trunk/tengDissertation/dissertation.bib

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@ARTICLE{Torre2003,
  author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez
        and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez},
  title = {Calculation of the solution properties of flexible macromolecules:
        methods and applications},
  journal = {European Biophysics Journal with Biophysics Letters},
  year = {2003},
  volume = {32},
  pages = {477-486},
  number = {5},
  month = {Aug},
  abstract = {While the prediction of hydrodynamic properties of rigid particles
        is nowadays feasible using simple and efficient computer programs,
        the calculation of such properties and, in general, the dynamic
        behavior of flexible macromolecules has not reached a similar situation.
        Although the theories are available, usually the computational work
        is done using solutions specific for each problem. We intend to
        develop computer programs that would greatly facilitate the task
        of predicting solution behavior of flexible macromolecules. In this
        paper, we first present an overview of the two approaches that are
        most practical: the Monte Carlo rigid-body treatment, and the Brownian
        dynamics simulation technique. The Monte Carlo procedure is based
        on the calculation of properties for instantaneous conformations
        of the macromolecule that are regarded as if they were instantaneously
        rigid. We describe how a Monte Carlo program can be interfaced to
        the programs in the HYDRO suite for rigid particles, and provide
        an example of such calculation, for a hypothetical particle: a protein
        with two domains connected by a flexible linker. We also describe
        briefly the essentials of Brownian dynamics, and propose a general
        mechanical model that includes several kinds of intramolecular interactions,
        such as bending, internal rotation, excluded volume effects, etc.
        We provide an example of the application of this methodology to
        the dynamics of a semiflexible, wormlike DNA.},
  annote = {724XK Times Cited:6 Cited References Count:64},
  issn = {0175-7571},
  uri = {<Go to ISI>://000185513400011},
}

@ARTICLE{Alakent2005,
  author = {B. Alakent and M. C. Camurdan and P. Doruker},
  title = {Hierarchical structure of the energy landscape of proteins revisited
        by time series analysis. II. Investigation of explicit solvent effects},
  journal = {Journal of Chemical Physics},
  year = {2005},
  volume = {123},
  pages = {-},
  number = {14},
  month = {Oct 8},
  abstract = {Time series analysis tools are employed on the principal modes obtained
        from the C-alpha trajectories from two independent molecular-dynamics
        simulations of alpha-amylase inhibitor (tendamistat). Fluctuations
        inside an energy minimum (intraminimum motions), transitions between
        minima (interminimum motions), and relaxations in different hierarchical
        energy levels are investigated and compared with those encountered
        in vacuum by using different sampling window sizes and intervals.
        The low-frequency low-indexed mode relationship, established in
        vacuum, is also encountered in water, which shows the reliability
        of the important dynamics information offered by principal components
        analysis in water. It has been shown that examining a short data
        collection period (100 ps) may result in a high population of overdamped
        modes, while some of the low-frequency oscillations (< 10 cm(-1))
        can be captured in water by using a longer data collection period
        (1200 ps). Simultaneous analysis of short and long sampling window
        sizes gives the following picture of the effect of water on protein
        dynamics. Water makes the protein lose its memory: future conformations
        are less dependent on previous conformations due to the lowering
        of energy barriers in hierarchical levels of the energy landscape.
        In short-time dynamics (< 10 ps), damping factors extracted from
        time series model parameters are lowered. For tendamistat, the friction
        coefficient in the Langevin equation is found to be around 40-60
        cm(-1) for the low-indexed modes, compatible with literature. The
        fact that water has increased the friction and that on the other
        hand has lubrication effect at first sight contradicts. However,
        this comes about because water enhances the transitions between
        minima and forces the protein to reduce its already inherent inability
        to maintain oscillations observed in vacuum. Some of the frequencies
        lower than 10 cm(-1) are found to be overdamped, while those higher
        than 20 cm(-1) are slightly increased. As for the long-time dynamics
        in water, it is found that random-walk motion is maintained for
        approximately 200 ps (about five times of that in vacuum) in the
        low-indexed modes, showing the lowering of energy barriers between
        the higher-level minima.},
  annote = {973OH Times Cited:1 Cited References Count:33},
  issn = {0021-9606},
  uri = {<Go to ISI>://000232532000064},
}

@BOOK{Alexander1987,
  title = {A Pattern Language: Towns, Buildings, Construction},
  publisher = {Oxford University Press},
  year = {1987},
  author = {C. Alexander},
  address = {New York},
}

@BOOK{Allen1987,
  title = {Computer Simulations of Liquids},
  publisher = {Oxford University Press},
  year = {1987},
  author = {M.~P. Allen and D.~J. Tildesley},
  address = {New York},
}

@ARTICLE{Allison1991,
  author = {S. A. Allison},
  title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application
        to Polarized Dynamic Light-Scattering},
  journal = {Macromolecules},
  year = {1991},
  volume = {24},
  pages = {530-536},
  number = {2},
  month = {Jan 21},
  abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
        of rigid macromolecules. It is applied to polarized dynamic light
        scattering from rodlike sturctures and from a model of a DNA fragment
        (762 base pairs). A number of rod cases are examined in which the
        translational anisotropy is increased form zero to a large value.
        Simulated first cumulants as well as amplitudes and lifetimes of
        the dynamic form factor are compared with predictions of analytic
        theories and found to be in very good agreement with them. For DNA
        fragments 762 base pairs in length or longer, translational anisotropy
        does not contribute significantly to dynamic light scattering. In
        a comparison of rigid and flexible simulations on semistiff models
        of this fragment, it is shown directly that flexing contributes
        to the faster decay processes probed by light scattering and that
        the flexible model studies are in good agreement with experiment.},
  annote = {Eu814 Times Cited:8 Cited References Count:32},
  issn = {0024-9297},
  uri = {<Go to ISI>://A1991EU81400029},
}

@ARTICLE{Andersen1983,
  author = {H. C. Andersen},
  title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics
        Calculations},
  journal = {Journal of Computational Physics},
  year = {1983},
  volume = {52},
  pages = {24-34},
  number = {1},
  annote = {Rq238 Times Cited:559 Cited References Count:14},
  issn = {0021-9991},
  uri = {<Go to ISI>://A1983RQ23800002},
}

@ARTICLE{Auerbach2005,
  author = {A. Auerbach},
  title = {Gating of acetylcholine receptor channels: Brownian motion across
        a broad transition state},
  journal = {Proceedings of the National Academy of Sciences of the United States
        of America},
  year = {2005},
  volume = {102},
  pages = {1408-1412},
  number = {5},
  month = {Feb 1},
  abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
        stable #closed# and #open# conformations. In patch clamp recordings,
        diliganded AChR gating appears to be a simple, two-state reaction.
        However, mutagenesis studies indicate that during gating dozens
        of residues across the protein move asynchronously and are organized
        into rigid body gating domains (#blocks#). Moreover, there is an
        upper limit to the apparent channel opening rate constant. These
        observations suggest that the gating reaction has a broad, corrugated
        transition state region, with the maximum opening rate reflecting,
        in part, the mean first-passage time across this ensemble. Simulations
        reveal that a flat, isotropic energy profile for the transition
        state can account for many of the essential features of AChR gating.
        With this mechanism, concerted, local structural transitions that
        occur on the broad transition state ensemble give rise to fractional
        measures of reaction progress (Phi values) determined by rate-equilibrium
        free energy relationship analysis. The results suggest that the
        coarse-grained AChR gating conformational change propagates through
        the protein with dynamics that are governed by the Brownian motion
        of individual gating blocks.},
  annote = {895QF Times Cited:9 Cited References Count:33},
  issn = {0027-8424},
  uri = {<Go to ISI>://000226877300030},
}

@ARTICLE{Baber1995,
  author = {J. Baber and J. F. Ellena and D. S. Cafiso},
  title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined
        Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
  journal = {Biochemistry},
  year = {1995},
  volume = {34},
  pages = {6533-6539},
  number = {19},
  month = {May 16},
  abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
        on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine
        membranes in the liquid crystalline phase was investigated using
        H-2 NMR. Upon the addition of the anesthetics, the first five methylene
        units near the interface generally show a very small increase in
        segmental order, while segments deeper within the bilayer show a
        small decrease in segmental order. From the H-2 NMR results, the
        chain length for the perdeuterated palmitoyl chain in the absence
        of anesthetic was found to be 12.35 Angstrom. Upon the addition
        of halothane enflurane, or isoflurane, the acyl chain undergoes
        slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively,
        at 50 mol % anesthetic. A simple model was used to estimate the
        relative amounts of anesthetic located near the interface and deeper
        in the bilayer hydrocarbon region, and only a slight preference
        for an interfacial location was observed. Intermolecular H-1-H-1
        nuclear Overhauser effects (NOEs) were measured between phospholipid
        and halothane protons. These NOEs are consistent with the intramembrane
        location of the anesthetics suggested by the H-2 NMR data. In addition,
        the NOE data indicate that anesthetics prefer the interfacial and
        hydrocarbon regions of the membrane and are not found in high concentrations
        in the phospholipid headgroup.},
  annote = {Qz716 Times Cited:38 Cited References Count:37},
  issn = {0006-2960},
  uri = {<Go to ISI>://A1995QZ71600035},
}

@ARTICLE{Banerjee2004,
  author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
  title = {Solution of quantum Langevin equation: Approximations, theoretical
        and numerical aspects},
  journal = {Journal of Chemical Physics},
  year = {2004},
  volume = {120},
  pages = {8960-8972},
  number = {19},
  month = {May 15},
  abstract = {Based on a coherent state representation of noise operator and an
        ensemble averaging procedure using Wigner canonical thermal distribution
        for harmonic oscillators, a generalized quantum Langevin equation
        has been recently developed [Phys. Rev. E 65, 021109 (2002); 66,
        051106 (2002)] to derive the equations of motion for probability
        distribution functions in c-number phase-space. We extend the treatment
        to explore several systematic approximation schemes for the solutions
        of the Langevin equation for nonlinear potentials for a wide range
        of noise correlation, strength and temperature down to the vacuum
        limit. The method is exemplified by an analytic application to harmonic
        oscillator for arbitrary memory kernel and with the help of a numerical
        calculation of barrier crossing, in a cubic potential to demonstrate
        the quantum Kramers' turnover and the quantum Arrhenius plot. (C)
        2004 American Institute of Physics.},
  annote = {816YY Times Cited:8 Cited References Count:35},
  issn = {0021-9606},
  uri = {<Go to ISI>://000221146400009},
}

@ARTICLE{Barojas1973,
  author = {J. Barojas and D. Levesque},
  title = {Simulation of Diatomic Homonuclear Liquids},
  journal = {Phys. Rev. A},
  year = {1973},
  volume = {7},
  pages = {1092-1105},
}

@ARTICLE{Barth1998,
  author = {E. Barth and T. Schlick},
  title = {Overcoming stability limitations in biomolecular dynamics. I. Combining
        force splitting via extrapolation with Langevin dynamics in LN},
  journal = {Journal of Chemical Physics},
  year = {1998},
  volume = {109},
  pages = {1617-1632},
  number = {5},
  month = {Aug 1},
  abstract = {We present an efficient new method termed LN for propagating biomolecular
        dynamics according to the Langevin equation that arose fortuitously
        upon analysis of the range of harmonic validity of our normal-mode
        scheme LIN. LN combines force linearization with force splitting
        techniques and disposes of LIN'S computationally intensive minimization
        (anharmonic correction) component. Unlike the competitive multiple-timestepping
        (MTS) schemes today-formulated to be symplectic and time-reversible-LN
        merges the slow and fast forces via extrapolation rather than impulses;
        the Langevin heat bath prevents systematic energy drifts. This combination
        succeeds in achieving more significant speedups than these MTS methods
        which are Limited by resonance artifacts to an outer timestep less
        than some integer multiple of half the period of the fastest motion
        (around 4-5 fs for biomolecules). We show that LN achieves very
        good agreement with small-timestep solutions of the Langevin equation
        in terms of thermodynamics (energy means and variances), geometry,
        and dynamics (spectral densities) for two proteins in vacuum and
        a large water system. Significantly, the frequency of updating the
        slow forces extends to 48 fs or more, resulting in speedup factors
        exceeding 10. The implementation of LN in any program that employs
        force-splitting computations is straightforward, with only partial
        second-derivative information required, as well as sparse Hessian/vector
        multiplication routines. The linearization part of LN could even
        be replaced by direct evaluation of the fast components. The application
        of LN to biomolecular dynamics is well suited for configurational
        sampling, thermodynamic, and structural questions. (C) 1998 American
        Institute of Physics.},
  annote = {105HH Times Cited:29 Cited References Count:49},
  issn = {0021-9606},
  uri = {<Go to ISI>://000075066300006},
}

@ARTICLE{Batcho2001,
  author = {P. F. Batcho and T. Schlick},
  title = {Special stability advantages of position-Verlet over velocity-Verlet
        in multiple-time step integration},
  journal = {Journal of Chemical Physics},
  year = {2001},
  volume = {115},
  pages = {4019-4029},
  number = {9},
  month = {Sep 1},
  abstract = {We present an analysis for a simple two-component harmonic oscillator
        that compares the use of position-Verlet to velocity-Verlet for
        multiple-time step integration. The numerical stability analysis
        based on the impulse-Verlet splitting shows that position-Verlet
        has enhanced stability, in terms of the largest allowable time step,
        for cases where an ample separation of time scales exists. Numerical
        investigations confirm the advantages of the position-Verlet scheme
        when used for the fastest time scales of the system. Applications
        to a biomolecule. a solvated protein, for both Newtonian and Langevin
        dynamics echo these trends over large outer time-step regimes. (C)
        2001 American Institute of Physics.},
  annote = {469KV Times Cited:6 Cited References Count:30},
  issn = {0021-9606},
  uri = {<Go to ISI>://000170813800005},
}

@ARTICLE{Bates2005,
  author = {M. A. Bates and G. R. Luckhurst},
  title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation
        study},
  journal = {Physical Review E},
  year = {2005},
  volume = {72},
  pages = {-},
  number = {5},
  month = {Nov},
  abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
        can exhibit the elusive biaxial nematic phase, we have developed
        a generic simulation model for such systems. This contains the features
        of the molecule that are essential to its liquid crystal behavior,
        namely the anisotropies of the two arms and the angle between them.
        The behavior of the model has been investigated using Monte Carlo
        simulations for a wide range of these structural parameters. This
        allows us to establish the relationship between the V-shaped molecule
        and its ability to form a biaxial nematic phase. Of particular importance
        are the criteria of geometry and the relative anisotropy necessary
        for the system to exhibit a Landau point, at which the biaxial nematic
        is formed directly from the isotropic phase. The simulations have
        also been used to determine the orientational order parameters for
        a selection of molecular axes. These are especially important because
        they reveal the phase symmetry and are connected to the experimental
        determination of this. The simulation results show that, whereas
        some positions are extremely sensitive to the phase biaxiality,
        others are totally blind to this.},
  annote = {Part 1 988LQ Times Cited:0 Cited References Count:38},
  issn = {1539-3755},
  uri = {<Go to ISI>://000233603100030},
}

@ARTICLE{Beard2003,
  author = {D. A. Beard and T. Schlick},
  title = {Unbiased rotational moves for rigid-body dynamics},
  journal = {Biophysical Journal},
  year = {2003},
  volume = {85},
  pages = {2973-2976},
  number = {5},
  month = {Nov 1},
  abstract = {We introduce an unbiased protocol for performing rotational moves
        in rigid-body dynamics simulations. This approach - based on the
        analytic solution for the rotational equations of motion for an
        orthogonal coordinate system at constant angular velocity - removes
        deficiencies that have been largely ignored in Brownian dynamics
        simulations, namely errors for finite rotations that result from
        applying the noncommuting rotational matrices in an arbitrary order.
        Our algorithm should thus replace standard approaches to rotate
        local coordinate frames in Langevin and Brownian dynamics simulations.},
  annote = {736UA Times Cited:0 Cited References Count:11},
  issn = {0006-3495},
  uri = {<Go to ISI>://000186190500018},
}

@ARTICLE{Beloborodov1998,
  author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev},
  title = {Effect of coupling between rotational and translational Brownian
        motions on NMR spin relaxation: Consideration using green function
        of rigid body diffusion},
  journal = {Journal of Magnetic Resonance},
  year = {1998},
  volume = {132},
  pages = {328-329},
  number = {2},
  month = {Jun},
  abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
        Biopolymers 33, 409-436, 1993), it was analytically shown that coupling
        between translation and rotation diffusion degrees of freedom does
        not affect the correlation functions relevant to the NMR intramolecular
        relaxation. It follows that spectral densities usually used for
        the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37,
        647-654, 1962) can be regarded as exact in respect to the rotation-translation
        coupling for the spin system connected with a rigid body. (C) 1998
        Academic Press.},
  annote = {Zu605 Times Cited:2 Cited References Count:6},
  issn = {1090-7807},
  uri = {<Go to ISI>://000074214800017},
}

