |
small separation of particles. Preliminary numerical examination |
| 3042 |
> |
of the various computational methods for a single configuration |
| 3043 |
> |
of a model BPTI-water system containing about 24,000 particles indicates |
| 3044 |
> |
that both of the PPPM methods give far more accurate values with |
| 3045 |
> |
reasonable computational cost than do the conventional truncation |
| 3046 |
> |
methods. It is concluded the two PPPM methods are nearly comparable |
| 3047 |
> |
in overall performance for the many-particle systems, although the |
| 3048 |
> |
first method has the drawback that the accuracy in the total electrostatic |
| 3049 |
> |
energy is not high for configurations of charged particles randomly |
| 3050 |
> |
generated.}, |
| 3051 |
|
annote = {Lh164 Times Cited:27 Cited References Count:47}, |
| 3052 |
|
issn = {0192-8651}, |
| 3053 |
|
uri = {<Go to ISI>://A1993LH16400011}, |
| 3063 |
|
number = {24}, |
| 3064 |
|
month = {Dec 20}, |
| 3065 |
|
abstract = {The best simple method for Newtonian molecular dynamics is indisputably |
| 3066 |
< |
the leapfrog Stormer-Verlet method. The appropriate generalization |
| 3067 |
< |
to simple Langevin dynamics is unclear. An analysis is presented |
| 3068 |
< |
comparing an 'impulse method' (kick; fluctuate; kick), the 1982 |
| 3069 |
< |
method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus |
| 3070 |
< |
(BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen |
| 3071 |
< |
methods can be implemented as efficiently as the BBK method. Other |
| 3072 |
< |
considerations suggest that the impulse method is the best basic |
| 3073 |
< |
method for simple Langevin dynamics, with the van Gunsteren-Berendsen |
| 3074 |
< |
method a close contender.}, |
| 3066 |
> |
the leapfrog Stormer-Verlet method. The appropriate generalization |
| 3067 |
> |
to simple Langevin dynamics is unclear. An analysis is presented |
| 3068 |
> |
comparing an 'impulse method' (kick; fluctuate; kick), the 1982 |
| 3069 |
> |
method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus |
| 3070 |
> |
(BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen |
| 3071 |
> |
methods can be implemented as efficiently as the BBK method. Other |
| 3072 |
> |
considerations suggest that the impulse method is the best basic |
| 3073 |
> |
method for simple Langevin dynamics, with the van Gunsteren-Berendsen |
| 3074 |
> |
method a close contender.}, |
| 3075 |
|
annote = {633RX Times Cited:8 Cited References Count:22}, |
| 3076 |
|
issn = {0026-8976}, |
| 3077 |
|
uri = {<Go to ISI>://000180297200014}, |
| 3080 |
|
@ARTICLE{Skeel1997, |
| 3081 |
|
author = {R. D. Skeel and G. H. Zhang and T. Schlick}, |
| 3082 |
|
title = {A family of symplectic integrators: Stability, accuracy, and molecular |
| 3083 |
< |
dynamics applications}, |
| 3083 |
> |
dynamics applications}, |
| 3084 |
|
journal = {Siam Journal on Scientific Computing}, |
| 3085 |
|
year = {1997}, |
| 3086 |
|
volume = {18}, |
| 3088 |
|
number = {1}, |
| 3089 |
|
month = {Jan}, |
| 3090 |
|
abstract = {The following integration methods for special second-order ordinary |
| 3091 |
< |
differential equations are studied: leapfrog, implicit midpoint, |
| 3092 |
< |
trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all |
| 3093 |
< |
are members, or equivalent to members, of a one-parameter family |
| 3094 |
< |
of schemes. Some methods have more than one common form, and we |
| 3095 |
< |
discuss a systematic enumeration of these forms. We also present |
| 3096 |
< |
a stability and accuracy analysis based on the idea of ''modified |
| 3097 |
< |
equations'' and a proof of symplecticness. It follows that Cowell-Numerov |
| 3098 |
< |
and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic. |
| 3099 |
< |
