trunk/langevin/langevin.bib

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@ARTICLE{2003,
  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},
}

@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{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{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{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{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{Berkov2005,
  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{Berkov2005a,
  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{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{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{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{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{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{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{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},
}

@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{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{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{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{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{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{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{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},
}

@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{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{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{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{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{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},
}

@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},
}

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