@ARTICLE{Berardi1996,
  author = {R. Berardi and S. Orlandi and C. Zannoni},
  title = {Antiphase structures in polar smectic liquid crystals and their molecular
        origin},
  journal = {Chemical Physics Letters},
  year = {1996},
  volume = {261},
  pages = {357-362},
  number = {3},
  month = {Oct 18},
  abstract = {We demonstrate that the overall molecular dipole organization in a
        smectic liquid crystal formed of polar molecules can be strongly
        influenced by the position of the dipole in the molecule. We study
        by large scale Monte Carlo simulations systems of attractive-repulsive
        ''Gay-Berne'' elongated ellipsoids with an axial dipole at the center
        or near the end of the molecule and we show that monolayer smectic
        liquid crystals and modulated antiferroelectric bilayer stripe domains
        similar to the experimentally observed ''antiphase'' structures
        are obtained in the two cases.},
  annote = {Vn637 Times Cited:49 Cited References Count:26},
  issn = {0009-2614},
  uri = {<Go to ISI>://A1996VN63700023},
}

@ARTICLE{Berkov2005,
  author = {D. V. Berkov and N. L. Gorn},
  title = {Magnetization precession due to a spin-polarized current in a thin
        nanoelement: Numerical simulation study},
  journal = {Physical Review B},
  year = {2005},
  volume = {72},
  pages = {-},
  number = {9},
  month = {Sep},
  abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
        formalism) of magnetization oscillations driven by a spin-polarized
        current through a thin elliptical nanoelement is presented. We show
        that a sophisticated micromagnetic model, where a polycrystalline
        structure of a nanoelement is taken into account, can explain qualitatively
        all most important features of the magnetization oscillation spectra
        recently observed experimentally [S. I. Kiselev , Nature 425, 380
        (2003)], namely, existence of several equidistant spectral bands,
        sharp onset and abrupt disappearance of magnetization oscillations
        with increasing current, absence of the out-of-plane regime predicted
        by a macrospin model, and the relation between frequencies of so-called
        small-angle and quasichaotic oscillations. However, a quantitative
        agreement with experimental results (especially concerning the frequency
        of quasichaotic oscillations) could not be achieved in the region
        of reasonable parameter values, indicating that further model refinement
        is necessary for a complete understanding of the spin-driven magnetization
        precession even in this relatively simple experimental situation.},
  annote = {969IT Times Cited:2 Cited References Count:55},
  issn = {1098-0121},
  uri = {<Go to ISI>://000232228500058},
}

@ARTICLE{Berkov2005a,
  author = {D. V. Berkov and N. L. Gorn},
  title = {Stochastic dynamic simulations of fast remagnetization processes:
        recent advances and applications},
  journal = {Journal of Magnetism and Magnetic Materials},
  year = {2005},
  volume = {290},
  pages = {442-448},
  month = {Apr},
  abstract = {Numerical simulations of fast remagnetization processes using stochastic
        dynamics are widely used to study various magnetic systems. In this
        paper, we first address several crucial methodological problems
        of such simulations: (i) the influence of finite-element discretization
        on simulated dynamics, (ii) choice between Ito and Stratonovich
        stochastic calculi by the solution of micromagnetic stochastic equations
        of motion and (iii) non-trivial correlation properties of the random
        (thermal) field. Next, we discuss several examples to demonstrate
        the great potential of the Langevin dynamics for studying fast remagnetization
        processes in technically relevant applications: we present numerical
        analysis of equilibrium magnon spectra in patterned structures,
        study thermal noise effects on the magnetization dynamics of nanoelements
        in pulsed fields and show some results for a remagnetization dynamics
        induced by a spin-polarized current. (c) 2004 Elsevier B.V. All
        rights reserved.},
  annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
  issn = {0304-8853},
  uri = {<Go to ISI>://000228837600109},
}

@ARTICLE{Berkov2002,
  author = {D. V. Berkov and N. L. Gorn and P. Gornert},
  title = {Magnetization dynamics in nanoparticle systems: Numerical simulation
        using Langevin dynamics},
  journal = {Physica Status Solidi a-Applied Research},
  year = {2002},
  volume = {189},
  pages = {409-421},
  number = {2},
  month = {Feb 16},
  abstract = {We report on recent progress achieved by the development of numerical
        methods based on the stochastic (Langevin) dynamics applied to systems
        of interacting magnetic nanoparticles. The method enables direct
        simulations of the trajectories of magnetic moments taking into
        account (i) all relevant interactions, (ii) precession dynamics,
        and (iii) temperature fluctuations included via the random (thermal)
        field. We present several novel results obtained using new methods
        developed for the solution of the Langevin equations. In particular,
        we have investigated magnetic nanodots and disordered granular systems
        of single-domain magnetic particles. For the first case we have
        calculated the spectrum and the spatial distribution of spin excitations.
        For the second system the complex ac susceptibility chi(omega, T)
        for various particle concentrations and particle anisotropies were
        computed and compared with numerous experimental results.},
  annote = {526TF Times Cited:4 Cited References Count:37},
  issn = {0031-8965},
  uri = {<Go to ISI>://000174145200026},
}

@ARTICLE{Bernal1980,
  author = {J.M. Bernal and J. G. {de la Torre}},
  title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules
        with Arbitrary Shape},
  journal = {Biopolymers},
  year = {1980},
  volume = {19},
  pages = {751-766},
}

@ARTICLE{Brenner1967,
  author = {H. Brenner },
  title = {Coupling between the Translational and Rotational Brownian Motions
        of Rigid Particles of Arbitrary shape},
  journal = {J. Collid. Int. Sci.},
  year = {1967},
  volume = {23},
  pages = {407-436},
}

@ARTICLE{Brooks1983,
  author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States
        and S. Swaminathan and M. Karplus},
  title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics
        Calculations},
  journal = {Journal of Computational Chemistry},
  year = {1983},
  volume = {4},
  pages = {187-217},
  number = {2},
  annote = {Qp423 Times Cited:6414 Cited References Count:96},
  issn = {0192-8651},
  uri = {<Go to ISI>://A1983QP42300010},
}

@ARTICLE{Brunger1984,
  author = {A. Brunger and C. L. Brooks and M. Karplus},
  title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations
        of St2 Water},
  journal = {Chemical Physics Letters},
  year = {1984},
  volume = {105},
  pages = {495-500},
  number = {5},
  annote = {Sm173 Times Cited:143 Cited References Count:22},
  issn = {0009-2614},
  uri = {<Go to ISI>://A1984SM17300007},
}

@ARTICLE{Budd1999,
  author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell},
  title = {Self-similar numerical solutions of the porous-medium equation using
        moving mesh methods},
  journal = {Philosophical Transactions of the Royal Society of London Series
        a-Mathematical Physical and Engineering Sciences},
  year = {1999},
  volume = {357},
  pages = {1047-1077},
  number = {1754},
  month = {Apr 15},
  abstract = {This paper examines a synthesis of adaptive mesh methods with the
        use of symmetry to study a partial differential equation. In particular,
        it considers methods which admit discrete self-similar solutions,
        examining the convergence of these to the true self-similar solution
        as well as their stability. Special attention is given to the nonlinear
        diffusion equation describing flow in a porous medium.},
  annote = {199EE Times Cited:4 Cited References Count:14},
  issn = {1364-503X},
  uri = {<Go to ISI>://000080466800005},
}

@ARTICLE{Camp1999,
  author = {P. J. Camp and M. P. Allen and A. J. Masters},
  title = {Theory and computer simulation of bent-core molecules},
  journal = {Journal of Chemical Physics},
  year = {1999},
  volume = {111},
  pages = {9871-9881},
  number = {21},
  month = {Dec 1},
  abstract = {Fluids of hard bent-core molecules have been studied using theory
        and computer simulation. The molecules are composed of two hard
        spherocylinders, with length-to-breadth ratio L/D, joined by their
        ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20
        degrees, the simulations show isotropic, nematic, smectic, and solid
        phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic,
        and solid phases are in evidence, which suggests that there is a
        nematic-smectic-solid triple point at an angle in the range 20 degrees
        < gamma < 30 degrees. In all of the orientationally ordered fluid
        phases the order is purely uniaxial. For gamma = 10 degrees and
        20 degrees, at the studied densities, the solid is also uniaxially
        ordered, whilst for gamma = 30 degrees the solid layers are biaxially
        ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find
        no spontaneous orientational ordering. This is shown to be due to
        the interlocking of dimer pairs which precludes alignment. We find
        similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial
        nematic transition is predicted by Onsager theory. Simulations in
        the biaxial nematic phase show it to be at least mechanically stable
        with respect to the isotropic phase, however. We have compared the
        quasi-exact simulation results in the isotropic phase with the predicted
        equations of state from three theories: the virial expansion containing
        the second and third virial coefficients; the Parsons-Lee equation
        of state; an application of Wertheim's theory of associating fluids
        in the limit of infinite attractive association energy. For all
        of the molecule elongations and geometries we have simulated, the
        Wertheim theory proved to be the most accurate. Interestingly, the
        isotropic equation of state is virtually independent of the dimer
        bond angle-a feature that is also reflected in the lack of variation
        with angle of the calculated second and third virial coefficients.
        (C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].},
  annote = {255TC Times Cited:24 Cited References Count:38},
  issn = {0021-9606},
  uri = {<Go to ISI>://000083685400056},
}

@ARTICLE{Care2005,
  author = {C. M. Care and D. J. Cleaver},
  title = {Computer simulation of liquid crystals},
  journal = {Reports on Progress in Physics},
  year = {2005},
  volume = {68},
  pages = {2665-2700},
  number = {11},
  month = {Nov},
  abstract = {A review is presented of molecular and mesoscopic computer simulations
        of liquid crystalline systems. Molecular simulation approaches applied
        to such systems are described, and the key findings for bulk phase
        behaviour are reported. Following this, recently developed lattice
        Boltzmann approaches to the mesoscale modelling of nemato-dynanics
        are reviewed. This paper concludes with a discussion of possible
        areas for future development in this field.},
  annote = {989TU Times Cited:2 Cited References Count:258},
  issn = {0034-4885},
  uri = {<Go to ISI>://000233697600004},
}

@ARTICLE{Carrasco1999,
  author = {B. Carrasco and J. G. {de la Torre}},
  title = {Hydrodynamic properties of rigid particles: Comparison of different
        modeling and computational procedures},
  journal = {Biophysical Journal},
  year = {1999},
  volume = {76},
  pages = {3044-3057},
  number = {6},
  month = {Jun},
  abstract = {The hydrodynamic properties of rigid particles are calculated from
        models composed of spherical elements (beads) using theories developed
        by Kirkwood, Bloomfield, and their coworkers. Bead models have usually
        been built in such a way that the beads fill the volume occupied
        by the particles. Sometimes the beads are few and of varying sizes
        (bead models in the strict sense), and other times there are many
        small beads (filling models). Because hydrodynamic friction takes
        place at the molecular surface, another possibility is to use shell
        models, as originally proposed by Bloomfield. In this work, we have
        developed procedures to build models of the various kinds, and we
        describe the theory and methods for calculating their hydrodynamic
        properties, including approximate methods that may be needed to
        treat models with a very large number of elements. By combining
        the various possibilities of model building and hydrodynamic calculation,
        several strategies can be designed. We have made a quantitative
        comparison of the performance of the various strategies by applying
        them to some test cases, for which the properties are known a priori.
        We provide guidelines and computational tools for bead modeling.},
  annote = {200TT Times Cited:46 Cited References Count:57},
  issn = {0006-3495},
  uri = {<Go to ISI>://000080556700016},
}

@ARTICLE{Chandra1999,
  author = {A. Chandra and T. Ichiye},
  title = {Dynamical properties of the soft sticky dipole model of water: Molecular
        dynamics simulations},
  journal = {Journal of Chemical Physics},
  year = {1999},
  volume = {111},
  pages = {2701-2709},
  number = {6},
  month = {Aug 8},
  abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
        are calculated by means of molecular dynamics simulations. Since
        this is not a simple point model, the forces and torques arising
        from the SSD potential are derived here. Simulations are carried
        out in the microcanonical ensemble employing the Ewald method for
        the electrostatic interactions. Various time correlation functions
        and dynamical quantities associated with the translational and rotational
        motion of water molecules are evaluated and compared with those
        of two other commonly used models of liquid water, namely the transferable
        intermolecular potential-three points (TIP3P) and simple point charge/extended
        (SPC/E) models, and also with experiments. The dynamical properties
        of the SSD water model are found to be in good agreement with the
        experimental results and appear to be better than the TIP3P and
        SPC/E models in most cases, as has been previously shown for its
        thermodynamic, structural, and dielectric properties. Also, molecular
        dynamics simulations of the SSD model are found to run much faster
        than TIP3P, SPC/E, and other multisite models. (C) 1999 American
        Institute of Physics. [S0021-9606(99)51430-X].},
  annote = {221EN Times Cited:14 Cited References Count:66},
  issn = {0021-9606},
  uri = {<Go to ISI>://000081711200038},
}

@ARTICLE{Channell1990,
  author = {P. J. Channell and C. Scovel},
  title = {Symplectic Integration of Hamiltonian-Systems},
  journal = {Nonlinearity},
  year = {1990},
  volume = {3},
  pages = {231-259},
  number = {2},
  month = {may},
  annote = {Dk631 Times Cited:152 Cited References Count:34},
  issn = {0951-7715},
  uri = {<Go to ISI>://A1990DK63100001},
}

@ARTICLE{Chen2003,
  author = {B. Chen and F. Solis},
  title = {Explicit mixed finite order Runge-Kutta methods},
  journal = {Applied Numerical Mathematics},
  year = {2003},
  volume = {44},
  pages = {21-30},
  number = {1-2},
  month = {Jan},
  abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
        equations and introduce a family of mixed methods from combinations
        of explicit Runge-Kutta methods. These methods have better stability
        behavior than traditional Runge-Kutta methods and generally extend
        the range of validity of the calculated solutions. These methods
        also give a way of determining if the numerical solutions are real
        or spurious. Emphasis is put on examples coming from mathematical
        models in ecology. (C) 2002 IMACS. Published by Elsevier Science
        B.V. All rights reserved.},
  annote = {633ZD Times Cited:0 Cited References Count:9},
  issn = {0168-9274},
  uri = {<Go to ISI>://000180314200002},
}

@ARTICLE{Cheung2004,
  author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
  title = {Calculation of flexoelectric coefficients for a nematic liquid crystal
        by atomistic simulation},
  journal = {Journal of Chemical Physics},
  year = {2004},
  volume = {121},
  pages = {9131-9139},
  number = {18},
  month = {Nov 8},
  abstract = {Equilibrium molecular dynamics calculations have been performed for
        the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile
        (PCH5) using a fully atomistic model. Simulation data have been
        obtained for a series of temperatures in the nematic phase. The
        simulation data have been used to calculate the flexoelectric coefficients
        e(s) and e(b) using the linear response formalism of Osipov and
        Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr.
        31, 125 (1986)]. The temperature and order parameter dependence
        of e(s) and e(b) are examined, as are separate contributions from
        different intermolecular interactions. Values of e(s) and e(b) calculated
        from simulation are consistent with those found from experiment.
        (C) 2004 American Institute of Physics.},
  annote = {866UM Times Cited:4 Cited References Count:61},
  issn = {0021-9606},
  uri = {<Go to ISI>://000224798900053},
}

@ARTICLE{Cheung2002,
  author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
  title = {Calculation of the rotational viscosity of a nematic liquid crystal},
  journal = {Chemical Physics Letters},
  year = {2002},
  volume = {356},
  pages = {140-146},
  number = {1-2},
  month = {Apr 15},
  abstract = {Equilibrium molecular dynamics calculations have been performed for
        the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile
        (PCH5) using a fully atomistic model. Simulation data has been obtained
        for a series of temperatures in the nematic phase. The rotational
        viscosity co-efficient gamma(1), has been calculated using the angular
        velocity correlation function of the nematic director, n, the mean
        squared diffusion of n and statistical mechanical methods based
        on the rotational diffusion co-efficient. We find good agreement
        between the first two methods and experimental values. (C) 2002
        Published by Elsevier Science B.V.},
  annote = {547KF Times Cited:8 Cited References Count:31},
  issn = {0009-2614},
  uri = {<Go to ISI>://000175331000020},
}

@ARTICLE{Chin2004,
  author = {S. A. Chin},
  title = {Dynamical multiple-time stepping methods for overcoming resonance
        instabilities},
  journal = {Journal of Chemical Physics},
  year = {2004},
  volume = {120},
  pages = {8-13},
  number = {1},
  month = {Jan 1},
  abstract = {Current molecular dynamics simulations of biomolecules using multiple
        time steps to update the slowly changing force are hampered by instabilities
        beginning at time steps near the half period of the fastest vibrating
        mode. These #resonance# instabilities have became a critical barrier
        preventing the long time simulation of biomolecular dynamics. Attempts
        to tame these instabilities by altering the slowly changing force
        and efforts to damp them out by Langevin dynamics do not address
        the fundamental cause of these instabilities. In this work, we trace
        the instability to the nonanalytic character of the underlying spectrum
        and show that a correct splitting of the Hamiltonian, which renders
        the spectrum analytic, restores stability. The resulting Hamiltonian
        dictates that in addition to updating the momentum due to the slowly
        changing force, one must also update the position with a modified
        mass. Thus multiple-time stepping must be done dynamically. (C)
        2004 American Institute of Physics.},
  annote = {757TK Times Cited:1 Cited References Count:22},
  issn = {0021-9606},
  uri = {<Go to ISI>://000187577400003},
}

