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David Chandler

Bio: David Chandler is an academic researcher from Sandia National Laboratories. The author has contributed to research in topics: Excited state & Transition path sampling. The author has an hindex of 107, co-authored 424 publications receiving 52396 citations. Previous affiliations of David Chandler include University of Pennsylvania & University of Sussex.


Papers
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Journal ArticleDOI
TL;DR: In this paper, the Fourier transform of the pair correlation function is used to calculate the structure factor of a reference system in which the intermolecular forces are entirely repulsive and identical to the repulsive forces in a Lennard-Jones fluid.
Abstract: The different roles the attractive and repulsive forces play in forming the equilibrium structure of a Lennard‐Jones liquid are discussed. It is found that the effects of these forces are most easily separated by considering the structure factor (or equivalently, the Fourier transform of the pair‐correlation function) rather than the pair‐correlation function itself. At intermediate and large wave vectors, the repulsive forces dominate the quantitative behavior of the liquid structure factor. The attractions are manifested primarily in the small wave vector part of the structure factor; but this effect decreases as the density increases and is almost negligible at reduced densities higher than 0.65. These conclusions are established by considering the structure factor of a hypothetical reference system in which the intermolecular forces are entirely repulsive and identical to the repulsive forces in a Lennard‐Jones fluid. This reference system structure factor is calculated with the aid of a simple but accurate approximation described herein. The conclusions lead to a very simple prescription for calculating the radial distribution function of dense liquids which is more accurate than that obtained by any previously reported theory. The thermodynamic ramifications of the conclusions are presented in the form of calculations of the free energy, the internal energy (from the energy equation), and the pressure (from the virial equation). The implications of our conclusions to perturbation theories for liquids and to the interpretation of x‐ray scattering experiments are discussed.

4,462 citations

Journal ArticleDOI
29 Sep 2005-Nature
TL;DR: The hydrophobic effect — the tendency for oil and water to segregate — is important in diverse phenomena, from the cleaning of laundry to the creation of micro-emulsions to make new materials, to the assembly of proteins into functional complexes.
Abstract: The hydrophobic effect — the tendency for oil and water to segregate — is important in diverse phenomena, from the cleaning of laundry, to the creation of micro-emulsions to make new materials, to the assembly of proteins into functional complexes. This effect is multifaceted depending on whether hydrophobic molecules are individually hydrated or driven to assemble into larger structures. Despite the basic principles underlying the hydrophobic effect being qualitatively well understood, only recently have theoretical developments begun to explain and quantify many features of this ubiquitous phenomenon.

3,162 citations

Book
01 Jan 1987
TL;DR: In this paper, the fundamentals conditions for equilibrium and stability of non-equilibrium systems are defined. And the Monte Carlo method in statistical mechanics is used for non-interacting (ideal) systems.
Abstract: Thermodynamics, fundamentals conditions for equilibrium and stability statistical mechanics non-interacting (ideal) systems statistical mechanical theory of phase transitions Monte Carlo method in statistical mechanics classical fluids statistical mechanics of non-equilibrium systems.

2,510 citations

Journal ArticleDOI
TL;DR: This article reviews the concepts and methods of transition path sampling, which allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states.
Abstract: This article reviews the concepts and methods of transition path sampling. These methods allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states. Based upon a statistical mechanics of trajectory space, they provide a perspective with which time dependent phenomena, even for systems driven far from equilibrium, can be examined with the same types of importance sampling tools that in the past have been applied so successfully to static equilibrium properties.

1,843 citations

Journal ArticleDOI
01 Jan 1996-Nature
TL;DR: In this paper, an interplay between diffusion and hydrogen-bond dynamics is proposed to explain the non-exponential kinetics of hydrogen bond formation and breaking in liquid water.
Abstract: HYDROGEN bonds play a crucial role in the behaviour of water1–4; their spatial patterns and fluctuations characterize the structure and dynamics of the liquid5–7. The processes of breaking and making hydrogen bonds in the condensed phase can be probed indirectly by a variety of experimental techniques8, and more quantitative information can be obtained from computer simulations9. In particular, simulations have revealed that on long timescales the relaxation behaviour of hydrogen bonds in liquid water exhibit non-exponential kinetics7,10–13, suggesting that bond making and breaking are not simple processes characterized by well defined rate constants. Here we show that these kinetics can be understood in terms of an interplay between diffusion and hydrogen-bond dynamics. In our model, which can be extended to other hydrogen-bonded liquids, diffusion governs whether a specific pair of water molecules are near neighbours, and hydrogen bonds between such pairs form and persist at random with average lifetimes determined by rate constants for bond making and breaking.

1,583 citations


Cited by
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01 May 1993
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

29,323 citations

28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
Abstract: The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

17,897 citations

Journal ArticleDOI
TL;DR: This paper presents a meta-modelling procedure called "Continuum Methods within MD and MC Simulations 3072", which automates the very labor-intensive and therefore time-heavy and expensive process of integrating discrete and continuous components into a discrete-time model.
Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

13,286 citations

Journal ArticleDOI
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
Abstract: This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.

13,116 citations