A different interpretation of the values used by these integrators |
| 3100 |
< |
leads to higher accuracy and better energy conservation. Hence, |
| 3101 |
< |
we suggest that the straightforward analysis of energy conservation |
| 3102 |
< |
is misleading.}, |
| 3091 |
> |
differential equations are studied: leapfrog, implicit midpoint, |
| 3092 |
> |
trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all |
| 3093 |
> |
are members, or equivalent to members, of a one-parameter family |
| 3094 |
> |
of schemes. Some methods have more than one common form, and we |
| 3095 |
> |
discuss a systematic enumeration of these forms. We also present |
| 3096 |
> |
a stability and accuracy analysis based on the idea of ''modified |
| 3097 |
> |
equations'' and a proof of symplecticness. It follows that Cowell-Numerov |
| 3098 |
> |
and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic. |
| 3099 |
> |
A different interpretation of the values used by these integrators |
| 3100 |
> |
leads to higher accuracy and better energy conservation. Hence, |
| 3101 |
> |
we suggest that the straightforward analysis of energy conservation |
| 3102 |
> |
is misleading.}, |
| 3103 |
|
annote = {We981 Times Cited:30 Cited References Count:35}, |
| 3104 |
|
issn = {1064-8275}, |
| 3105 |
|
uri = {<Go to ISI>://A1997WE98100012}, |
| 3107 |
|
|
| 3108 |
|
@ARTICLE{Tao2005, |
| 3109 |
|
author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont |
| 3110 |
< |
and W. J. Briels}, |
| 3110 |
> |
and W. J. Briels}, |
| 3111 |
|
title = {Brownian dynamics simulations of the self- and collective rotational |
| 3112 |
< |
diffusion coefficients of rigid long thin rods}, |
| 3112 |
> |
diffusion coefficients of rigid long thin rods}, |
| 3113 |
|
journal = {Journal of Chemical Physics}, |
| 3114 |
|
year = {2005}, |
| 3115 |
|
volume = {122}, |
| 3117 |
|
number = {24}, |
| 3118 |
|
month = {Jun 22}, |
| 3119 |
|
abstract = {Recently a microscopic theory for the dynamics of suspensions of long |
| 3120 |
< |
thin rigid rods was presented, confirming and expanding the well-known |
| 3121 |
< |
theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, |
| 3122 |
< |
Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here |
| 3123 |
< |
this theory is put to the test by comparing it against computer |
| 3124 |
< |
simulations. A Brownian dynamics simulation program was developed |
| 3125 |
< |
to follow the dynamics of the rods, with a length over a diameter |
| 3126 |
< |
ratio of 60, on the Smoluchowski time scale. The model accounts |
| 3127 |
< |
for excluded volume interactions between rods, but neglects hydrodynamic |
| 3128 |
< |
interactions. The self-rotational diffusion coefficients D-r(phi) |
| 3129 |
< |
of the rods were calculated by standard methods and by a new, more |
| 3130 |
< |
efficient method based on calculating average restoring torques. |
| 3131 |
< |
Collective decay of orientational order was calculated by means |
| 3132 |
< |
of equilibrium and nonequilibrium simulations. Our results show |
| 3133 |
< |
that, for the currently accessible volume fractions, the decay times |
| 3134 |
< |
in both cases are virtually identical. Moreover, the observed decay |
| 3135 |
< |
of diffusion coefficients with volume fraction is much quicker than |
| 3136 |
< |
predicted by the theory, which is attributed to an oversimplification |
| 3137 |
< |
of dynamic correlations in the theory. (c) 2005 American Institute |
| 3138 |
< |
of Physics.}, |
| 3120 |
> |
thin rigid rods was presented, confirming and expanding the well-known |
| 3121 |
> |
theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, |
| 3122 |
> |
Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here |
| 3123 |
> |
this theory is put to the test by comparing it against computer |