@ARTICLE{Cook2000,
  author = {M. J. Cook and M. R. Wilson},
  title = {Simulation studies of dipole correlation in the isotropic liquid
        phase},
  journal = {Liquid Crystals},
  year = {2000},
  volume = {27},
  pages = {1573-1583},
  number = {12},
  month = {Dec},
  abstract = {The Kirkwood correlation factor g(1) determines the preference for
        local parallel or antiparallel dipole association in the isotropic
        phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood
        factors greater than 1 have an enhanced effective dipole moment
        along the molecular long axis. This leads to higher values of Delta
        epsilon in the nematic phase. This paper describes state-of-the-art
        molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile
        (PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl)
        in the isotropic liquid phase using an all-atom force field and
        taking long range electrostatics into account using an Ewald summation.
        Using this methodology, PCH5 is seen to prefer antiparallel dipole
        alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel
        dipole alignment with a positive g(1); this is in accordance with
        experimental dielectric measurements. Analysis of the molecular
        dynamics trajectories allows an assessment of why these molecules
        behave differently.},
  annote = {376BF Times Cited:10 Cited References Count:16},
  issn = {0267-8292},
  uri = {<Go to ISI>://000165437800002},
}

@ARTICLE{Cui2003,
  author = {B. X. Cui and M. Y. Shen and K. F. Freed},
  title = {Folding and misfolding of the papillomavirus E6 interacting peptide
        E6ap},
  journal = {Proceedings of the National Academy of Sciences of the United States
        of America},
  year = {2003},
  volume = {100},
  pages = {7087-7092},
  number = {12},
  month = {Jun 10},
  abstract = {All-atom Langevin dynamics simulations have been performed to study
        the folding pathways of the 18-residue binding domain fragment E6ap
        of the human papillomavirus E6 interacting peptide. Six independent
        folding trajectories, with a total duration of nearly 2 mus, all
        lead to the same native state in which the E6ap adopts a fluctuating
        a-helix structure in the central portion (Ser-4-Leu-13) but with
        very flexible N and C termini. Simulations starting from different
        core configurations exhibit the E6ap folding dynamics as either
        a two- or three-state folder with an intermediate misfolded state.
        The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13)
        is well conserved in the native-state structure but absent in the
        intermediate structure, suggesting that the leucine core is not
        only essential for the binding activity of E6ap but also important
        for the stability of the native structure. The free energy landscape
        reveals a significant barrier between the basins separating the
        native and misfolded states. We also discuss the various underlying
        forces that drive the peptide into its native state.},
  annote = {689LC Times Cited:3 Cited References Count:48},
  issn = {0027-8424},
  uri = {<Go to ISI>://000183493500037},
}

@ARTICLE{Denisov2003,
  author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou},
  title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
  journal = {Physical Review B},
  year = {2003},
  volume = {67},
  pages = {-},
  number = {1},
  month = {Jan 1},
  abstract = {We study the slow phase of thermally activated magnetic relaxation
        in finite two-dimensional ensembles of dipolar interacting ferromagnetic
        nanoparticles whose easy axes of magnetization are perpendicular
        to the distribution plane. We develop a method to numerically simulate
        the magnetic relaxation for the case that the smallest heights of
        the potential barriers between the equilibrium directions of the
        nanoparticle magnetic moments are much larger than the thermal energy.
        Within this framework, we analyze in detail the role that the correlations
        of the nanoparticle magnetic moments and the finite size of the
        nanoparticle ensemble play in magnetic relaxation.},
  annote = {642XH Times Cited:11 Cited References Count:31},
  issn = {1098-0121},
  uri = {<Go to ISI>://000180830400056},
}

@ARTICLE{Derreumaux1998,
  author = {P. Derreumaux and T. Schlick},
  title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
  journal = {Biophysical Journal},
  year = {1998},
  volume = {74},
  pages = {72-81},
  number = {1},
  month = {Jan},
  abstract = {To explore the origin of the large-scale motion of triosephosphate
        isomerase's flexible loop (residues 166 to 176) at the active site,
        several simulation protocols are employed both for the free enzyme
        in vacuo and for the free enzyme with some solvent modeling: high-temperature
        Langevin dynamics simulations, sampling by a #dynamics##driver#
        approach, and potential-energy surface calculations. Our focus is
        on obtaining the energy barrier to the enzyme's motion and establishing
        the nature of the loop movement. Previous calculations did not determine
        this energy barrier and the effect of solvent on the barrier. High-temperature
        molecular dynamics simulations and crystallographic studies have
        suggested a rigid-body motion with two hinges located at both ends
        of the loop; Brownian dynamics simulations at room temperature pointed
        to a very flexible behavior. The present simulations and analyses
        reveal that although solute/solvent hydrogen bonds play a crucial
        role in lowering the energy along the pathway, there still remains
        a high activation barrier, This finding clearly indicates that,
        if the loop opens and closes in the absence of a substrate at standard
        conditions (e.g., room temperature, appropriate concentration of
        isomerase), the time scale for transition is not in the nanosecond
        but rather the microsecond range. Our results also indicate that
        in the context of spontaneous opening in the free enzyme, the motion
        is of rigid-body type and that the specific interaction between
        residues Ala(176) and Tyr(208) plays a crucial role in the loop
        opening/closing mechanism.},
  annote = {Zl046 Times Cited:30 Cited References Count:29},
  issn = {0006-3495},
  uri = {<Go to ISI>://000073393400009},
}

@ARTICLE{Dullweber1997,
  author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
  title = {Symplectic splitting methods for rigid body molecular dynamics},
  journal = {Journal of Chemical Physics},
  year = {1997},
  volume = {107},
  pages = {5840-5851},
  number = {15},
  month = {Oct 15},
  abstract = {Rigid body molecular models possess symplectic structure and time-reversal
        symmetry. Standard numerical integration methods destroy both properties,
        introducing nonphysical dynamical behavior such as numerically induced
        dissipative states and drift in the energy during long term simulations.
        This article describes the construction, implementation, and practical
        application of fast explicit symplectic-reversible integrators for
        multiple rigid body molecular simulations, These methods use a reduction
        to Euler equations for the free rigid body, together with a symplectic
        splitting technique. In every time step, the orientational dynamics
        of each rigid body is integrated by a sequence of planar rotations.
        Besides preserving the symplectic and reversible structures of the
        flow, this scheme accurately conserves the total angular momentum
        of a system of interacting rigid bodies. Excellent energy conservation
        fan be obtained relative to traditional methods, especially in long-time
        simulations. The method is implemented in a research code, ORIENT
        and compared with a quaternion/extrapolation scheme for the TIP4P
        model of water. Our experiments show that the symplectic-reversible
        scheme is far superior to the more traditional quaternion method.
        (C) 1997 American Institute of Physics.},
  annote = {Ya587 Times Cited:35 Cited References Count:32},
  issn = {0021-9606},
  uri = {<Go to ISI>://A1997YA58700024},
}

@BOOK{Gamma1994,
  title = {Design Patterns: Elements of Reusable Object-Oriented Software},
  publisher = {Perason Education},
  year = {1994},
  author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
  address = {London},
  chapter = {7},
}

@ARTICLE{Edwards2005,
  author = {S. A. Edwards and D. R. M. Williams},
  title = {Stretching a single diblock copolymer in a selective solvent: Langevin
        dynamics simulations},
  journal = {Macromolecules},
  year = {2005},
  volume = {38},
  pages = {10590-10595},
  number = {25},
  month = {Dec 13},
  abstract = {Using the Langevin dynamics technique, we have carried out simulations
        of a single-chain flexible diblock copolymer. The polymer consists
        of two blocks of equal length, one very poorly solvated and the
        other close to theta-conditions. We study what happens when such
        a polymer is stretched, for a range of different stretching speeds,
        and correlate our observations with features in the plot of force
        vs extension. We find that at slow speeds this force profile does
        not increase monotonically, in disagreement with earlier predictions,
        and that at high speeds there is a strong dependence on which end
        of the polymer is pulled, as well as a high level of hysteresis.},
  annote = {992EC Times Cited:0 Cited References Count:13},
  issn = {0024-9297},
  uri = {<Go to ISI>://000233866200035},
}

@ARTICLE{Egberts1988,
  author = {E. Egberts and H. J. C. Berendsen},
  title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic
        Detail},
  journal = {Journal of Chemical Physics},
  year = {1988},
  volume = {89},
  pages = {3718-3732},
  number = {6},
  month = {Sep 15},
  annote = {Q0188 Times Cited:219 Cited References Count:43},
  issn = {0021-9606},
  uri = {<Go to ISI>://A1988Q018800036},
}

@ARTICLE{Ermak1978,
  author = {D. L. Ermak and J. A. Mccammon},
  title = {Brownian Dynamics with Hydrodynamic Interactions},
  journal = {Journal of Chemical Physics},
  year = {1978},
  volume = {69},
  pages = {1352-1360},
  number = {4},
  annote = {Fp216 Times Cited:785 Cited References Count:42},
  issn = {0021-9606},
  uri = {<Go to ISI>://A1978FP21600004},
}

@ARTICLE{Evans1977,
  author = {D. J. Evans},
  title = {Representation of Orientation Space},
  journal = {Molecular Physics},
  year = {1977},
  volume = {34},
  pages = {317-325},
  number = {2},
  annote = {Ds757 Times Cited:271 Cited References Count:18},
  issn = {0026-8976},
  uri = {<Go to ISI>://A1977DS75700002},
}

@ARTICLE{Fennell2004,
  author = {C. J. Fennell and J. D. Gezelter},
  title = {On the structural and transport properties of the soft sticky dipole
        and related single-point water models},
  journal = {Journal of Chemical Physics},
  year = {2004},
  volume = {120},
  pages = {9175-9184},
  number = {19},
  month = {May 15},
  abstract = {The density maximum and temperature dependence of the self-diffusion
        constant were investigated for the soft sticky dipole (SSD) water
        model and two related reparametrizations of this single-point model.
        A combination of microcanonical and isobaric-isothermal molecular
        dynamics simulations was used to calculate these properties, both
        with and without the use of reaction field to handle long-range
        electrostatics. The isobaric-isothermal simulations of the melting
        of both ice-I-h and ice-I-c showed a density maximum near 260 K.
        In most cases, the use of the reaction field resulted in calculated
        densities which were significantly lower than experimental densities.
        Analysis of self-diffusion constants shows that the original SSD
        model captures the transport properties of experimental water very
        well in both the normal and supercooled liquid regimes. We also
        present our reparametrized versions of SSD for use both with the
        reaction field or without any long-range electrostatic corrections.
        These are called the SSD/RF and SSD/E models, respectively. These
        modified models were shown to maintain or improve upon the experimental
        agreement with the structural and transport properties that can
        be obtained with either the original SSD or the density-corrected
        version of the original model (SSD1). Additionally, a novel low-density
        ice structure is presented which appears to be the most stable ice
        structure for the entire SSD family. (C) 2004 American Institute
        of Physics.},
  annote = {816YY Times Cited:5 Cited References Count:39},
  issn = {0021-9606},
  uri = {<Go to ISI>://000221146400032},
}

@ARTICLE{Fernandes2002,
  author = {M. X. Fernandes and J. G. {de la Torre}},
  title = {Brownian dynamics simulation of rigid particles of arbitrary shape
        in external fields},
  journal = {Biophysical Journal},
  year = {2002},
  volume = {83},
  pages = {3039-3048},
  number = {6},
  month = {Dec},
  abstract = {We have developed a Brownian dynamics simulation algorithm to generate
        Brownian trajectories of an isolated, rigid particle of arbitrary
        shape in the presence of electric fields or any other external agents.
        Starting from the generalized diffusion tensor, which can be calculated
        with the existing HYDRO software, the new program BROWNRIG (including
        a case-specific subprogram for the external agent) carries out a
        simulation that is analyzed later to extract the observable dynamic
        properties. We provide a variety of examples of utilization of this
        method, which serve as tests of its performance, and also illustrate
        its applicability. Examples include free diffusion, transport in
        an electric field, and diffusion in a restricting environment.},
  annote = {633AD Times Cited:2 Cited References Count:43},
  issn = {0006-3495},
  uri = {<Go to ISI>://000180256300012},
}

@BOOK{Frenkel1996,
  title = {Understanding Molecular Simulation : From Algorithms to Applications},
  publisher = {Academic Press},
  year = {1996},
  author = {D. Frenkel and B. Smit},
  address = {New York},
}

@ARTICLE{Gay1981,
  author = {J. G. Gay and B. J. Berne},
  title = {Modification of the Overlap Potential to Mimic a Linear Site-Site
        Potential},
  journal = {Journal of Chemical Physics},
  year = {1981},
  volume = {74},
  pages = {3316-3319},
  number = {6},
  annote = {Lj347 Times Cited:482 Cited References Count:13},
  issn = {0021-9606},
  uri = {<Go to ISI>://A1981LJ34700029},
}

@ARTICLE{Gelin1999,
  author = {M. F. Gelin},
  title = {Inertial effects in the Brownian dynamics with rigid constraints},
  journal = {Macromolecular Theory and Simulations},
  year = {1999},
  volume = {8},
  pages = {529-543},
  number = {6},
  month = {Nov},
  abstract = {To investigate the influence of inertial effects on the dynamics of
        an assembly of beads subjected to rigid constraints and placed in
        a buffer medium, a convenient method to introduce suitable generalized
        coordinates is presented. Without any restriction on the nature
        of the soft forces involved (both stochastic and deterministic),
        pertinent Langevin equations are derived. Provided that the Brownian
        forces are Gaussian and Markovian, the corresponding Fokker-Planck
        equation (FPE) is obtained in the complete phase space of generalized
        coordinates and momenta. The correct short time behavior for correlation
        functions (CFs) of generalized coordinates is established, and the
        diffusion equation with memory (DEM) is deduced from the FPE in
        the high friction Limit. The DEM is invoked to perform illustrative
        calculations in two dimensions of the orientational CFs for once
        broken nonrigid rods immobilized on a surface. These calculations
        reveal that the CFs under certain conditions exhibit an oscillatory
        behavior, which is irreproducible within the standard diffusion
        equation. Several methods are considered for the approximate solution
        of the DEM, and their application to three dimensional DEMs is discussed.},
  annote = {257MM Times Cited:2 Cited References Count:82},
  issn = {1022-1344},
  uri = {<Go to ISI>://000083785700002},
}

@ARTICLE{Goetz1998,
  author = {R. Goetz and R. Lipowsky},
  title = {Computer simulations of bilayer membranes: Self-assembly and interfacial
        tension},
  journal = {Journal of Chemical Physics},
  year = {1998},
  volume = {108},
  pages = {7397},
  number = {17},
}

@BOOK{Goldstein2001,
  title = {Classical Mechanics},
  publisher = {Addison Wesley},
  year = {2001},
  author = {H. Goldstein and C. Poole and J. Safko},
  address = {San Francisco},
  edition = {3rd},
}

@ARTICLE{Gray2003,
  author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and
        B. Kuhlman and C. A. Rohl and D. Baker},
  title = {Protein-protein docking with simultaneous optimization of rigid-body
        displacement and side-chain conformations},
  journal = {Journal of Molecular Biology},
  year = {2003},
  volume = {331},
  pages = {281-299},
  number = {1},
  month = {Aug 1},
  abstract = {Protein-protein docking algorithms provide a means to elucidate structural
        details for presently unknown complexes. Here, we present and evaluate
        a new method to predict protein-protein complexes from the coordinates
        of the unbound monomer components. The method employs a low-resolution,
        rigid-body, Monte Carlo search followed by simultaneous optimization
        of backbone displacement and side-chain conformations using Monte
        Carlo minimization. Up to 10(5) independent simulations are carried
        out, and the resulting #decoys# are ranked using an energy function
        dominated by van der Waals interactions, an implicit solvation model,
        and an orientation-dependent hydrogen bonding potential. Top-ranking
        decoys are clustered to select the final predictions. Small-perturbation
        studies reveal the formation of binding funnels in 42 of 54 cases
        using coordinates derived from the bound complexes and in 32 of
        54 cases using independently determined coordinates of one or both
        monomers. Experimental binding affinities correlate with the calculated
        score function and explain the predictive success or failure of
        many targets. Global searches using one or both unbound components
        predict at least 25% of the native residue-residue contacts in 28
        of the 32 cases where binding funnels exist. The results suggest
        that the method may soon be useful for generating models of biologically
        important complexes from the structures of the isolated components,
        but they also highlight the challenges that must be met to achieve
        consistent and accurate prediction of protein-protein interactions.
        (C) 2003 Elsevier Ltd. All rights reserved.},
  annote = {704QL Times Cited:48 Cited References Count:60},
  issn = {0022-2836},
  uri = {<Go to ISI>://000184351300022},
}

