https://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf

Fast parallel algorithms for short-range molecular dynamics

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.

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。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the one-electron states, (b) exact energy minimization and hence calculation of the exact Hellmann-Feynman forces after each molecular-dynamics step using preconditioned conjugate-gradient techniques, (c) accurate nonlocal pseudopotentials, and (d) Nos\'e dynamics for generating a canonical ensemble. This method gives perfect control of the adiabaticity of the electron-ion ensemble and allows us to perform simulations over more than 30 ps. The computer-generated ensemble describes the structural, dynamic, and electronic properties of liquid and amorphous Ge in very good agreement with experiment. The simulation allows us to study in detail the changes in the structure-property relationship through the metal-semiconductor transition. We report a detailed analysis of the local structural properties and their changes induced by an annealing process. The geometrical, bonding, and spectral properties of defects in the disordered tetrahedral network are investigated and compared with experiment.

Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium.

/pdf/self-assembled-monolayers-of-thiolates-on-metals-as-a-form-1neb0hj3k4.pdf

Self-assembled monolayers of thiolates on metals as a form of nanotechnology.

We present an extensive molecular‐dynamics simulation for a bead spring model of a melt of linear polymers. The number of monomers N covers the range from N=5 to N=400. Since the entanglement length Ne is found to be approximately 35, our chains cover the crossover from the nonentangled to the entangled regime. The Rouse model provides an excellent description for short chains N<Ne, while the dynamics of the long chains can be described by the reptation model. By mapping the model chains onto chemical species we give estimates of the times and distances of onset of the slowing down in motion due to reptation. Comparison to neutron spin‐echo data confirm our mapping procedure, resolving a discrepancy between various experiments. By considering the primitive chain we are able to directly visualize the confinement to a tube. Analyzing the Rouse mode relaxation allows us to exclude the generalized Rouse models, while the original reptation prediction gives a good description of the data.

Dynamics of entangled linear polymer melts: A molecular‐dynamics simulation

We describe an efficient and general algorithm for simulating polymers, which can be used for single, large chains as well as many-chain systems. It allows us to distinguish solvent effects from interchain effects on the dynamics of the chains. The method is tested for linear and cyclic chains of 50 to 200 monomers. We have confirmed two theoretical results which have not been observed numerically or experimentally, namely the anomalous behavior of S(q) for rings and the ${t}^{0.54}$ power law for the motion of a monomer in a self-avoiding chain undergoing Rouse relaxation.

Molecular dynamics simulation for polymers in the presence of a heat bath.

The free-volume model, which has been useful for describing the behavior of the viscosity $\ensuremath{\eta}$ of dense liquids and glasses, is extended to account for their thermodynamic behavior as well. Experimental results for the heat capacity ${C}_{p}$ and the volume $\overline{v}$ show that the system falls out of complete, metastable thermodynamic equilibrium at the glass transition temperature ${T}_{g}$. As a first step in understanding these universal phenomena, a theory of the underlying metastable phase, the amorphous phase, is developed. Recent molecular-dynamic calculations demonstrating the existence of a cellular structure in liquids and the properties of the local free energy of the molecular cells permit us to formulate more precisely and justify in more detail the standard free-volume model. In particular, it is possible to define the free volume and distinguish solid-like and liquidlike cells. This leads to the introduction of percolation theory, which is used to describe the gradual development of the communal entropy of the amorphous phase. We then determine the probability distribution of the cellular volume as a function of the fraction of liquidlike cells, $p$. The equilibrium liquid-glass transition is associated with the increase of $p$ with temperature. This occurs via a phase transition which is most probably first order. The results of our theory give a generalized equation for the viscosity which agrees accurately with experimental results at all temperatures. Results for ${C}_{p}$ and $\overline{v}$ are also obtained. This equilibrium theory can provide the basis for a relaxation theory of the kinetic effects observed around and below ${T}_{g}$. The relationship between the entropy theory and the free-volume model is also clarified.

Liquid-glass transition, a free-volume approach

Computer simulation of grain growth—I. Kinetics

We have performed a systematic, large-scale simulation study of granular media in two and three dimensions, investigating the rheology of cohesionless granular particles in inclined plane geometries, i.e., chute flows. We find that over a wide range of parameter space of interaction coefficients and inclination angles, a steady-state flow regime exists in which the energy input from gravity balances that dissipated from friction and inelastic collisions. In this regime, the bulk packing fraction (away from the top free surface and the bottom plate boundary) remains constant as a function of depth z, of the pile. The velocity profile in the direction of flow vx(z) scales with height of the pile H, according to vx(z) proportional to H(alpha), with alpha=1.52+/-0.05. However, the behavior of the normal stresses indicates that existing simple theories of granular flow do not capture all of the features evidenced in the simulations.

/pdf/granular-flow-down-an-inclined-plane-bagnold-scaling-and-4056jr0hsg.pdf

Gary S. Grest

Papers

Dynamics of entangled linear polymer melts: A molecular‐dynamics simulation

Molecular dynamics simulation for polymers in the presence of a heat bath.

Liquid-glass transition, a free-volume approach

Computer simulation of grain growth—I. Kinetics

Granular flow down an inclined plane: Bagnold scaling and rheology