| 3124 |
> |
simulations. A Brownian dynamics simulation program was developed |
| 3125 |
> |
to follow the dynamics of the rods, with a length over a diameter |
| 3126 |
> |
ratio of 60, on the Smoluchowski time scale. The model accounts |
| 3127 |
> |
for excluded volume interactions between rods, but neglects hydrodynamic |
| 3128 |
> |
interactions. The self-rotational diffusion coefficients D-r(phi) |
| 3129 |
> |
of the rods were calculated by standard methods and by a new, more |
| 3130 |
> |
efficient method based on calculating average restoring torques. |
| 3131 |
> |
Collective decay of orientational order was calculated by means |
| 3132 |
> |
of equilibrium and nonequilibrium simulations. Our results show |
| 3133 |
> |
that, for the currently accessible volume fractions, the decay times |
| 3134 |
> |
in both cases are virtually identical. Moreover, the observed decay |
| 3135 |
> |
of diffusion coefficients with volume fraction is much quicker than |
| 3136 |
> |
predicted by the theory, which is attributed to an oversimplification |
| 3137 |
> |
of dynamic correlations in the theory. (c) 2005 American Institute |
| 3138 |
> |
of Physics.}, |
| 3139 |
|
annote = {943DN Times Cited:3 Cited References Count:26}, |
| 3140 |
|
issn = {0021-9606}, |
| 3141 |
|
uri = {<Go to ISI>://000230332400077}, |
| 3154 |
|
@ARTICLE{Tu1995, |
| 3155 |
|
author = {K. Tu and D. J. Tobias and M. L. Klein}, |
| 3156 |
|
title = {Constant pressure and temperature molecular dynamics simulation of |
| 3157 |
< |
a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine |
| 3158 |
< |
bilayer}, |
| 3157 |
> |
a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine |
| 3158 |
> |
bilayer}, |
| 3159 |
|
journal = {Biophysical Journal}, |
| 3160 |
|
year = {1995}, |
| 3161 |
|
volume = {69}, |
| 3163 |
|
number = {6}, |
| 3164 |
|
month = {Dec}, |
| 3165 |
|
abstract = {We report a constant pressure and temperature molecular dynamics simulation |
| 3166 |
< |
of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine |
| 3167 |
< |
at 50 degrees C and 28 water molecules/lipid. We have shown that |
| 3168 |
< |
the bilayer is stable throughout the 1550-ps simulation and have |
| 3169 |
< |
demonstrated convergence of the system dimensions. Several important |
| 3170 |
< |
aspects of the bilayer structure have been investigated and compared |
| 3171 |
< |
favorably with experimental results. For example, the average positions |
| 3172 |
< |
of specific carbon atoms along the bilayer normal agree well with |
| 3173 |
< |
neutron diffraction data, and the electron density profile is in |
| 3174 |
< |
accord with x-ray diffraction results. The hydrocarbon chain deuterium |
| 3175 |
< |
order parameters agree reasonably well with NMR results for the |
| 3176 |
< |
middles of the chains, but the simulation predicts too much order |
| 3177 |
< |
at the chain ends. In spite of the deviations in the order parameters, |
| 3178 |
< |
the hydrocarbon chain packing density appears to be essentially |
| 3179 |
< |
correct, inasmuch as the area/lipid and bilayer thickness are in |
| 3180 |
< |
agreement with the most refined experimental estimates. The deuterium |
| 3181 |
< |
order parameters for the glycerol and choline groups, as well as |
| 3182 |
< |
the phosphorus chemical shift anisotropy, are in qualitative agreement |
| 3183 |
< |
with those extracted from NMR measurements.}, |
| 3166 |
> |
of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine |
| 3167 |
> |
at 50 degrees C and 28 water molecules/lipid. We have shown that |
| 3168 |
> |
the bilayer is stable throughout the 1550-ps simulation and have |
| 3169 |
> |
demonstrated convergence of the system dimensions. Several important |
| 3170 |
> |
aspects of the bilayer structure have been investigated and compared |