@ARTICLE{Greengard1994,
  author = {L. Greengard},
  title = {Fast Algorithms for Classical Physics},
  journal = {Science},
  year = {1994},
  volume = {265},
  pages = {909-914},
  number = {5174},
  month = {Aug 12},
  abstract = {Some of the recently developed fast summation methods that have arisen
        in scientific computing are described. These methods require an
        amount of work proportional to N or N log N to evaluate all pairwise
        interactions in an ensemble of N particles. Traditional methods,
        by contrast, require an amount of work proportional to N-2. AS a
        result, large-scale simulations can be carried out using only modest
        computer resources. In combination with supercomputers, it is possible
        to address questions that were previously out of reach. Problems
        from diffusion, gravitation, and wave propagation are considered.},
  annote = {Pb499 Times Cited:99 Cited References Count:44},
  issn = {0036-8075},
  uri = {<Go to ISI>://A1994PB49900031},
}

@ARTICLE{Greengard1987,
  author = {L. Greengard and V. Rokhlin},
  title = {A Fast Algorithm for Particle Simulations},
  journal = {Journal of Computational Physics},
  year = {1987},
  volume = {73},
  pages = {325-348},
  number = {2},
  month = {Dec},
  annote = {L0498 Times Cited:899 Cited References Count:7},
  issn = {0021-9991},
  uri = {<Go to ISI>://A1987L049800006},
}

@ARTICLE{Hairer1997,
  author = {E. Hairer and C. Lubich},
  title = {The life-span of backward error analysis for numerical integrators},
  journal = {Numerische Mathematik},
  year = {1997},
  volume = {76},
  pages = {441-462},
  number = {4},
  month = {Jun},
  abstract = {Backward error analysis is a useful tool for the study of numerical
        approximations to ordinary differential equations. The numerical
        solution is formally interpreted as the exact solution of a perturbed
        differential equation, given as a formal and usually divergent series
        in powers of the step size. For a rigorous analysis, this series
        has to be truncated. In this article we study the influence of this
        truncation to the difference between the numerical solution and
        the exact solution of the perturbed differential equation. Results
        on the long-time behaviour of numerical solutions are obtained in
        this way. We present applications to the numerical phase portrait
        near hyperbolic equilibrium points, to asymptotically stable periodic
        orbits and Hopf bifurcation, and to energy conservation and approximation
        of invariant tori in Hamiltonian systems.},
  annote = {Xj488 Times Cited:50 Cited References Count:19},
  issn = {0029-599X},
  uri = {<Go to ISI>://A1997XJ48800002},
}

@ARTICLE{Hao1993,
  author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga},
  title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic
        Trypsin-Inhibitor Studied by Computer-Simulations},
  journal = {Biochemistry},
  year = {1993},
  volume = {32},
  pages = {9614-9631},
  number = {37},
  month = {Sep 21},
  abstract = {A new procedure for studying the folding and unfolding of proteins,
        with an application to bovine pancreatic trypsin inhibitor (BPTI),
        is reported. The unfolding and refolding of the native structure
        of the protein are characterized by the dimensions of the protein,
        expressed in terms of the three principal radii of the structure
        considered as an ellipsoid. A dynamic equation, describing the variations
        of the principal radii on the unfolding path, and a numerical procedure
        to solve this equation are proposed. Expanded and distorted conformations
        are refolded to the native structure by a dimensional-constraint
        energy minimization procedure. A unique and reproducible unfolding
        pathway for an intermediate of BPTI lacking the [30,51] disulfide
        bond is obtained. The resulting unfolded conformations are extended;
        they contain near-native local structure, but their longest principal
        radii are more than 2.5 times greater than that of the native structure.
        The most interesting finding is that the majority of expanded conformations,
        generated under various conditions, can be refolded closely to the
        native structure, as measured by the correct overall chain fold,
        by the rms deviations from the native structure of only 1.9-3.1
        angstrom, and by the energy differences of about 10 kcal/mol from
        the native structure. Introduction of the [30,51] disulfide bond
        at this stage, followed by minimization, improves the closeness
        of the refolded structures to the native structure, reducing the
        rms deviations to 0.9-2.0 angstrom. The unique refolding of these
        expanded structures over such a large conformational space implies
        that the folding is strongly dictated by the interactions in the
        amino acid sequence of BPTI. The simulations indicate that, under
        conditions that favor a compact structure as mimicked by the volume
        constraints in our algorithm; the expanded conformations have a
        strong tendency to move toward the native structure; therefore,
        they probably would be favorable folding intermediates. The results
        presented here support a general model for protein folding, i.e.,
        progressive formation of partially folded structural units, followed
        by collapse to the compact native structure. The general applicability
        of the procedure is also discussed.},
  annote = {Ly294 Times Cited:27 Cited References Count:57},
  issn = {0006-2960},
  uri = {<Go to ISI>://A1993LY29400014},
}

@ARTICLE{Hinsen2000,
  author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel
        and G. R. Kneller},
  title = {Harmonicity in slow protein dynamics},
  journal = {Chemical Physics},
  year = {2000},
  volume = {261},
  pages = {25-37},
  number = {1-2},
  month = {Nov 1},
  abstract = {The slow dynamics of proteins around its native folded state is usually
        described by diffusion in a strongly anharmonic potential. In this
        paper, we try to understand the form and origin of the anharmonicities,
        with the principal aim of gaining a better understanding of the
        principal motion types, but also in order to develop more efficient
        numerical methods for simulating neutron scattering spectra of large
        proteins. First, we decompose a molecular dynamics (MD) trajectory
        of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water
        into three contributions that we expect to be independent: the global
        motion of the residues, the rigid-body motion of the sidechains
        relative to the backbone, and the internal deformations of the sidechains.
        We show that they are indeed almost independent by verifying the
        factorization of the incoherent intermediate scattering function.
        Then, we show that the global residue motions, which include all
        large-scale backbone motions, can be reproduced by a simple harmonic
        model which contains two contributions: a short-time vibrational
        term, described by a standard normal mode calculation in a local
        minimum, and a long-time diffusive term, described by Brownian motion
        in an effective harmonic potential. The potential and the friction
        constants were fitted to the MD data. The major anharmonic contribution
        to the incoherent intermediate scattering function comes from the
        rigid-body diffusion of the sidechains. This model can be used to
        calculate scattering functions for large proteins and for long-time
        scales very efficiently, and thus provides a useful complement to
        MD simulations, which are best suited for detailed studies on smaller
        systems or for shorter time scales. (C) 2000 Elsevier Science B.V.
        All rights reserved.},
  annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31},
  issn = {0301-0104},
  uri = {<Go to ISI>://000090121700003},
}

@ARTICLE{Ho1992,
  author = {C. Ho and C. D. Stubbs},
  title = {Hydration at the Membrane Protein-Lipid Interface},
  journal = {Biophysical Journal},
  year = {1992},
  volume = {63},
  pages = {897-902},
  number = {4},
  month = {Oct},
  abstract = {Evidence has been found for the existence water at the protein-lipid
        hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome
        C, using two related fluorescence spectroscopic approaches. The
        first approach exploited the fact that the presence of water in
        the excited state solvent cage of a fluorophore increases the rate
        of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl)
        phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores
        are located in the hydrophobic core of the lipid bilayer, the introduction
        of gramicidin reduced the fluorescence lifetime, indicative of an
        increased presence of water in the bilayer. Since a high protein:lipid
        ratio was used, the fluorophores were forced to be adjacent to the
        protein hydrophobic surface, hence the presence of water in this
        region could be inferred. Cholesterol is known to reduce the water
        content of lipid bilayers and this effect was maintained at the
        protein-lipid interface with both gramicidin and apocytochrome C,
        again suggesting hydration in this region. The second approach was
        to use the fluorescence enhancement induced by exchanging deuterium
        oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH,
        located in the lipid head group region, and of the gramicidin intrinsic
        tryptophans were greater in a D2O buffer compared with H2O, showing
        that the fluorophores were exposed to water in the bilayer at the
        protein-lipid interface. In the presence of cholesterol the fluorescence
        intensity ratio of D2O to H2O decreased, indicating a removal of
        water by the cholesterol, in keeping with the lifetime data. Altered
        hydration at the protein-lipid interface could affect conformation,
        thereby offering a new route by which membrane protein functioning
        may be modified.},
  annote = {Ju251 Times Cited:55 Cited References Count:44},
  issn = {0006-3495},
  uri = {<Go to ISI>://A1992JU25100002},
}

@BOOK{Hockney1981,
  title = {Computer Simulation Using Particles},
  publisher = {McGraw-Hill},
  year = {1981},
  author = {R.W. Hockney and J.W. Eastwood},
  address = {New York},
}

@ARTICLE{Hoover1985,
  author = {W. G. Hoover},
  title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
  journal = {Physical Review A},
  year = {1985},
  volume = {31},
  pages = {1695-1697},
  number = {3},
  annote = {Acr30 Times Cited:1809 Cited References Count:11},
  issn = {1050-2947},
  uri = {<Go to ISI>://A1985ACR3000056},
}

@ARTICLE{Huh2004,
  author = {Y. Huh and N. M. Cann},
  title = {Discrimination in isotropic, nematic, and smectic phases of chiral
        calamitic molecules: A computer simulation study},
  journal = {Journal of Chemical Physics},
  year = {2004},
  volume = {121},
  pages = {10299-10308},
  number = {20},
  month = {Nov 22},
  abstract = {Racemic fluids of chiral calamitic molecules are investigated with
        molecular dynamics simulations. In particular, the phase behavior
        as a function of density is examined for eight racemates. The relationship
        between chiral discrimination and orientational order in the phase
        is explored. We find that the transition from the isotropic phase
        to a liquid crystal phase is accompanied by an increase in chiral
        discrimination, as measured by differences in radial distributions.
        Among ordered phases, discrimination is largest for smectic phases
        with a significant preference for heterochiral contact within the
        layers. (C) 2004 American Institute of Physics.},
  annote = {870FJ Times Cited:0 Cited References Count:63},
  issn = {0021-9606},
  uri = {<Go to ISI>://000225042700059},
}

@ARTICLE{Humphrey1996,
  author = {W. Humphrey and A. Dalke and K. Schulten},
  title = {VMD: Visual molecular dynamics},
  journal = {Journal of Molecular Graphics},
  year = {1996},
  volume = {14},
  pages = {33-\&},
  number = {1},
  month = {Feb},
  abstract = {VMD is a molecular graphics program designed for the display and analysis
        of molecular assemblies, in particular biopolymers such as proteins
        and nucleic acids. VMD can simultaneously display any number of
        structures using a wide variety of rendering styles and coloring
        methods. Molecules are displayed as one or more ''representations,''
        in which each representation embodies a particular rendering method
        and coloring scheme for a selected subset of atoms. The atoms displayed
        in each representation are chosen using an extensive atom selection
        syntax, which includes Boolean operators and regular expressions.
        VMD provides a complete graphical user interface for program control,
        as well as a text interface using the Tcl embeddable parser to allow
        for complex scripts with variable substitution, control loops, and
        function calls. Full session logging is supported, which produces
        a VMD command script for later playback. High-resolution raster
        images of displayed molecules may be produced by generating input
        scripts for use by a number of photorealistic image-rendering applications.
        VMD has also been expressly designed with the ability to animate
        molecular dynamics (MD) simulation trajectories, imported either
        from files or from a direct connection to a running MD simulation.
        VMD is the visualization component of MDScope, a set of tools for
        interactive problem solving in structural biology, which also includes
        the parallel MD program NAMD, and the MDCOMM software used to connect
        the visualization and simulation programs. VMD is written in C++,
        using an object-oriented design; the program, including source code
        and extensive documentation, is freely available via anonymous ftp
        and through the World Wide Web.},
  annote = {Uh515 Times Cited:1418 Cited References Count:19},
  issn = {0263-7855},
  uri = {<Go to ISI>://A1996UH51500005},
}

@ARTICLE{Izaguirre2001,
  author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
  title = {Langevin stabilization of molecular dynamics},
  journal = {Journal of Chemical Physics},
  year = {2001},
  volume = {114},
  pages = {2090-2098},
  number = {5},
  month = {Feb 1},
  abstract = {In this paper we show the possibility of using very mild stochastic
        damping to stabilize long time step integrators for Newtonian molecular
        dynamics. More specifically, stable and accurate integrations are
        obtained for damping coefficients that are only a few percent of
        the natural decay rate of processes of interest, such as the velocity
        autocorrelation function. Two new multiple time stepping integrators,
        Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are
        introduced in this paper. Both use the mollified impulse method
        for the Newtonian term. LM uses a discretization of the Langevin
        equation that is exact for the constant force, and BBK-M uses the
        popular Brunger-Brooks-Karplus integrator (BBK). These integrators,
        along with an extrapolative method called LN, are evaluated across
        a wide range of damping coefficient values. When large damping coefficients
        are used, as one would for the implicit modeling of solvent molecules,
        the method LN is superior, with LM closely following. However, with
        mild damping of 0.2 ps(-1), LM produces the best results, allowing
        long time steps of 14 fs in simulations containing explicitly modeled
        flexible water. With BBK-M and the same damping coefficient, time
        steps of 12 fs are possible for the same system. Similar results
        are obtained for a solvated protein-DNA simulation of estrogen receptor
        ER with estrogen response element ERE. A parallel version of BBK-M
        runs nearly three times faster than the Verlet-I/r-RESPA (reversible
        reference system propagator algorithm) when using the largest stable
        time step on each one, and it also parallelizes well. The computation
        of diffusion coefficients for flexible water and ER/ERE shows that
        when mild damping of up to 0.2 ps-1 is used the dynamics are not
        significantly distorted. (C) 2001 American Institute of Physics.},
  annote = {397CQ Times Cited:14 Cited References Count:36},
  issn = {0021-9606},
  uri = {<Go to ISI>://000166676100020},
}

@ARTICLE{Torre1977,
  author = {Jose Garcia De La Torre, V.A. Bloomfield},
  title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
  journal = {Biopolymers},
  year = {1977},
  volume = {16},
  pages = {1747-1763},
}

@ARTICLE{Kale1999,
  author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy
        and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan
        and K. Schulten},
  title = {NAMD2: Greater scalability for parallel molecular dynamics},
  journal = {Journal of Computational Physics},
  year = {1999},
  volume = {151},
  pages = {283-312},
  number = {1},
  month = {May 1},
  abstract = {Molecular dynamics programs simulate the behavior of biomolecular
        systems, leading to understanding of their functions. However, the
        computational complexity of such simulations is enormous. Parallel
        machines provide the potential to meet this computational challenge.
        To harness this potential, it is necessary to develop a scalable
        program. It is also necessary that the program be easily modified
        by application-domain programmers. The NAMD2 program presented in
        this paper seeks to provide these desirable features. It uses spatial
        decomposition combined with force decomposition to enhance scalability.
        It uses intelligent periodic load balancing, so as to maximally
        utilize the available compute power. It is modularly organized,
        and implemented using Charm++, a parallel C++ dialect, so as to
        enhance its modifiability. It uses a combination of numerical techniques
        and algorithms to ensure that energy drifts are minimized, ensuring
        accuracy in long running calculations. NAMD2 uses a portable run-time
        framework called Converse that also supports interoperability among
        multiple parallel paradigms. As a result, different components of
        applications can be written in the most appropriate parallel paradigms.
        NAMD2 runs on most parallel machines including workstation clusters
        and has yielded speedups in excess of 180 on 220 processors. This
        paper also describes the performance obtained on some benchmark
        applications. (C) 1999 Academic Press.},
  annote = {194FM Times Cited:373 Cited References Count:51},
  issn = {0021-9991},
  uri = {<Go to ISI>://000080181500013},
}

@ARTICLE{Kane2000,
  author = {C. Kane and J. E. Marsden and M. Ortiz and M. West},
  title = {Variational integrators and the Newmark algorithm for conservative
        and dissipative mechanical systems},
  journal = {International Journal for Numerical Methods in Engineering},
  year = {2000},
  volume = {49},
  pages = {1295-1325},
  number = {10},
  month = {Dec 10},
  abstract = {The purpose of this work is twofold. First, we demonstrate analytically
        that the classical Newmark family as well as related integration
        algorithms are variational in the sense of the Veselov formulation
        of discrete mechanics. Such variational algorithms are well known
        to be symplectic and momentum preserving and to often have excellent
        global energy behaviour. This analytical result is verified through
        numerical examples and is believed to be one of the primary reasons
        that this class of algorithms performs so well. Second, we develop
        algorithms for mechanical systems with forcing, and in particular,
        for dissipative systems. In this case, we develop integrators that
        are based on a discretization of the Lagrange d'Alembert principle
        as well as on a variational formulation of dissipation. It is demonstrated
        that these types of structured integrators have good numerical behaviour
        in terms of obtaining the correct amounts by which the energy changes
        over the integration run. Copyright (C) 2000 John Wiley & Sons,
        Ltd.},
  annote = {373CJ Times Cited:30 Cited References Count:41},
  issn = {0029-5981},
  uri = {<Go to ISI>://000165270600004},
}

@ARTICLE{Klimov1997,
  author = {D. K. Klimov and D. Thirumalai},
  title = {Viscosity dependence of the folding rates of proteins},
  journal = {Physical Review Letters},
  year = {1997},
  volume = {79},
  pages = {317-320},
  number = {2},
  month = {Jul 14},
  abstract = {The viscosity (eta) dependence of the folding rates for four sequences
        (the native state of three sequences is a beta sheet, while the
        fourth forms an alpha helix) is calculated for off-lattice models
        of proteins. Assuming that the dynamics is given by the Langevin
        equation, we show that the folding rates increase linearly at low
        viscosities eta, decrease as 1/eta at large eta, and have a maximum
        at intermediate values. The Kramers' theory of barrier crossing
        provides a quantitative fit of the numerical results. By mapping
        the simulation results to real proteins we estimate that for optimized
        sequences the time scale for forming a four turn alpha-helix topology
        is about 500 ns, whereas for beta sheet it is about 10 mu s.},
  annote = {Xk293 Times Cited:77 Cited References Count:17},
  issn = {0031-9007},
  uri = {<Go to ISI>://A1997XK29300035},
}

