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.

Fast parallel algorithms for short-range molecular dynamics

Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

Molecular self-assembly and nanochemistry: A chemical strategy for the synthesis of nanostructures

Structure and nanostructure in ionic liquids.

Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate systems. Such anomalous diffusion can have different physical origins, which can be identified from careful data analysis. In particular, single particle tracking provides the entire trajectory of the traced particle, which allows one to evaluate different observables to quantify the dynamics of the system under observation. We here provide an extensive overview over different popular anomalous diffusion models and their properties. We pay special attention to their ergodic properties, highlighting the fact that in several of these models the long time averaged mean squared displacement shows a distinct disparity to the regular, ensemble averaged mean squared displacement. In these cases, data obtained from time averages cannot be interpreted by the standard theoretical results for the ensemble averages. Here we therefore provide a comparison of the main properties of the time averaged mean squared displacement and its statistical behaviour in terms of the scatter of the amplitudes between the time averages obtained from different trajectories. We especially demonstrate how anomalous dynamics may be identified for systems, which, on first sight, appear to be Brownian. Moreover, we discuss the ergodicity breaking parameters for the different anomalous stochastic processes and showcase the physical origins for the various behaviours. This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion.

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Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking.

Theory of polyelectrolytes in solutions and at surfaces

A new coarse-grained (CG) model is developed for water. Each CG unit consists of three charged sites, and there is an additional nonelectrostatic soft interaction between central sites on different units. The interactions are chosen to mimic the properties of 4-water clusters in atomistic simulations: the nonelectrostatic component is modeled using a modified Born−Mayer−Huggins potential, and the charges are chosen to reproduce the dipole moment and quadrupole moment tensor of 4-water clusters from atomistic simulations. The parameters are optimized to reproduce experimental data for the compressibility, density, and permittivity of bulk water and the surface tension and interface potential for the air−water interface. This big multipole water (BMW) model represents a qualitative improvement over existing CG water models; for example, it reproduces the dipole potential in membrane−water interface when compared to experiment, with modest additional computational cost as compared to the popular MARTINI CG m...

A new coarse-grained model for water: the importance of electrostatic interactions.

The effect of salt on the dynamics of water molecules follows the Hofmeister series. For some “structure-making” salts, the self-diffusion coefficient of the water molecules, D, decreases with increasing salt concentration. For other “structure-breaking” salts, D increases with increasing salt concentration. In this work, the concentration and temperature dependence of the self-diffusion of water in electrolyte solutions is studied using molecular dynamics simulations and pulsed-field-gradient NMR experiments; temperature-dependent viscosities are also independently measured. Simulations of rigid, nonpolarizable models at room temperature show that none of the many models tested can reproduce the experimentally observed trend for the concentration dependence of D; that is, the models predict that D decreases with increasing salt concentration for both structure-breaking and structure-making salts. Predictions of polarizable models are not in agreement with experiment either. These results suggest that man...

Self-diffusion and viscosity in electrolyte solutions.

A theory for nonuniform polymer melts is presented, which combines density functional theory with Monte Carlo methods. The theory treats the ideal gas functional exactly via a single chain simulation and uses the weighted density approximation for the excess free energy functional. The bulk fluid properties required in the theory are obtained from a generalized Flory equation of state. The predictions of the theory are compared to Monte Carlo simulations for the density profiles of semiflexible polymer melts confined between flat plates. Good agreement between theory and simulation is found for 3mers and 20mers and for several densities and molecular stiffnesses.

Arun Yethiraj

Papers

A new coarse-grained model for water: the importance of electrostatic interactions.

Self-diffusion and viscosity in electrolyte solutions.

Monte Carlo density functional theory of nonuniform polymer melts

Monte-Carlo simulation of polymers confined between flat plates

Effect of macromolecular crowding on reaction rates: a computational and theoretical study.