| 3171 |
> |
favorably with experimental results. For example, the average positions |
| 3172 |
> |
of specific carbon atoms along the bilayer normal agree well with |
| 3173 |
> |
neutron diffraction data, and the electron density profile is in |
| 3174 |
> |
accord with x-ray diffraction results. The hydrocarbon chain deuterium |
| 3175 |
> |
order parameters agree reasonably well with NMR results for the |
| 3176 |
> |
middles of the chains, but the simulation predicts too much order |
| 3177 |
> |
at the chain ends. In spite of the deviations in the order parameters, |
| 3178 |
> |
the hydrocarbon chain packing density appears to be essentially |
| 3179 |
> |
correct, inasmuch as the area/lipid and bilayer thickness are in |
| 3180 |
> |
agreement with the most refined experimental estimates. The deuterium |
| 3181 |
> |
order parameters for the glycerol and choline groups, as well as |
| 3182 |
> |
the phosphorus chemical shift anisotropy, are in qualitative agreement |
| 3183 |
> |
with those extracted from NMR measurements.}, |
| 3184 |
|
annote = {Tv018 Times Cited:108 Cited References Count:34}, |
| 3185 |
|
issn = {0006-3495}, |
| 3186 |
|
uri = {<Go to ISI>://A1995TV01800037}, |
| 3196 |
|
number = {3}, |
| 3197 |
|
month = {Aug 1}, |
| 3198 |
|
abstract = {The Trotter factorization of the Liouville propagator is used to generate |
| 3199 |
< |
new reversible molecular dynamics integrators. This strategy is |
| 3200 |
< |
applied to derive reversible reference system propagator algorithms |
| 3201 |
< |
(RESPA) that greatly accelerate simulations of systems with a separation |
| 3202 |
< |
of time scales or with long range forces. The new algorithms have |
| 3203 |
< |
all of the advantages of previous RESPA integrators but are reversible, |
| 3204 |
< |
and more stable than those methods. These methods are applied to |
| 3205 |
< |
a set of paradigmatic systems and are shown to be superior to earlier |
| 3206 |
< |
methods. It is shown how the new RESPA methods are related to predictor-corrector |
| 3207 |
< |
integrators. Finally, we show how these methods can be used to accelerate |
| 3208 |
< |
the integration of the equations of motion of systems with Nose |
| 3209 |
< |
thermostats.}, |
| 3199 |
> |
new reversible molecular dynamics integrators. This strategy is |
| 3200 |
> |
applied to derive reversible reference system propagator algorithms |
| 3201 |
> |
(RESPA) that greatly accelerate simulations of systems with a separation |
| 3202 |
> |
of time scales or with long range forces. The new algorithms have |
| 3203 |
> |
all of the advantages of previous RESPA integrators but are reversible, |
| 3204 |
> |
and more stable than those methods. These methods are applied to |
| 3205 |
> |
a set of paradigmatic systems and are shown to be superior to earlier |
| 3206 |
> |
methods. It is shown how the new RESPA methods are related to predictor-corrector |
| 3207 |
> |
integrators. Finally, we show how these methods can be used to accelerate |
| 3208 |
> |
the integration of the equations of motion of systems with Nose |
| 3209 |
> |
thermostats.}, |
| 3210 |
|
annote = {Je891 Times Cited:680 Cited References Count:19}, |
| 3211 |
|
issn = {0021-9606}, |
| 3212 |
|
uri = {<Go to ISI>://A1992JE89100044}, |
| 3220 |
|
address = {New York}, |
| 3221 |
|
} |
| 3222 |
|
|
| 3223 |
+ |
@ARTICLE{Vincent1995, |
| 3224 |
+ |
author = {J. J. Vincent and K. M. Merz}, |
| 3225 |
+ |
title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing |
| 3226 |
+ |
Interface Standard}, |
| 3227 |
+ |
journal = {Journal of Computational Chemistry}, |
| 3228 |
+ |
year = {1995}, |
| 3229 |
+ |
volume = {16}, |
| 3230 |
+ |
pages = {1420-1427}, |
| 3231 |
+ |
number = {11}, |
| 3232 |
+ |
month = {Nov}, |