@ARTICLE{Kol1997,
  author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
  title = {A symplectic method for rigid-body molecular simulation},
  journal = {Journal of Chemical Physics},
  year = {1997},
  volume = {107},
  pages = {2580-2588},
  number = {7},
  month = {Aug 15},
  abstract = {Rigid-body molecular dynamics simulations typically are performed
        in a quaternion representation. The nonseparable form of the Hamiltonian
        in quaternions prevents the use of a standard leapfrog (Verlet)
        integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation
        methods are generally used, This is unfortunate since symplectic
        methods like Verlet exhibit superior energy conservation in long-time
        integrations. In this article, we describe an alternative method,
        which we call RSHAKE (for rotation-SHAKE), in which the entire rotation
        matrix is evolved (using the scheme of McLachlan and Scovel [J.
        Nonlin. Sci, 16 233 (1995)]) in tandem with the particle positions.
        We employ a fast approximate Newton solver to preserve the orthogonality
        of the rotation matrix. We test our method on a system of soft-sphere
        dipoles and compare with quaternion evolution using a 4th-order
        predictor-corrector integrator, Although the short-time error of
        the quaternion algorithm is smaller for fixed time step than that
        for RSHAKE, the quaternion scheme exhibits an energy drift which
        is not observed in simulations with RSHAKE, hence a fixed energy
        tolerance can be achieved by using a larger time step, The superiority
        of RSHAKE increases with system size. (C) 1997 American Institute
        of Physics.},
  annote = {Xq332 Times Cited:11 Cited References Count:18},
  issn = {0021-9606},
  uri = {<Go to ISI>://A1997XQ33200046},
}

@ARTICLE{Lansac2001,
  author = {Y. Lansac and M. A. Glaser and N. A. Clark},
  title = {Microscopic structure and dynamics of a partial bilayer smectic liquid
        crystal},
  journal = {Physical Review E},
  year = {2001},
  volume = {6405},
  pages = {-},
  number = {5},
  month = {Nov},
  abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
        class of mesogens. Many of the peculiar properties of nCB's (e.g.,
        the occurence of the partial bilayer smectic-A(d) phase) are thought
        to be a manifestation of short-range antiparallel association of
        neighboring molecules, resulting from strong dipole-dipole interactions
        between cyano groups. To test and extend existing models of microscopic
        ordering in nCB's, we carry out large-scale atomistic simulation
        studies of the microscopic structure and dynamics of the Sm-A(d)
        phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of
        thermodynamic, structural, and dynamical properties for this material,
        and make a detailed comparison of our results with experimental
        measurements in order to validate our molecular model. Semiquantitative
        agreement with experiment is found: the smectic layer spacing and
        mass density are well reproduced, translational diffusion constants
        are similar to experiment, but the orientational ordering of alkyl
        chains is overestimated. This simulation provides a detailed picture
        of molecular conformation, smectic layer structure, and intermolecular
        correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range
        antiparallel association of molecules arising from dipole-dipole
        interactions plays a dominant role in determining the molecular-scale
        structure of 8CB.},
  annote = {Part 1 496QF Times Cited:10 Cited References Count:60},
  issn = {1063-651X},
  uri = {<Go to ISI>://000172406900063},
}

@ARTICLE{Lansac2003,
  author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser},
  title = {Phase behavior of bent-core molecules},
  journal = {Physical Review E},
  year = {2003},
  volume = {67},
  pages = {-},
  number = {1},
  month = {Jan},
  abstract = {Recently, a new class of smectic liquid crystal phases characterized
        by the spontaneous formation of macroscopic chiral domains from
        achiral bent-core molecules has been discovered. We have carried
        out Monte Carlo simulations of a minimal hard spherocylinder dimer
        model to investigate the role of excluded volume interactions in
        determining the phase behavior of bent-core materials and to probe
        the molecular origins of polar and chiral symmetry breaking. We
        present the phase diagram of hard spherocylinder dimers of length-diameter
        ratio of 5 as a function of pressure or density and dimer opening
        angle psi. With decreasing psi, a transition from a nonpolar to
        a polar smectic A phase is observed near psi=167degrees, and the
        nematic phase becomes thermodynamically unstable for psi<135degrees.
        Free energy calculations indicate that the antipolar smectic A (SmAP(A))
        phase is more stable than the polar smectic A phase (SmAP(F)). No
        chiral smectic or biaxial nematic phases were found.},
  annote = {Part 1 646CM Times Cited:15 Cited References Count:38},
  issn = {1063-651X},
  uri = {<Go to ISI>://000181017300042},
}

@BOOK{Leach2001,
  title = {Molecular Modeling: Principles and Applications},
  publisher = {Pearson Educated Limited},
  year = {2001},
  author = {A. Leach},
  address = {Harlow, England},
  edition = {2nd},
}

@ARTICLE{Leimkuhler1999,
  author = {B. Leimkuhler},
  title = {Reversible adaptive regularization: perturbed Kepler motion and classical
        atomic trajectories},
  journal = {Philosophical Transactions of the Royal Society of London Series
        a-Mathematical Physical and Engineering Sciences},
  year = {1999},
  volume = {357},
  pages = {1101-1133},
  number = {1754},
  month = {Apr 15},
  abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
        regularization and modified Sundman transformations are applied
        to simulate general perturbed Kepler motion and to compute classical
        trajectories of atomic systems (e.g. Rydberg atoms). The new family
        of reversible adaptive regularization methods also conserves angular
        momentum and exhibits superior energy conservation and numerical
        stability in long-time integrations. The schemes are appropriate
        for scattering, for astronomical calculations of escape time and
        long-term stability, and for classical and semiclassical studies
        of atomic dynamics. The components of an algorithm for trajectory
        calculations are described. Numerical experiments illustrate the
        effectiveness of the reversible approach.},
  annote = {199EE Times Cited:11 Cited References Count:48},
  issn = {1364-503X},
  uri = {<Go to ISI>://000080466800007},
}

@BOOK{Leimkuhler2004,
  title = {Simulating Hamiltonian Dynamics},
  publisher = {Cambridge University Press},
  year = {2004},
  author = {B. Leimkuhler and S. Reich},
  address = {Cambridge},
}

@ARTICLE{Levelut1981,
  author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard
        and G. Sigaud},
  title = {Number of Sa Phases},
  journal = {Physical Review A},
  year = {1981},
  volume = {24},
  pages = {2180-2186},
  number = {4},
  annote = {Ml751 Times Cited:96 Cited References Count:16},
  issn = {1050-2947},
  uri = {<Go to ISI>://A1981ML75100057},
}

@ARTICLE{Lieb1982,
  author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
  title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers -
        Evidence from Raman-Scattering},
  journal = {Biochimica Et Biophysica Acta},
  year = {1982},
  volume = {688},
  pages = {388-398},
  number = {2},
  annote = {Nu461 Times Cited:40 Cited References Count:28},
  issn = {0006-3002},
  uri = {<Go to ISI>://A1982NU46100012},
}

@ARTICLE{Link1997,
  author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A.
        Clark and E. Korblova and D. M. Walba},
  title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic
        phase of achiral molecules},
  journal = {Science},
  year = {1997},
  volume = {278},
  pages = {1924-1927},
  number = {5345},
  month = {Dec 12},
  abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
        cores was found to have fluid layers that exhibit two spontaneous
        symmetry-breaking instabilities: polar molecular orientational ordering
        about the layer normal and molecular tilt. These instabilities combine
        to form a chiral layer structure with a handedness that depends
        on the sign of the tilt. The bulk states are either antiferroelectric-racemic,
        with the layer polar direction and handedness alternating in sign
        from layer to layer, or antiferroelectric-chiral, which is of uniform
        layer handedness. Both states exhibit an electric field-induced
        transition from antiferroelectric to ferroelectric.},
  annote = {Yl002 Times Cited:407 Cited References Count:25},
  issn = {0036-8075},
  uri = {<Go to ISI>://A1997YL00200028},
}

@ARTICLE{Liwo2005,
  author = {A. Liwo and M. Khalili and H. A. Scheraga},
  title = {Ab initio simulations of protein folding pathways by molecular dynamics
        with the united-residue (UNRES) model of polypeptide chains},
  journal = {Febs Journal},
  year = {2005},
  volume = {272},
  pages = {359-360},
  month = {Jul},
  annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
  issn = {1742-464X},
  uri = {<Go to ISI>://000234826102043},
}

@ARTICLE{Luty1994,
  author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
  title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods
        for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
  journal = {Molecular Simulation},
  year = {1994},
  volume = {14},
  pages = {11-20},
  number = {1},
  abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
        for calculating electrostatic interactions in periodic molecular
        systems. A brief comparison of the theories shows that the methods
        are very similar differing mainly in the technique which is used
        to perform the ''k-space'' or mesh calculation. Because the PPPM
        utilizes the highly efficient numerical Fast Fourier Transform (FFT)
        method it requires significantly less computational effort than
        the Ewald method and scale's almost linearly with system size.},
  annote = {Qf464 Times Cited:50 Cited References Count:20},
  issn = {0892-7022},
  uri = {<Go to ISI>://A1994QF46400002},
}

@BOOK{Marion1990,
  title = {Classical Dynamics of Particles and Systems},
  publisher = {Academic Press},
  year = {1990},
  author = {J.~B. Marion},
  address = {New York},
  edition = {2rd},
}

@ARTICLE{Marrink1994,
  author = {S. J. Marrink and H. J. C. Berendsen},
  title = {Simulation of Water Transport through a Lipid-Membrane},
  journal = {Journal of Physical Chemistry},
  year = {1994},
  volume = {98},
  pages = {4155-4168},
  number = {15},
  month = {Apr 14},
  abstract = {To obtain insight in the process of water permeation through a lipid
        membrane, we performed molecular dynamics simulations on a phospholipid
        (DPPC)/water system with atomic detail. Since the actual process
        of permeation is too slow to be studied directly, we deduced the
        permeation rate indirectly via computation of the free energy and
        diffusion rate profiles of a water molecule across the bilayer.
        We conclude that the permeation of water through a lipid membrane
        cannot be described adequately by a simple homogeneous solubility-diffusion
        model. Both the excess free energy and the diffusion rate strongly
        depend on the position in the membrane, as a result from the inhomogeneous
        nature of the membrane. The calculated excess free energy profile
        has a shallow slope and a maximum height of 26 kJ/mol. The diffusion
        rate is highest in the middle of the membrane where the lipid density
        is low. In the interfacial region almost all water molecules are
        bound by the lipid headgroups, and the diffusion turns out to be
        1 order of magnitude smaller. The total transport process is essentially
        determined by the free energy barrier. The rate-limiting step is
        the permeation through the dense part of the lipid tails, where
        the resistance is highest. We found a permeation rate of 7(+/-3)
        x 10(-2) cm/s at 350 K, comparable to experimental values for DPPC
        membranes, if corrected for the temperature of the simulation. Taking
        the inhomogeneity of the membrane into account, we define a new
        ''four-region'' model which seems to be more realistic than the
        ''two-phase'' solubility-diffusion model.},
  annote = {Ng219 Times Cited:187 Cited References Count:25},
  issn = {0022-3654},
  uri = {<Go to ISI>://A1994NG21900040},
}

@ARTICLE{Marrink2004,
  author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
  title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
  journal = {J. Phys. Chem. B},
  year = {2004},
  volume = {108},
  pages = {750-760},
}

@ARTICLE{Marsden1998,
  author = {J. E. Marsden and G. W. Patrick and S. Shkoller},
  title = {Multisymplectic geometry, variational integrators, and nonlinear
        PDEs},
  journal = {Communications in Mathematical Physics},
  year = {1998},
  volume = {199},
  pages = {351-395},
  number = {2},
  month = {Dec},
  abstract = {This paper presents a geometric-variational approach to continuous
        and discrete mechanics and field theories. Using multisymplectic
        geometry, we show that the existence of the fundamental geometric
        structures as well as their preservation along solutions can be
        obtained directly from the variational principle. In particular,
        we prove that a unique multisymplectic structure is obtained by
        taking the derivative of an action function, and use this structure
        to prove covariant generalizations of conservation of symplecticity
        and Noether's theorem. Natural discretization schemes for PDEs,
        which have these important preservation properties, then follow
        by choosing a discrete action functional. In the case of mechanics,
        we recover the variational symplectic integrators of Veselov type,
        while for PDEs we obtain covariant spacetime integrators which conserve
        the corresponding discrete multisymplectic form as well as the discrete
        momentum mappings corresponding to symmetries. We show that the
        usual notion of symplecticity along an infinite-dimensional space
        of fields can be naturally obtained by making a spacetime split.
        All of the aspects of our method are demonstrated with a nonlinear
        sine-Gordon equation, including computational results and a comparison
        with other discretization schemes.},
  annote = {154RH Times Cited:88 Cited References Count:36},
  issn = {0010-3616},
  uri = {<Go to ISI>://000077902200006},
}

@ARTICLE{Matthey2004,
  author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and
        M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
  title = {ProtoMol, an object-oriented framework for prototyping novel algorithms
        for molecular dynamics},
  journal = {Acm Transactions on Mathematical Software},
  year = {2004},
  volume = {30},
  pages = {237-265},
  number = {3},
  month = {Sep},
  abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
        of novel algorithms for molecular dynamics and related applications.
        Its flexibility is achieved primarily through the use of inheritance
        and design patterns (object-oriented programming): Performance is
        obtained by using templates that enable generation of efficient
        code for sections critical to performance (generic programming).
        The framework encapsulates important optimizations that can be used
        by developers, such as parallelism in the force computation. Its
        design is based on domain analysis of numerical integrators for
        molecular dynamics (MD) and of fast solvers for the force computation,
        particularly due to electrostatic interactions. Several new and
        efficient algorithms are implemented in PROTOMOL. Finally, it is
        shown that PROTOMOL'S sequential performance is excellent when compared
        to a leading MD program, and that it scales well for moderate number
        of processors. Binaries and source codes for Windows, Linux, Solaris,
        IRIX, HP-UX, and AIX platforms are available under open source license
        at http://protomol.sourceforge.net.},
  annote = {860EP Times Cited:2 Cited References Count:52},
  issn = {0098-3500},
  uri = {<Go to ISI>://000224325600001},
}

@ARTICLE{McLachlan1993,
  author = {R.~I McLachlan},
  title = {Explicit Lie-Poisson integration and the Euler equations},
  journal = {prl},
  year = {1993},
  volume = {71},
  pages = {3043-3046},
}

@ARTICLE{McLachlan1998,
  author = {R. I. McLachlan and G. R. W. Quispel},
  title = {Generating functions for dynamical systems with symmetries, integrals,
        and differential invariants},
  journal = {Physica D},
  year = {1998},
  volume = {112},
  pages = {298-309},
  number = {1-2},
  month = {Jan 15},
  abstract = {We give a survey and some new examples of generating functions for
        systems with symplectic structure, systems with a first integral,
        systems that preserve volume, and systems with symmetries and/or
        time-reversing symmetries. Both ODEs and maps are treated, and we
        discuss how generating functions may be used in the structure-preserving
        numerical integration of ODEs with the above properties.},
  annote = {Yt049 Times Cited:7 Cited References Count:26},
  issn = {0167-2789},
  uri = {<Go to ISI>://000071558900021},
}

@ARTICLE{McLachlan1998a,
  author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner},
  title = {Numerical integrators that preserve symmetries and reversing symmetries},
  journal = {Siam Journal on Numerical Analysis},
  year = {1998},
  volume = {35},
  pages = {586-599},
  number = {2},
  month = {Apr},
  abstract = {We consider properties of flows, the relationships between them, and
        whether numerical integrators can be made to preserve these properties.
        This is done in the context of automorphisms and antiautomorphisms
        of a certain group generated by maps associated to vector fields.
        This new framework unifies several known constructions. We also
        use the concept of #covariance# of a numerical method with respect
        to a group of coordinate transformations. The main application is
        to explore the relationship between spatial symmetries, reversing
        symmetries, and time symmetry of flows and numerical integrators.},
  annote = {Zc449 Times Cited:14 Cited References Count:33},
  issn = {0036-1429},
  uri = {<Go to ISI>://000072580500010},
}

@ARTICLE{McLachlan2005,
  author = {R. I. McLachlan and A. Zanna},
  title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
  journal = {Foundations of Computational Mathematics},
  year = {2005},
  volume = {5},
  pages = {87-123},
  number = {1},
  month = {Feb},
  abstract = {In this paper we revisit the Moser-Veselov description of the free
        rigid body in body coordinates, which, in the 3 x 3 case, can be
        implemented as an explicit, second-order, integrable approximation
        of the continuous solution. By backward error analysis, we study
        the modified vector field which is integrated exactly by the discrete
        algorithm. We deduce that the discrete Moser-Veselov (DMV) is well
        approximated to higher order by time reparametrizations of the continuous
        equations (modified vector field). We use the modified vector field
        to scale the initial data of the DMV to improve the order of the
        approximation and show the equivalence of the DMV and the RATTLE
        algorithm. Numerical integration with these preprocessed initial
        data is several orders of magnitude more accurate than the original
        DMV and RATTLE approach.},
  annote = {911NS Times Cited:0 Cited References Count:14},
  issn = {1615-3375},
  uri = {<Go to ISI>://000228011900003},
}

@ARTICLE{Meineke2005,
  author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and
        J. D. Gezelter},
  title = {OOPSE: An object-oriented parallel simulation engine for molecular
        dynamics},
  journal = {Journal of Computational Chemistry},
  year = {2005},
  volume = {26},
  pages = {252-271},
  number = {3},
  month = {Feb},
  abstract = {OOPSE is a new molecular dynamics simulation program that is capable
        of efficiently integrating equations of motion for atom types with
        orientational degrees of freedom (e.g. #sticky# atoms and point
        dipoles). Transition metals can also be simulated using the embedded
        atom method (EAM) potential included in the code. Parallel simulations
        are carried out using the force-based decomposition method. Simulations
        are specified using a very simple C-based meta-data language. A
        number of advanced integrators are included, and the basic integrator
        for orientational dynamics provides substantial improvements over
        older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.},
  annote = {891CF Times Cited:1 Cited References Count:56},
  issn = {0192-8651},
  uri = {<Go to ISI>://000226558200006},
}

@ARTICLE{Melchionna1993,
  author = {S. Melchionna and G. Ciccotti and B. L. Holian},
  title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
  journal = {Molecular Physics},
  year = {1993},
  volume = {78},
  pages = {533-544},
  number = {3},
  month = {Feb 20},
  abstract = {In this paper we write down equations of motion (following the approach
        pioneered by Hoover) for an exact isothermal-isobaric molecular
        dynamics simulation, and we extend them to multiple thermostating
        rates, to a shape-varying cell and to molecular systems, coherently
        with the previous 'extended system method'. An integration scheme
        is proposed together with a numerical illustration of the method.},
  annote = {Kq355 Times Cited:172 Cited References Count:17},
  issn = {0026-8976},
  uri = {<Go to ISI>://A1993KQ35500002},
}

@ARTICLE{Memmer2002,
  author = {R. Memmer},
  title = {Liquid crystal phases of achiral banana-shaped molecules: a computer
        simulation study},
  journal = {Liquid Crystals},
  year = {2002},
  volume = {29},
  pages = {483-496},
  number = {4},
  month = {Apr},
  abstract = {The phase behaviour of achiral banana-shaped molecules was studied
        by computer simulation. The banana-shaped molecules were described
        by model intermolecular interactions based on the Gay-Berne potential.
        The characteristic molecular structure was considered by joining
        two calamitic Gay-Berne particles through a bond to form a biaxial
        molecule of point symmetry group C-2v with a suitable bending angle.
        The dependence on temperature of systems of N=1024 rigid banana-shaped
        molecules with bending angle phi=140degrees has been studied by
        means of Monte Carlo simulations in the isobaric-isothermal ensemble
        (NpT). On cooling an isotropic system, two phase transitions characterized
        by phase transition enthalpy, entropy and relative volume change
        have been observed. For the first time by computer simulation of
        a many-particle system of banana-shaped molecules, at low temperature
        an untilted smectic phase showing a global phase biaxiality and
        a spontaneous local polarization in the layers, i.e. a local polar
        arrangement of the steric dipoles, with an antiferroelectric-like
        superstructure could be proven, a phase structure which recently
        has been discovered experimentally. Additionally, at intermediate
        temperature a nematic-like phase has been proved, whereas close
        to the transition to the smectic phase hints of a spontaneous achiral
        symmetry breaking have been determined. Here, in the absence of
        a layered structure a helical superstructure has been formed. All
        phases have been characterized by visual representations of selected
        configurations, scalar and pseudoscalar correlation functions, and
        order parameters.},
  annote = {531HT Times Cited:12 Cited References Count:37},
  issn = {0267-8292},
  uri = {<Go to ISI>://000174410500001},
}

@ARTICLE{Metropolis1949,
  author = {N. Metropolis and S. Ulam},
  title = {The $\mbox{Monte Carlo}$ Method},
  journal = {J. Am. Stat. Ass.},
  year = {1949},
  volume = {44},
  pages = {335-341},
}

@ARTICLE{Mielke2004,
  author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen
        and C. J. Benham},
  title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian
        dynamics study},
  journal = {Journal of Chemical Physics},
  year = {2004},
  volume = {121},
  pages = {8104-8112},
  number = {16},
  month = {Oct 22},
  abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
        DNA can potentially induce long-range structural deformations integral
        to mechanisms of biological significance in both prokaryotes and
        eukaryotes. In this paper, we introduce a dynamic computer model
        for investigating this phenomenon. Duplex DNA is represented as
        a chain of hydrodynamic beads interacting through potentials of
        linearly elastic stretching, bending, and twisting, as well as excluded
        volume. The chain, linear when relaxed, is looped to form two open
        but topologically constrained subdomains. This permits the dynamic
        introduction of torsional stress via a centrally applied torque.
        We simulate by Brownian dynamics the 100 mus response of a 477-base
        pair B-DNA template to the localized torque generated by the prokaryotic
        transcription ensemble. Following a sharp rise at early times, the
        distributed twist assumes a nearly constant value in both subdomains,
        and a succession of supercoiling deformations occurs as superhelical
        stress is increasingly partitioned to writhe. The magnitude of writhe
        surpasses that of twist before also leveling off when the structure
        reaches mechanical equilibrium with the torsional load. Superhelicity
        is simultaneously right handed in one subdomain and left handed
        in the other, as predicted by the #transcription-induced##twin-supercoiled-domain#
        model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84,
        7024 (1987)]. The properties of the chain at the onset of writhing
        agree well with predictions from theory, and the generated stress
        is ample for driving secondary structural transitions in physiological
        DNA. (C) 2004 American Institute of Physics.},
  annote = {861ZF Times Cited:3 Cited References Count:34},
  issn = {0021-9606},
  uri = {<Go to ISI>://000224456500064},
}

@ARTICLE{Naess2001,
  author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter},
  title = {Brownian dynamics simulation of rigid bodies and segmented polymer
        chains. Use of Cartesian rotation vectors as the generalized coordinates
        describing angular orientations},
  journal = {Physica A},
  year = {2001},
  volume = {294},
  pages = {323-339},
  number = {3-4},
  month = {May 15},
  abstract = {The three Eulerian angles constitute the classical choice of generalized
        coordinates used to describe the three degrees of rotational freedom
        of a rigid body, but it has long been known that this choice yields
        singular equations of motion. The latter is also true when Eulerian
        angles are used in Brownian dynamics analyses of the angular orientation
        of single rigid bodies and segmented polymer chains. Starting from
        kinetic theory we here show that by instead employing the three
        components of Cartesian rotation vectors as the generalized coordinates
        describing angular orientation, no singularity appears in the configuration
        space diffusion equation and the associated Brownian dynamics algorithm.
        The suitability of Cartesian rotation vectors in Brownian dynamics
        simulations of segmented polymer chains with spring-like or ball-socket
        joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.},
  annote = {433TA Times Cited:7 Cited References Count:19},
  issn = {0378-4371},
  uri = {<Go to ISI>://000168774800005},
}

@ARTICLE{Niori1996,
  author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe},
  title = {Distinct ferroelectric smectic liquid crystals consisting of banana
        shaped achiral molecules},
  journal = {Journal of Materials Chemistry},
  year = {1996},
  volume = {6},
  pages = {1231-1233},
  number = {7},
  month = {Jul},
  abstract = {The synthesis of a banana-shaped molecule is reported and it is found
        that the smectic phase which it forms is biaxial with the molecules
        packed in the best,direction into a layer. Because of this characteristic
        packing, spontaneous polarization appears parallel to the layer
        and switches on reversal of an applied electric field. This is the
        first obvious example of ferroelectricity in an achiral smectic
        phase and is ascribed to the C-2v symmetry of the molecular packing.},
  annote = {Ux855 Times Cited:447 Cited References Count:18},
  issn = {0959-9428},
  uri = {<Go to ISI>://A1996UX85500025},
}

@ARTICLE{Noguchi2002,
  author = {H. Noguchi and M. Takasu},
  title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
  journal = {Physical Review E},
  year = {2002},
  volume = {65},
  pages = {-},
  number = {5},
  month = {may},
  abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
        forces using a Brownian dynamics simulation. Two nanoparticles,
        which interact repulsively with amphiphilic molecules, are put inside
        a vesicle. The position of one nanoparticle is fixed, and the other
        is moved by a constant force as in optical-trapping experiments.
        First, the pulled vesicle stretches into a pear or tube shape. Then
        the inner monolayer in the tube-shaped region is deformed, and a
        cylindrical structure is formed between two vesicles. After stretching
        the cylindrical region, fission occurs near the moved vesicle. Soon
        after this the cylindrical region shrinks. The trapping force similar
        to 100 pN is needed to induce the formation of the cylindrical structure
        and fission.},
  annote = {Part 1 568PX Times Cited:5 Cited References Count:39},
  issn = {1063-651X},
  uri = {<Go to ISI>://000176552300084},
}

@ARTICLE{Noguchi2001,
  author = {H. Noguchi and M. Takasu},
  title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
  journal = {Journal of Chemical Physics},
  year = {2001},
  volume = {115},
  pages = {9547-9551},
  number = {20},
  month = {Nov 22},
  abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
        simulation. Amphiphilic molecules spontaneously form vesicles with
        a bilayer structure. Two vesicles come into contact and form a stalk
        intermediate, in which a necklike structure only connects the outer
        monolayers, as predicted by the stalk hypothesis. We have found
        a new pathway of pore opening from stalks at high temperature: the
        elliptic stalk bends and contact between the ends of the arc-shaped
        stalk leads to pore opening. On the other hand, we have clarified
        that the pore-opening process at low temperature agrees with the
        modified stalk model: a pore is induced by contact between the inner
        monolayers inside the stalk. (C) 2001 American Institute of Physics.},
  annote = {491UW Times Cited:48 Cited References Count:25},
  issn = {0021-9606},
  uri = {<Go to ISI>://000172129300049},
}

@BOOK{Olver1986,
  title = {Applications of Lie groups to differential equatitons},
  publisher = {Springer},
  year = {1986},
  author = {P.J. Olver},
  address = {New York},
}

@ARTICLE{Omelyan1998,
  author = {I. P. Omelyan},
  title = {On the numerical integration of motion for rigid polyatomics: The
        modified quaternion approach},
  journal = {Computers in Physics},
  year = {1998},
  volume = {12},
  pages = {97-103},
  number = {1},
  month = {Jan-Feb},
  abstract = {A revised version of the quaternion approach for numerical integration
        of the equations of motion for rigid polyatomic molecules is proposed.
        The modified approach is based on a formulation of the quaternion
        dynamics with constraints. This allows one to resolve the rigidity
        problem rigorously using constraint forces. It is shown that the
        procedure for preservation of molecular rigidity can be realized
        particularly simply within the Verlet algorithm in velocity form.
        We demonstrate that the method presented leads to an improved numerical
        stability with respect to the usual quaternion rescaling scheme
        and it is roughly as good as the cumbersome atomic-constraint technique.
        (C) 1998 American Institute of Physics.},
  annote = {Yx279 Times Cited:12 Cited References Count:28},
  issn = {0894-1866},
  uri = {<Go to ISI>://000072024300025},
}

@ARTICLE{Omelyan1998a,
  author = {I. P. Omelyan},
  title = {Algorithm for numerical integration of the rigid-body equations of
        motion},
  journal = {Physical Review E},
  year = {1998},
  volume = {58},
  pages = {1169-1172},
  number = {1},
  month = {Jul},
  abstract = {An algorithm for numerical integration of the rigid-body equations
        of motion is proposed. The algorithm uses the leapfrog scheme and
        the quantities involved are angular velocities and orientational
        variables that can be expressed in terms of either principal axes
        or quaternions. Due to specific features of the algorithm, orthonormality
        and unit norms of the orientational variables are integrals of motion,
        despite an approximate character of the produced trajectories. It
        is shown that the method presented appears to be the most efficient
        among all such algorithms known.},
  annote = {101XL Times Cited:8 Cited References Count:22},
  issn = {1063-651X},
  uri = {<Go to ISI>://000074893400151},
}

@ARTICLE{Orlandi2006,
  author = {S. Orlandi and R. Berardi and J. Steltzer and C. Zannoni},
  title = {A Monte Carlo study of the mesophases formed by polar bent-shaped
        molecules},
  journal = {Journal of Chemical Physics},
  year = {2006},
  volume = {124},
  pages = {-},
  number = {12},
  month = {Mar 28},
  abstract = {Liquid crystal phases formed by bent-shaped (or #banana#) molecules
        are currently of great interest. Here we investigate by Monte Carlo
        computer simulations the phases formed by rigid banana molecules
        modeled combining three Gay-Berne sites and containing either one
        central or two lateral and transversal dipoles. We show that changing
        the dipole position and orientation has a profound effect on the
        mesophase stability and molecular organization. In particular, we
        find a uniaxial nematic phase only for off-center dipolar models
        and tilted phases only for the one with terminal dipoles. (c) 2006
        American Institute of Physics.},
  annote = {028CP Times Cited:0 Cited References Count:42},
  issn = {0021-9606},
  uri = {<Go to ISI>://000236464000072},
}

@ARTICLE{Owren1992,
  author = {B. Owren and M. Zennaro},
  title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
  journal = {Siam Journal on Scientific and Statistical Computing},
  year = {1992},
  volume = {13},
  pages = {1488-1501},
  number = {6},
  month = {Nov},
  abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
        stages are considered. These methods are continuously differentiable
        if and only if one of the stages is the FSAL evaluation. A characterization
        of a subclass of these methods is developed for orders 3, 4, and
        5. It is shown how the free parameters of these methods can be used
        either to minimize the continuous truncation error coefficients
        or to maximize the stability region. As a representative for these
        methods the fifth-order method with minimized error coefficients
        is chosen, supplied with an error estimation method, and analysed
        by using the DETEST software. The results are compared with a similar
        implementation of the Dormand-Prince 5(4) pair with interpolant,
        showing a significant advantage in the new method for the chosen
        problems.},
  annote = {Ju936 Times Cited:25 Cited References Count:20},
  issn = {0196-5204},
  uri = {<Go to ISI>://A1992JU93600013},
}

@ARTICLE{Palacios1998,
  author = {J. L. Garcia-Palacios and F. J. Lazaro},
  title = {Langevin-dynamics study of the dynamical properties of small magnetic
        particles},
  journal = {Physical Review B},
  year = {1998},
  volume = {58},
  pages = {14937-14958},
  number = {22},
  month = {Dec 1},
  abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
        magnetic moment is numerically solved (properly observing the customary
        interpretation of it as a Stratonovich stochastic differential equation),
        in order to study the dynamics of magnetic nanoparticles. The corresponding
        Langevin-dynamics approach allows for the study of the fluctuating
        trajectories of individual magnetic moments, where we have encountered
        remarkable phenomena in the overbarrier rotation process, such as
        crossing-back or multiple crossing of the potential barrier, rooted
        in the gyromagnetic nature of the system. Concerning averaged quantities,
        we study the linear dynamic response of the archetypal ensemble
        of noninteracting classical magnetic moments with axially symmetric
        magnetic anisotropy. The results are compared with different analytical
        expressions used to model the relaxation of nanoparticle ensembles,
        assessing their accuracy. It has been found that, among a number
        of heuristic expressions for the linear dynamic susceptibility,
        only the simple formula proposed by Shliomis and Stepanov matches
        the coarse features of the susceptibility reasonably. By comparing
        the numerical results with the asymptotic formula of Storonkin {Sov.
        Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]},
        the effects of the intra-potential-well relaxation modes on the
        low-temperature longitudinal dynamic response have been assessed,
        showing their relatively small reflection in the susceptibility
        curves but their dramatic influence on the phase shifts. Comparison
        of the numerical results with the exact zero-damping expression
        for the transverse susceptibility by Garanin, Ishchenko, and Panina
        {Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242
        (1990)]}, reveals a sizable contribution of the spread of the precession
        frequencies of the magnetic moment in the anisotropy field to the
        dynamic response at intermediate-to-high temperatures. [S0163-1829
        (98)00446-9].},
  annote = {146XW Times Cited:66 Cited References Count:45},
  issn = {0163-1829},
  uri = {<Go to ISI>://000077460000052},
}