| 3233 |
+ |
abstract = {We have implemented a portable parallel version of the macromolecular |
| 3234 |
+ |
modeling package AMBER4. The message passing paradigm was used. |
| 3235 |
+ |
All message passing constructs are compliant with the Message Passing |
| 3236 |
+ |
Interface (MPI) standard. The molecular dynamics/minimization module |
| 3237 |
+ |
MINMD and the free-energy perturbation module Gibbs have been implemented |
| 3238 |
+ |
in parallel on a number of machines, including a Gray T3D, an IBM |
| 3239 |
+ |
SP1/SP2, and a collection of networked workstations. In addition, |
| 3240 |
+ |
the code has been tested with an MPI implementation from Argonne |
| 3241 |
+ |
National Laboratories/Mississippi State University which runs on |
| 3242 |
+ |
many parallel machines. The goal of this work is to decrease the |
| 3243 |
+ |
amount of time required to perform molecular dynamics simulations. |
| 3244 |
+ |
Performance results for a Lipid bilayer molecular dynamics simulation |
| 3245 |
+ |
on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995 |
| 3246 |
+ |
by John Wiley & Sons, Inc.}, |
| 3247 |
+ |
annote = {Ta403 Times Cited:16 Cited References Count:23}, |
| 3248 |
+ |
issn = {0192-8651}, |
| 3249 |
+ |
uri = {<Go to ISI>://A1995TA40300009}, |
| 3250 |
+ |
} |
| 3251 |
+ |
|
| 3252 |
|
@ARTICLE{Wegener1979, |
| 3253 |
|
author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben}, |
| 3254 |
|
title = {A general ellipsoid can not always serve as a modle for the rotational |
| 3255 |
< |
diffusion properties of arbitrary shaped rigid molecules}, |
| 3255 |
> |
diffusion properties of arbitrary shaped rigid molecules}, |
| 3256 |
|
journal = {Proc. Natl. Acad. Sci.}, |
| 3257 |
|
year = {1979}, |
| 3258 |
|
volume = {76}, |
| 3260 |
|
number = {12}, |
| 3261 |
|
} |
| 3262 |
|
|
| 3263 |
+ |
@ARTICLE{Wilson2006, |
| 3264 |
+ |
author = {G.~V. Wilson }, |
| 3265 |
+ |
title = {Where's the Real Bottleneck in Scientific Computing?}, |
| 3266 |
+ |
journal = {American Scientist}, |
| 3267 |
+ |
year = {2006}, |
| 3268 |
+ |
volume = {94}, |
| 3269 |
+ |
} |
| 3270 |
+ |
|
| 3271 |
|
@ARTICLE{Withers2003, |
| 3272 |
|
author = {I. M. Withers}, |
| 3273 |
|
title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne |
| 3274 |
< |
fluid}, |
| 3274 |
> |
fluid}, |
| 3275 |
|
journal = {Journal of Chemical Physics}, |
| 3276 |
|
year = {2003}, |
| 3277 |
|
volume = {119}, |
| 3279 |
|
number = {19}, |
| 3280 |
|
month = {Nov 15}, |
| 3281 |
|
abstract = {The effects of longitudinal quadrupole moments on the formation of |
| 3282 |
< |
liquid crystalline phases are studied by means of constant NPT Monte |
| 3283 |
< |
Carlo simulation methods. The popular Gay-Berne model mesogen is |
| 3284 |
< |
used as the reference fluid, which displays the phase sequences |
| 3285 |
< |
isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0) |
| 3286 |
< |
and low (T*=1.5) temperatures, respectively. With increasing quadrupole |
| 3287 |
< |
magnitude the smectic phases are observed to be stabilized with |
| 3288 |
< |
respect to the isotropic liquid, while the smectic B is destabilized |
| 3289 |
< |
with respect to the smectic A. At the lower temperature, a sufficiently |
| 3290 |
< |
large quadrupole magnitude results in the injection of the smectic |
| 3291 |
< |
A phase into the phase sequence and the replacement of the smectic |
| 3292 |
< |
B phase by the tilted smectic J phase. The nematic phase is also |
| 3293 |
< |
injected into the phase sequence at both temperatures considered, |
| 3294 |
< |
and ultimately for sufficiently large quadrupole magnitudes no coherent |
| 3295 |
< |
layered structures were observed. The stabilization of the smectic |
| 3296 |
< |
A phase supports the commonly held belief that, while the inclusion |