@ARTICLE{Parr1995,
  author = {T. J. Parr and R. W. Quong},
  title = {Antlr - a Predicated-Ll(K) Parser Generator},
  journal = {Software-Practice \& Experience},
  year = {1995},
  volume = {25},
  pages = {789-810},
  number = {7},
  month = {Jul},
  abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
        often choose to write recursive-descent parsers by hand to obtain
        increased flexibility, better error handling, and ease of debugging.
        We introduce ANTLR, a public-domain parser generator that combines
        the flexibility of hand-coded parsing with the convenience of a
        parser generator, which is a component of PCCTS. ANTLR has many
        features that make it easier to use than other language tools. Most
        important, ANTLR provides predicates which let the programmer systematically
        direct the parse via arbitrary expressions using semantic and syntactic
        context; in practice, the use of predicates eliminates the need
        to hand-tweak the ANTLR output, even for difficult parsing problems.
        ANTLR also integrates the description of lexical and syntactic analysis,
        accepts LL(k) grammars for k > 1 with extended BNF notation, and
        can automatically generate abstract syntax trees. ANTLR is widely
        used, with over 1000 registered industrial and academic users in
        37 countries. It has been ported to many popular systems such as
        the PC, Macintosh, and a variety of UNIX platforms; a commercial
        C++ front-end has been developed as a result of one of our industrial
        collaborations.},
  annote = {Rk104 Times Cited:19 Cited References Count:10},
  issn = {0038-0644},
  uri = {<Go to ISI>://A1995RK10400004},
}

@ARTICLE{Pastor1988,
  author = {R. W. Pastor and B. R. Brooks and A. Szabo},
  title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
  journal = {Molecular Physics},
  year = {1988},
  volume = {65},
  pages = {1409-1419},
  number = {6},
  month = {Dec 20},
  annote = {T1302 Times Cited:61 Cited References Count:26},
  issn = {0026-8976},
  uri = {<Go to ISI>://A1988T130200011},
}

@ARTICLE{Pelzl1999,
  author = {G. Pelzl and S. Diele and W. Weissflog},
  title = {Banana-shaped compounds - A new field of liquid crystals},
  journal = {Advanced Materials},
  year = {1999},
  volume = {11},
  pages = {707-724},
  number = {9},
  month = {Jul 5},
  annote = {220RC Times Cited:313 Cited References Count:49},
  issn = {0935-9648},
  uri = {<Go to ISI>://000081680400007},
}

@ARTICLE{Perram1985,
  author = {J. W. Perram and M. S. Wertheim},
  title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and
        the Contact Function},
  journal = {Journal of Computational Physics},
  year = {1985},
  volume = {58},
  pages = {409-416},
  number = {3},
  annote = {Akb93 Times Cited:71 Cited References Count:12},
  issn = {0021-9991},
  uri = {<Go to ISI>://A1985AKB9300008},
}

@ARTICLE{Rotne1969,
  author = {F. Perrin},
  title = {Variational treatment of hydrodynamic interaction in polymers},
  journal = {J. Chem. Phys.},
  year = {1969},
  volume = {50},
  pages = {4831�C4837},
}

@ARTICLE{Perrin1936,
  author = {F. Perrin},
  title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation
        des fluorescences. Translation et diffusion de moleculese ellipsoidales},
  journal = {J. Phys. Radium},
  year = {1936},
  volume = {7},
  pages = {1-11},
}

@ARTICLE{Perrin1934,
  author = {F. Perrin},
  title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour
        des molecules ellipsoidales},
  journal = {J. Phys. Radium},
  year = {1934},
  volume = {5},
  pages = {497-511},
}

@ARTICLE{Petrache2000,
  author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
  title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines
        Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
  journal = {Biophysical Journal},
  year = {2000},
  volume = {79},
  pages = {3172-3192},
}

@ARTICLE{Petrache1998,
  author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
  title = {Fluid phase structure of EPC and DMPC bilayers},
  journal = {Chemistry and Physics of Lipids},
  year = {1998},
  volume = {95},
  pages = {83-94},
  number = {1},
  month = {Sep},
  abstract = {X-ray diffraction data taken at high instrumental resolution were
        obtained for EPC and DMPC under various osmotic pressures, primarily
        at T = 30 degrees C. The headgroup thickness D-HH was obtained from
        relative electron density profiles. By using volumetric results
        and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4
        +/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The
        analysis also gives estimates for the areal compressibility K-A.
        The A(F) results lead to other structural results regarding membrane
        thickness and associated waters. Using the recently determined absolute
        electrons density profile of DPPC, the AF results also lead to absolute
        electron density profiles and absolute continuous transforms \F(q)\
        for EPC and DMPC, Limited measurements of temperature dependence
        show directly that fluctuations increase with increasing temperature
        and that a small decrease in bending modulus K-c accounts for the
        increased water spacing reported by Simon et al. (1995) Biophys.
        J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights
        reserved.},
  annote = {130AT Times Cited:98 Cited References Count:39},
  issn = {0009-3084},
  uri = {<Go to ISI>://000076497600007},
}

@ARTICLE{Powles1973,
  author = {J.~G. Powles},
  title = {A general ellipsoid can not always serve as a modle for the rotational
        diffusion properties of arbitrary shaped rigid molecules},
  journal = {Advan. Phys.},
  year = {1973},
  volume = {22},
  pages = {1-56},
}

@ARTICLE{Recio2004,
  author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
  title = {Identification of protein-protein interaction sites from docking
        energy landscapes},
  journal = {Journal of Molecular Biology},
  year = {2004},
  volume = {335},
  pages = {843-865},
  number = {3},
  month = {Jan 16},
  abstract = {Protein recognition is one of the most challenging and intriguing
        problems in structural biology. Despite all the available structural,
        sequence and biophysical information about protein-protein complexes,
        the physico-chemical patterns, if any, that make a protein surface
        likely to be involved in protein-protein interactions, remain elusive.
        Here, we apply protein docking simulations and analysis of the interaction
        energy landscapes to identify protein-protein interaction sites.
        The new protocol for global docking based on multi-start global
        energy optimization of an allatom model of the ligand, with detailed
        receptor potentials and atomic solvation parameters optimized in
        a training set of 24 complexes, explores the conformational space
        around the whole receptor without restrictions. The ensembles of
        the rigid-body docking solutions generated by the simulations were
        subsequently used to project the docking energy landscapes onto
        the protein surfaces. We found that highly populated low-energy
        regions consistently corresponded to actual binding sites. The procedure
        was validated on a test set of 21 known protein-protein complexes
        not used in the training set. As much as 81% of the predicted high-propensity
        patch residues were located correctly in the native interfaces.
        This approach can guide the design of mutations on the surfaces
        of proteins, provide geometrical details of a possible interaction,
        and help to annotate protein surfaces in structural proteomics.
        (C) 2003 Elsevier Ltd. All rights reserved.},
  annote = {763GQ Times Cited:21 Cited References Count:59},
  issn = {0022-2836},
  uri = {<Go to ISI>://000188066900016},
}

@ARTICLE{Reddy2006,
  author = {R. A. Reddy and C. Tschierske},
  title = {Bent-core liquid crystals: polar order, superstructural chirality
        and spontaneous desymmetrisation in soft matter systems},
  journal = {Journal of Materials Chemistry},
  year = {2006},
  volume = {16},
  pages = {907-961},
  number = {10},
  abstract = {An overview on the recent developments in the field of liquid crystalline
        bent-core molecules (so-called banana liquid crystals) is given.
        After some basic issues, dealing with general aspects of the systematisation
        of the mesophases, development of polar order and chirality in this
        class of LC systems and explaining some general structure-property
        relationships, we focus on fascinating new developments in this
        field, such as modulated, undulated and columnar phases, so-called
        B7 phases, phase biaxiality, ferroelectric and antiferroelectric
        polar order in smectic and columnar phases, amplification and switching
        of chirality and the spontaneous formation of superstructural and
        supramolecular chirality.},
  annote = {021NS Times Cited:2 Cited References Count:316},
  issn = {0959-9428},
  uri = {<Go to ISI>://000235990500001},
}

@ARTICLE{Reich1999,
  author = {S. Reich},
  title = {Backward error analysis for numerical integrators},
  journal = {Siam Journal on Numerical Analysis},
  year = {1999},
  volume = {36},
  pages = {1549-1570},
  number = {5},
  month = {Sep 8},
  abstract = {Backward error analysis has become an important tool for understanding
        the long time behavior of numerical integration methods. This is
        true in particular for the integration of Hamiltonian systems where
        backward error analysis can be used to show that a symplectic method
        will conserve energy over exponentially long periods of time. Such
        results are typically based on two aspects of backward error analysis:
        (i) It can be shown that the modified vector fields have some qualitative
        properties which they share with the given problem and (ii) an estimate
        is given for the difference between the best interpolating vector
        field and the numerical method. These aspects have been investigated
        recently, for example, by Benettin and Giorgilli in [J. Statist.
        Phys., 74 (1994), pp. 1117-1143], by Hairer in [Ann. Numer. Math.,
        1 (1994), pp. 107-132], and by Hairer and Lubich in [Numer. Math.,
        76 (1997), pp. 441-462]. In this paper we aim at providing a unifying
        framework and a simplification of the existing results and corresponding
        proofs. Our approach to backward error analysis is based on a simple
        recursive definition of the modified vector fields that does not
        require explicit Taylor series expansion of the numerical method
        and the corresponding flow maps as in the above-cited works. As
        an application we discuss the long time integration of chaotic Hamiltonian
        systems and the approximation of time averages along numerically
        computed trajectories.},
  annote = {237HV Times Cited:43 Cited References Count:41},
  issn = {0036-1429},
  uri = {<Go to ISI>://000082650600010},
}

@ARTICLE{Ros2005,
  author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
  title = {Banana-shaped liquid crystals: a new field to explore},
  journal = {Journal of Materials Chemistry},
  year = {2005},
  volume = {15},
  pages = {5093-5098},
  number = {48},
  abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
        mesogenic materials represent a bewitching and stimulating field
        of research that is interesting both academically and in terms of
        applications. Numerous topics are open to investigation in this
        area because of the rich phenomenology and new possibilities that
        these materials offer. The principal concepts in this area are reviewed
        along with recent results. In addition, new directions to stimulate
        further research activities are highlighted.},
  annote = {990XA Times Cited:3 Cited References Count:72},
  issn = {0959-9428},
  uri = {<Go to ISI>://000233775500001},
}

@ARTICLE{Roux1991,
  author = {B. Roux and M. Karplus},
  title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
  journal = {Journal of Physical Chemistry},
  year = {1991},
  volume = {95},
  pages = {4856-4868},
  number = {12},
  month = {Jun 13},
  abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
        poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin
        channel. Because of the different dynamical regimes for the three
        species (high barrier for Na+, low barrier for K+, almost free diffusion
        for water), different methods are used to calculate the mobilities.
        By use of activated dynamics and a potential of mean force determined
        previously (Roux, B.; Karplus, M. Biophys. J. 1991, 59, 961), the
        barrier crossing rate of Na+ ion is determined. The motion of Na+
        at the transition state is controlled by local interactions and
        collisions with the neighboring carbonyls and the two nearest water
        molecules. There are significant deviations from transition-state
        theory; the transmission coefficient is equal to 0.11. The water
        and K+ motions are found to be well described by a diffusive model;
        the motion of K+ appears to be controlled by the diffusion of water.
        The time-dependent friction functions of Na+ and K+ ions in the
        periodic beta-helix are calculated and analyzed by using a generalized
        Langevin equation approach. Both Na+ and K+ suffer many rapid collisions,
        and their dynamics is overdamped and noninertial. Thus, the selectivity
        sequence of ions in the beta-helix is not influenced strongly by
        their masses.},
  annote = {Fr756 Times Cited:97 Cited References Count:65},
  issn = {0022-3654},
  uri = {<Go to ISI>://A1991FR75600049},
}

@ARTICLE{Roy2005,
  author = {A. Roy and N. V. Madhusudana},
  title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases
        in banana shaped molecules},
  journal = {European Physical Journal E},
  year = {2005},
  volume = {18},
  pages = {253-258},
  number = {3},
  month = {Nov},
  abstract = {A vast majority of compounds with bent core or banana shaped molecules
        exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased
        in a homologous series. The B-6 phase has an intercalated fluid
        lamellar structure with a layer spacing of half the molecular length.
        The B-1 phase has a two dimensionally periodic rectangular columnar
        structure. The B-2 phase has a monolayer fluid lamellar structure
        with molecules tilted with respect to the layer normal. Neglecting
        the tilt order of the molecules in the B-2 phase, we have developed
        a frustrated packing model to describe this phase sequence qualitatively.
        The model has some analogy with that of the frustrated smectics
        exhibited by highly polar rod like molecules.},
  annote = {985FW Times Cited:0 Cited References Count:30},
  issn = {1292-8941},
  uri = {<Go to ISI>://000233363300002},
}

@ARTICLE{Ryckaert1977,
  author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
  title = {Numerical-Integration of Cartesian Equations of Motion of a System
        with Constraints - Molecular-Dynamics of N-Alkanes},
  journal = {Journal of Computational Physics},
  year = {1977},
  volume = {23},
  pages = {327-341},
  number = {3},
  annote = {Cz253 Times Cited:3680 Cited References Count:7},
  issn = {0021-9991},
  uri = {<Go to ISI>://A1977CZ25300007},
}

@ARTICLE{Sagui1999,
  author = {C. Sagui and T. A. Darden},
  title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic
        effects},
  journal = {Annual Review of Biophysics and Biomolecular Structure},
  year = {1999},
  volume = {28},
  pages = {155-179},
  abstract = {Current computer simulations of biomolecules typically make use of
        classical molecular dynamics methods, as a very large number (tens
        to hundreds of thousands) of atoms are involved over timescales
        of many nanoseconds. The methodology for treating short-range bonded
        and van der Waals interactions has matured. However, long-range
        electrostatic interactions still represent a bottleneck in simulations.
        In this article, we introduce the basic issues for an accurate representation
        of the relevant electrostatic interactions. In spite of the huge
        computational time demanded by most biomolecular systems, it is
        no longer necessary to resort to uncontrolled approximations such
        as the use of cutoffs. In particular, we discuss the Ewald summation
        methods, the fast particle mesh methods, and the fast multipole
        methods. We also review recent efforts to understand the role of
        boundary conditions in systems with long-range interactions, and
        conclude with a short perspective on future trends.},
  annote = {213KJ Times Cited:126 Cited References Count:73},
  issn = {1056-8700},
  uri = {<Go to ISI>://000081271400008},
}

@ARTICLE{Sandu1999,
  author = {A. Sandu and T. Schlick},
  title = {Masking resonance artifacts in force-splitting methods for biomolecular
        simulations by extrapolative Langevin dynamics},
  journal = {Journal of Computational Physics},
  year = {1999},
  volume = {151},
  pages = {74-113},
  number = {1},
  month = {May 1},
  abstract = {Numerical resonance artifacts have become recognized recently as a
        limiting factor to increasing the timestep in multiple-timestep
        (MTS) biomolecular dynamics simulations. At certain timesteps correlated
        to internal motions (e.g., 5 fs, around half the period of the fastest
        bond stretch, T-min), visible inaccuracies or instabilities can
        occur. Impulse-MTS schemes are vulnerable to these resonance errors
        since large energy pulses are introduced to the governing dynamics
        equations when the slow forces are evaluated. We recently showed
        that such resonance artifacts can be masked significantly by applying
        extrapolative splitting to stochastic dynamics. Theoretical and
        numerical analyses of force-splitting integrators based on the Verlet
        discretization are reported here for linear models to explain these
        observations and to suggest how to construct effective integrators
        for biomolecular dynamics that balance stability with accuracy.
        Analyses for Newtonian dynamics demonstrate the severe resonance
        patterns of the Impulse splitting, with this severity worsening
        with the outer timestep. Delta t: Constant Extrapolation is generally
        unstable, but the disturbances do not grow with Delta t. Thus. the
        stochastic extrapolative combination can counteract generic instabilities
        and largely alleviate resonances with a sufficiently strong Langevin
        heat-bath coupling (gamma), estimates for which are derived here
        based on the fastest and slowest motion periods. These resonance
        results generally hold for nonlinear test systems: a water tetramer
        and solvated protein. Proposed related approaches such as Extrapolation/Correction
        and Midpoint Extrapolation work better than Constant Extrapolation
        only for timesteps less than T-min/2. An effective extrapolative
        stochastic approach for biomolecules that balances long-timestep
        stability with good accuracy for the fast subsystem is then applied
        to a biomolecule using a three-class partitioning: the medium forces
        are treated by Midpoint Extrapolation via position Verlet, and the
        slow forces are incorporated by Constant Extrapolation. The resulting
        algorithm (LN) performs well on a solvated protein system in terms
        of thermodynamic properties and yields an order of magnitude speedup
        with respect to single-timestep Langevin trajectories. Computed
        spectral density functions also show how the Newtonian modes can
        be approximated by using a small gamma in the range Of 5-20 ps(-1).
        (C) 1999 Academic Press.},
  annote = {194FM Times Cited:14 Cited References Count:32},
  issn = {0021-9991},
  uri = {<Go to ISI>://000080181500004},
}

@ARTICLE{Sasaki2004,
  author = {Y. Sasaki and R. Shukla and B. D. Smith},
  title = {Facilitated phosphatidylserine flip-flop across vesicle and cell
        membranes using urea-derived synthetic translocases},
  journal = {Organic \& Biomolecular Chemistry},
  year = {2004},
  volume = {2},
  pages = {214-219},
  number = {2},
  abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
        groups are shown to facilitate the translocation of fluorescent
        phospholipid probes and endogenous phosphatidylserine across vesicle
        and erythrocyte cell membranes. The synthetic translocases appear
        to operate by binding to the phospholipid head groups and forming
        lipophilic supramolecular complexes which diffuse through the non-polar
        interior of the bilayer membrane.},
  annote = {760PX Times Cited:8 Cited References Count:25},
  issn = {1477-0520},
  uri = {<Go to ISI>://000187843800012},
}