| 3297 |
< |
of polar groups is not a prerequisite for the formation of the smectic |
| 3298 |
< |
A phase, quadrupolar interactions help to increase the temperature |
| 3299 |
< |
and pressure range for which the smectic A phase is observed. The |
| 3300 |
< |
quality of the layered structure is worsened with increasing quadrupole |
| 3301 |
< |
magnitude. This behavior, along with the injection of the nematic |
| 3302 |
< |
phase into the phase sequence, indicate that the general tendency |
| 3303 |
< |
of the quadrupolar interactions is to destabilize the layered structure. |
| 3304 |
< |
A pressure dependence upon the smectic layer spacing is observed. |
| 3305 |
< |
This behavior is in much closer agreement with experimental findings |
| 3306 |
< |
than has been observed previously for nonpolar Gay-Berne and hard |
| 3307 |
< |
spherocylinder models. (C) 2003 American Institute of Physics.}, |
| 3282 |
> |
liquid crystalline phases are studied by means of constant NPT Monte |
| 3283 |
> |
Carlo simulation methods. The popular Gay-Berne model mesogen is |
| 3284 |
> |
used as the reference fluid, which displays the phase sequences |
| 3285 |
> |
isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0) |
| 3286 |
> |
and low (T*=1.5) temperatures, respectively. With increasing quadrupole |
| 3287 |
> |
magnitude the smectic phases are observed to be stabilized with |
| 3288 |
> |
respect to the isotropic liquid, while the smectic B is destabilized |
| 3289 |
> |
with respect to the smectic A. At the lower temperature, a sufficiently |
| 3290 |
> |
large quadrupole magnitude results in the injection of the smectic |
| 3291 |
> |
A phase into the phase sequence and the replacement of the smectic |
| 3292 |
> |
B phase by the tilted smectic J phase. The nematic phase is also |
| 3293 |
> |
injected into the phase sequence at both temperatures considered, |
| 3294 |
> |
and ultimately for sufficiently large quadrupole magnitudes no coherent |
| 3295 |
> |
layered structures were observed. The stabilization of the smectic |
| 3296 |
> |
A phase supports the commonly held belief that, while the inclusion |
| 3297 |
> |
of polar groups is not a prerequisite for the formation of the smectic |
| 3298 |
> |
A phase, quadrupolar interactions help to increase the temperature |
| 3299 |
> |
and pressure range for which the smectic A phase is observed. The |
| 3300 |
> |
quality of the layered structure is worsened with increasing quadrupole |
| 3301 |
> |
magnitude. This behavior, along with the injection of the nematic |
| 3302 |
> |
phase into the phase sequence, indicate that the general tendency |
| 3303 |
> |
of the quadrupolar interactions is to destabilize the layered structure. |
| 3304 |
> |
A pressure dependence upon the smectic layer spacing is observed. |
| 3305 |
> |
This behavior is in much closer agreement with experimental findings |
| 3306 |
> |
than has been observed previously for nonpolar Gay-Berne and hard |
| 3307 |
> |
spherocylinder models. (C) 2003 American Institute of Physics.}, |
| 3308 |
|
annote = {738EF Times Cited:3 Cited References Count:43}, |
| 3309 |
|
issn = {0021-9606}, |
| 3310 |
|
uri = {<Go to ISI>://000186273200027}, |
| 3313 |
|
@ARTICLE{Wolf1999, |
| 3314 |
|
author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht}, |
| 3315 |
|
title = {Exact method for the simulation of Coulombic systems by spherically |
| 3316 |
< |
truncated, pairwise r(-1) summation}, |
| 3316 |
> |
truncated, pairwise r(-1) summation}, |
| 3317 |
|
journal = {Journal of Chemical Physics}, |
| 3318 |
|
year = {1999}, |
| 3319 |
|
volume = {110}, |
| 3321 |
|
number = {17}, |
| 3322 |
|
month = {May 1}, |
| 3323 |
|
abstract = {Based on a recent result showing that the net Coulomb potential in |
| 3324 |
< |
condensed ionic systems is rather short ranged, an exact and physically |
| 3325 |
< |
transparent method permitting the evaluation of the Coulomb potential |
| 3326 |
< |
by direct summation over the r(-1) Coulomb pair potential is presented. |
| 3327 |
< |
The key observation is that the problems encountered in determining |
| 3328 |
< |
the Coulomb energy by pairwise, spherically truncated r(-1) summation |
| 3329 |
< |
are a direct consequence of the fact that the system summed over |
| 3330 |
< |
is practically never neutral. A simple method is developed that |
| 3331 |
< |
achieves charge neutralization wherever the r(-1) pair potential |
| 3332 |
< |
is truncated. This enables the extraction of the Coulomb energy, |
| 3333 |
< |
forces, and stresses from a spherically truncated, usually charged |
| 3334 |
< |
environment in a manner that is independent of the grouping of the |
| 3335 |
< |
pair terms. The close connection of our approach with the Ewald |
| 3336 |
< |
method is demonstrated and exploited, providing an efficient method |
| 3337 |
< |
for the simulation of even highly disordered ionic systems by direct, |
| 3338 |
< |
pairwise r(-1) summation with spherical truncation at rather short |
| 3339 |
< |
range, i.e., a method which fully exploits the short-ranged nature |
| 3340 |
< |
of the interactions in ionic systems. The method is validated by |
| 3341 |
< |
simulations of crystals, liquids, and interfacial systems, such |
| 3342 |
< |
as free surfaces and grain boundaries. (C) 1999 American Institute |
| 3343 |
< |
of Physics. [S0021-9606(99)51517-1].}, |
| 3324 |
> |
condensed ionic systems is rather short ranged, an exact and physically |
| 3325 |
> |
transparent method permitting the evaluation of the Coulomb potential |
| 3326 |
> |
by direct summation over the r(-1) Coulomb pair potential is presented. |
| 3327 |
> |
The key observation is that the problems encountered in determining |
| 3328 |
> |
the Coulomb energy by pairwise, spherically truncated r(-1) summation |
| 3329 |
> |
are a direct consequence of the fact that the system summed over |
| 3330 |
> |
is practically never neutral. A simple method is developed that |
| 3331 |
> |
achieves charge neutralization wherever the r(-1) pair potential |
| 3332 |
> |
is truncated. This enables the extraction of the Coulomb energy, |
| 3333 |
> |
forces, and stresses from a spherically truncated, usually charged |
| 3334 |
> |
environment in a manner that is independent of the grouping of the |
| 3335 |
> |
pair terms. The close connection of our approach with the Ewald |
| 3336 |
> |
method is demonstrated and exploited, providing an efficient method |
| 3337 |
> |
for the simulation of even highly disordered ionic systems by direct, |
| 3338 |
> |
pairwise r(-1) summation with spherical truncation at rather short |
| 3339 |
> |
range, i.e., a method which fully exploits the short-ranged nature |
| 3340 |
> |
of the interactions in ionic systems. The method is validated by |
| 3341 |
> |
simulations of crystals, liquids, and interfacial systems, such |
| 3342 |
> |
as free surfaces and grain boundaries. (C) 1999 American Institute |
| 3343 |
> |
of Physics. [S0021-9606(99)51517-1].}, |
| 3344 |
|
annote = {189PD Times Cited:70 Cited References Count:34}, |
| 3345 |
|
issn = {0021-9606}, |
| 3346 |
|
uri = {<Go to ISI>://000079913000008}, |
| 3360 |
|
uri = {<Go to ISI>://A1990EJ79800009}, |
| 3361 |
|
} |
| 3362 |
|
|
| 2943 |
– |
@Book{Frenkel1996, |
| 2944 |
– |
author = {D. Frenkel and B. Smit}, |
| 2945 |
– |
title = {Understanding Molecular Simulation : From Algorithms |
| 2946 |
– |
to Applications}, |
| 2947 |
– |
publisher = {Academic Press}, |
| 2948 |
– |
year = 1996, |
| 2949 |
– |
address = {New York} |
| 2950 |
– |
} |