@ARTICLE{Satoh1996,
  author = {K. Satoh and S. Mita and S. Kondo},
  title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect
        of terminal dipole moment on mesophase formation},
  journal = {Chemical Physics Letters},
  year = {1996},
  volume = {255},
  pages = {99-104},
  number = {1-3},
  month = {Jun 7},
  abstract = {The effects of dipole-dipole interaction on mesophase formation are
        investigated with a Monte Carlo simulation using the dipolar Gay-Berne
        potential. It is shown that the dipole moment at the end of a molecule
        causes a shift in the nematic-isotropic transition toward higher
        temperature and a spread of the temperature range of the nematic
        phase and that layer structures with various interdigitations are
        formed in the smectic phase.},
  annote = {Uq975 Times Cited:32 Cited References Count:33},
  issn = {0009-2614},
  uri = {<Go to ISI>://A1996UQ97500017},
}

@ARTICLE{Schaps1999,
  author = {G. L. Schaps},
  title = {Compiler construction with ANTLR and Java - Tools for building tools},
  journal = {Dr Dobbs Journal},
  year = {1999},
  volume = {24},
  pages = {84-+},
  number = {3},
  month = {Mar},
  annote = {163EC Times Cited:0 Cited References Count:0},
  issn = {1044-789X},
  uri = {<Go to ISI>://000078389200023},
}

@ARTICLE{Shen2002,
  author = {M. Y. Shen and K. F. Freed},
  title = {Long time dynamics of met-enkephalin: Comparison of explicit and
        implicit solvent models},
  journal = {Biophysical Journal},
  year = {2002},
  volume = {82},
  pages = {1791-1808},
  number = {4},
  month = {Apr},
  abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
        structure and receptor docking mechanism are still not well understood.
        The conformational dynamics of this neuron peptide in liquid water
        are studied here by using all-atom molecular dynamics (MID) and
        implicit water Langevin dynamics (LD) simulations with AMBER potential
        functions and the three-site transferable intermolecular potential
        (TIP3P) model for water. To achieve the same simulation length in
        physical time, the full MID simulations require 200 times as much
        CPU time as the implicit water LID simulations. The solvent hydrophobicity
        and dielectric behavior are treated in the implicit solvent LD simulations
        by using a macroscopic solvation potential, a single dielectric
        constant, and atomic friction coefficients computed using the accessible
        surface area method with the TIP3P model water viscosity as determined
        here from MID simulations for pure TIP3P water. Both the local and
        the global dynamics obtained from the implicit solvent LD simulations
        agree very well with those from the explicit solvent MD simulations.
        The simulations provide insights into the conformational restrictions
        that are associated with the bioactivity of the opiate peptide dermorphin
        for the delta-receptor.},
  annote = {540MH Times Cited:36 Cited References Count:45},
  issn = {0006-3495},
  uri = {<Go to ISI>://000174932400010},
}

@ARTICLE{Shillcock2005,
  author = {J. C. Shillcock and R. Lipowsky},
  title = {Tension-induced fusion of bilayer membranes and vesicles},
  journal = {Nature Materials},
  year = {2005},
  volume = {4},
  pages = {225-228},
  number = {3},
  month = {Mar},
  annote = {901QJ Times Cited:9 Cited References Count:23},
  issn = {1476-1122},
  uri = {<Go to ISI>://000227296700019},
}

@ARTICLE{Shimada1993,
  author = {J. Shimada and H. Kaneko and T. Takada},
  title = {Efficient Calculations of Coulombic Interactions in Biomolecular
        Simulations with Periodic Boundary-Conditions},
  journal = {Journal of Computational Chemistry},
  year = {1993},
  volume = {14},
  pages = {867-878},
  number = {7},
  month = {Jul},
  abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
        simulations, two possibilities are considered. The first is the
        famous particle-particle and particle-mesh (PPPM) method developed
        by Hockney and Eastwood, and the second is a new one developed here
        in their spirit but by the use of the multipole expansion technique
        suggested by Ladd. It is then numerically found that the new PPPM
        method gives more accurate results for a two-particle system at
        small separation of particles. Preliminary numerical examination
        of the various computational methods for a single configuration
        of a model BPTI-water system containing about 24,000 particles indicates
        that both of the PPPM methods give far more accurate values with
        reasonable computational cost than do the conventional truncation
        methods. It is concluded the two PPPM methods are nearly comparable
        in overall performance for the many-particle systems, although the
        first method has the drawback that the accuracy in the total electrostatic
        energy is not high for configurations of charged particles randomly
        generated.},
  annote = {Lh164 Times Cited:27 Cited References Count:47},
  issn = {0192-8651},
  uri = {<Go to ISI>://A1993LH16400011},
}

@ARTICLE{Skeel2002,
  author = {R. D. Skeel and J. A. Izaguirre},
  title = {An impulse integrator for Langevin dynamics},
  journal = {Molecular Physics},
  year = {2002},
  volume = {100},
  pages = {3885-3891},
  number = {24},
  month = {Dec 20},
  abstract = {The best simple method for Newtonian molecular dynamics is indisputably
        the leapfrog Stormer-Verlet method. The appropriate generalization
        to simple Langevin dynamics is unclear. An analysis is presented
        comparing an 'impulse method' (kick; fluctuate; kick), the 1982
        method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus
        (BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen
        methods can be implemented as efficiently as the BBK method. Other
        considerations suggest that the impulse method is the best basic
        method for simple Langevin dynamics, with the van Gunsteren-Berendsen
        method a close contender.},
  annote = {633RX Times Cited:8 Cited References Count:22},
  issn = {0026-8976},
  uri = {<Go to ISI>://000180297200014},
}

@ARTICLE{Skeel1997,
  author = {R. D. Skeel and G. H. Zhang and T. Schlick},
  title = {A family of symplectic integrators: Stability, accuracy, and molecular
        dynamics applications},
  journal = {Siam Journal on Scientific Computing},
  year = {1997},
  volume = {18},
  pages = {203-222},
  number = {1},
  month = {Jan},
  abstract = {The following integration methods for special second-order ordinary
        differential equations are studied: leapfrog, implicit midpoint,
        trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all
        are members, or equivalent to members, of a one-parameter family
        of schemes. Some methods have more than one common form, and we
        discuss a systematic enumeration of these forms. We also present
        a stability and accuracy analysis based on the idea of ''modified
        equations'' and a proof of symplecticness. It follows that Cowell-Numerov
        and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic.
        A different interpretation of the values used by these integrators
        leads to higher accuracy and better energy conservation. Hence,
        we suggest that the straightforward analysis of energy conservation
        is misleading.},
  annote = {We981 Times Cited:30 Cited References Count:35},
  issn = {1064-8275},
  uri = {<Go to ISI>://A1997WE98100012},
}

@ARTICLE{Tao2005,
  author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont
        and W. J. Briels},
  title = {Brownian dynamics simulations of the self- and collective rotational
        diffusion coefficients of rigid long thin rods},
  journal = {Journal of Chemical Physics},
  year = {2005},
  volume = {122},
  pages = {-},
  number = {24},
  month = {Jun 22},
  abstract = {Recently a microscopic theory for the dynamics of suspensions of long
        thin rigid rods was presented, confirming and expanding the well-known
        theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon,
        Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here
        this theory is put to the test by comparing it against computer
        simulations. A Brownian dynamics simulation program was developed
        to follow the dynamics of the rods, with a length over a diameter
        ratio of 60, on the Smoluchowski time scale. The model accounts
        for excluded volume interactions between rods, but neglects hydrodynamic
        interactions. The self-rotational diffusion coefficients D-r(phi)
        of the rods were calculated by standard methods and by a new, more
        efficient method based on calculating average restoring torques.
        Collective decay of orientational order was calculated by means
        of equilibrium and nonequilibrium simulations. Our results show
        that, for the currently accessible volume fractions, the decay times
        in both cases are virtually identical. Moreover, the observed decay
        of diffusion coefficients with volume fraction is much quicker than
        predicted by the theory, which is attributed to an oversimplification
        of dynamic correlations in the theory. (c) 2005 American Institute
        of Physics.},
  annote = {943DN Times Cited:3 Cited References Count:26},
  issn = {0021-9606},
  uri = {<Go to ISI>://000230332400077},
}

@BOOK{Tolman1979,
  title = {The Principles of Statistical Mechanics},
  publisher = {Dover Publications, Inc.},
  year = {1979},
  author = {R.~C. Tolman},
  address = {New York},
  chapter = {2},
  pages = {19-22},
}

@ARTICLE{Tu1995,
  author = {K. Tu and D. J. Tobias and M. L. Klein},
  title = {Constant pressure and temperature molecular dynamics simulation of
        a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine
        bilayer},
  journal = {Biophysical Journal},
  year = {1995},
  volume = {69},
  pages = {2558-2562},
  number = {6},
  month = {Dec},
  abstract = {We report a constant pressure and temperature molecular dynamics simulation
        of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine
        at 50 degrees C and 28 water molecules/lipid. We have shown that
        the bilayer is stable throughout the 1550-ps simulation and have
        demonstrated convergence of the system dimensions. Several important
        aspects of the bilayer structure have been investigated and compared
        favorably with experimental results. For example, the average positions
        of specific carbon atoms along the bilayer normal agree well with
        neutron diffraction data, and the electron density profile is in
        accord with x-ray diffraction results. The hydrocarbon chain deuterium
        order parameters agree reasonably well with NMR results for the
        middles of the chains, but the simulation predicts too much order
        at the chain ends. In spite of the deviations in the order parameters,
        the hydrocarbon chain packing density appears to be essentially
        correct, inasmuch as the area/lipid and bilayer thickness are in
        agreement with the most refined experimental estimates. The deuterium
        order parameters for the glycerol and choline groups, as well as
        the phosphorus chemical shift anisotropy, are in qualitative agreement
        with those extracted from NMR measurements.},
  annote = {Tv018 Times Cited:108 Cited References Count:34},
  issn = {0006-3495},
  uri = {<Go to ISI>://A1995TV01800037},
}

@ARTICLE{Tuckerman1992,
  author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
  title = {Reversible Multiple Time Scale Molecular-Dynamics},
  journal = {Journal of Chemical Physics},
  year = {1992},
  volume = {97},
  pages = {1990-2001},
  number = {3},
  month = {Aug 1},
  abstract = {The Trotter factorization of the Liouville propagator is used to generate
        new reversible molecular dynamics integrators. This strategy is
        applied to derive reversible reference system propagator algorithms
        (RESPA) that greatly accelerate simulations of systems with a separation
        of time scales or with long range forces. The new algorithms have
        all of the advantages of previous RESPA integrators but are reversible,
        and more stable than those methods. These methods are applied to
        a set of paradigmatic systems and are shown to be superior to earlier
        methods. It is shown how the new RESPA methods are related to predictor-corrector
        integrators. Finally, we show how these methods can be used to accelerate
        the integration of the equations of motion of systems with Nose
        thermostats.},
  annote = {Je891 Times Cited:680 Cited References Count:19},
  issn = {0021-9606},
  uri = {<Go to ISI>://A1992JE89100044},
}

@BOOK{Varadarajan1974,
  title = {Lie groups, Lie algebras, and their representations},
  publisher = {Prentice-Hall},
  year = {1974},
  author = {V.S. Varadarajan},
  address = {New York},
}

@ARTICLE{Vincent1995,
  author = {J. J. Vincent and K. M. Merz},
  title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing
        Interface Standard},
  journal = {Journal of Computational Chemistry},
  year = {1995},
  volume = {16},
  pages = {1420-1427},
  number = {11},
  month = {Nov},
  abstract = {We have implemented a portable parallel version of the macromolecular
        modeling package AMBER4. The message passing paradigm was used.
        All message passing constructs are compliant with the Message Passing
        Interface (MPI) standard. The molecular dynamics/minimization module
        MINMD and the free-energy perturbation module Gibbs have been implemented
        in parallel on a number of machines, including a Gray T3D, an IBM
        SP1/SP2, and a collection of networked workstations. In addition,
        the code has been tested with an MPI implementation from Argonne
        National Laboratories/Mississippi State University which runs on
        many parallel machines. The goal of this work is to decrease the
        amount of time required to perform molecular dynamics simulations.
        Performance results for a Lipid bilayer molecular dynamics simulation
        on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995
        by John Wiley & Sons, Inc.},
  annote = {Ta403 Times Cited:16 Cited References Count:23},
  issn = {0192-8651},
  uri = {<Go to ISI>://A1995TA40300009},
}

@ARTICLE{Wegener1979,
  author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
  title = {A general ellipsoid can not always serve as a modle for the rotational
        diffusion properties of arbitrary shaped rigid molecules},
  journal = {Proc. Natl. Acad. Sci.},
  year = {1979},
  volume = {76},
  pages = {6356-6360},
  number = {12},
}

@ARTICLE{Wilson2006,
  author = {G.~V. Wilson },
  title = {Where's the Real Bottleneck in Scientific Computing?},
  journal = {American Scientist},
  year = {2006},
  volume = {94},
}

@ARTICLE{Withers2003,
  author = {I. M. Withers},
  title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne
        fluid},
  journal = {Journal of Chemical Physics},
  year = {2003},
  volume = {119},
  pages = {10209-10223},
  number = {19},
  month = {Nov 15},
  abstract = {The effects of longitudinal quadrupole moments on the formation of
        liquid crystalline phases are studied by means of constant NPT Monte
        Carlo simulation methods. The popular Gay-Berne model mesogen is
        used as the reference fluid, which displays the phase sequences
        isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0)
        and low (T*=1.5) temperatures, respectively. With increasing quadrupole
        magnitude the smectic phases are observed to be stabilized with
        respect to the isotropic liquid, while the smectic B is destabilized
        with respect to the smectic A. At the lower temperature, a sufficiently
        large quadrupole magnitude results in the injection of the smectic
        A phase into the phase sequence and the replacement of the smectic
        B phase by the tilted smectic J phase. The nematic phase is also
        injected into the phase sequence at both temperatures considered,
        and ultimately for sufficiently large quadrupole magnitudes no coherent
        layered structures were observed. The stabilization of the smectic
        A phase supports the commonly held belief that, while the inclusion
        of polar groups is not a prerequisite for the formation of the smectic
        A phase, quadrupolar interactions help to increase the temperature
        and pressure range for which the smectic A phase is observed. The
        quality of the layered structure is worsened with increasing quadrupole
        magnitude. This behavior, along with the injection of the nematic
        phase into the phase sequence, indicate that the general tendency
        of the quadrupolar interactions is to destabilize the layered structure.
        A pressure dependence upon the smectic layer spacing is observed.
        This behavior is in much closer agreement with experimental findings
        than has been observed previously for nonpolar Gay-Berne and hard
        spherocylinder models. (C) 2003 American Institute of Physics.},
  annote = {738EF Times Cited:3 Cited References Count:43},
  issn = {0021-9606},
  uri = {<Go to ISI>://000186273200027},
}

@ARTICLE{Wolf1999,
  author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
  title = {Exact method for the simulation of Coulombic systems by spherically
        truncated, pairwise r(-1) summation},
  journal = {Journal of Chemical Physics},
  year = {1999},
  volume = {110},
  pages = {8254-8282},
  number = {17},
  month = {May 1},
  abstract = {Based on a recent result showing that the net Coulomb potential in
        condensed ionic systems is rather short ranged, an exact and physically
        transparent method permitting the evaluation of the Coulomb potential
        by direct summation over the r(-1) Coulomb pair potential is presented.
        The key observation is that the problems encountered in determining
        the Coulomb energy by pairwise, spherically truncated r(-1) summation
        are a direct consequence of the fact that the system summed over
        is practically never neutral. A simple method is developed that
        achieves charge neutralization wherever the r(-1) pair potential
        is truncated. This enables the extraction of the Coulomb energy,
        forces, and stresses from a spherically truncated, usually charged
        environment in a manner that is independent of the grouping of the
        pair terms. The close connection of our approach with the Ewald
        method is demonstrated and exploited, providing an efficient method
        for the simulation of even highly disordered ionic systems by direct,
        pairwise r(-1) summation with spherical truncation at rather short
        range, i.e., a method which fully exploits the short-ranged nature
        of the interactions in ionic systems. The method is validated by
        simulations of crystals, liquids, and interfacial systems, such
        as free surfaces and grain boundaries. (C) 1999 American Institute
        of Physics. [S0021-9606(99)51517-1].},
  annote = {189PD Times Cited:70 Cited References Count:34},
  issn = {0021-9606},
  uri = {<Go to ISI>://000079913000008},
}

@ARTICLE{Yoshida1990,
  author = {H. Yoshida},
  title = {Construction of Higher-Order Symplectic Integrators},
  journal = {Physics Letters A},
  year = {1990},
  volume = {150},
  pages = {262-268},
  number = {5-7},
  month = {Nov 12},
  annote = {Ej798 Times Cited:492 Cited References Count:9},
  issn = {0375-9601},
  uri = {<Go to ISI>://A1990EJ79800009},
}

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