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

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

LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

Numerical Initial Value Problems in Ordinary Differential Equations

https://www.cell.com/biophysj/pdf/S0006-3495(10)00228-6.pdf

A Multiscale Red Blood Cell Model with Accurate Mechanics, Rheology, and Dynamics

The viscosity of blood has long been used as an indicator in the understanding and treatment of disease, and the advent of modern viscometers allows its measurement with ever-improving clinical convenience. However, these advances have not been matched by theoretical developments that can yield a quantitative understanding of blood’s microrheology and its possible connection to relevant biomolecules (e.g., fibrinogen). Using coarse-grained molecular dynamics and two different red blood cell models, we accurately predict the dependence of blood viscosity on shear rate and hematocrit. We explicitly represent cell–cell interactions and identify the types and sizes of reversible rouleaux structures that yield a tremendous increase of blood viscosity at low shear rates. We also present the first quantitative estimates of the magnitude of adhesive forces between red cells. In addition, our simulations support the hypothesis, previously deduced from experiments, of yield stress as an indicator of cell aggregation. This non-Newtonian behavior is analyzed and related to the suspension’s microstructure, deformation, and dynamics of single red blood cells. The most complex cell dynamics occurs in the intermediate shear rate regime, where individual cells experience severe deformation and transient folded conformations. The generality of these cell models together with single-cell measurements points to the future prediction of blood-viscosity anomalies and the corresponding microstructures associated with various diseases (e.g., malaria, AIDS, and diabetes mellitus). The models can easily be adapted to tune the properties of a much wider class of complex fluids including capsule and vesicle suspensions.

/pdf/predicting-human-blood-viscosity-in-silico-2oviebiggo.pdf

Predicting human blood viscosity in silico

: The authors discuss the creation of a finite element program suitable for solving incompressible, viscous free surface problems in steady axisymmetric or plane flows. For convenience in extending program capability to non-Newtonian flow, non-zero Reynolds numbers, and transient flow, a Galerkin formulation of the governing equations is chosen, rather than an extremum principle. The resulting program is used to solve the Newtonian die-swell problem for creeping jets free of surface tension constraints. The authors conclude that a Newtonian jet expands about 13%, in substantial agreement with experiments made with both small finite Reynolds numbers and small ratios of surface tension to viscous forces. The solutions to the related stick-slip problem and the tube inlet problem, both of which also contain stress singularities, are also given. (Modified author abstract)

The solution of viscous incompressible jet and free-surface flows using finite-element methods

Systematic coarse-graining of spectrin-level red blood cell models

Blood is modeled as a suspension of red blood cells using the dissipative particle dynamics method. The red blood cell membrane is coarse-grained for efficient simulations of multiple cells, yet accurately describes its viscoelastic properties. Blood flow in microtubes ranging from 10 to 40 lm in diameter is simulated in three dimensions for values of hematocrit in the range of 0.15–0.45 and carefully compared with available experimental data. Velocity profiles for different hematocrit values show an increase in bluntness with an increase in hematocrit. Red blood cell center-of-mass distributions demonstrate cell migration away from the wall to the tube center. This results in the formation of a cell-free layer next to the tube wall corresponding to the experimentally observed Fahraeus and Fahraeus–Lindqvist effects. The predicted cell-free layer widths are in agreement with those found in in vitro experiments; the results are also in qualitative agreement with in vivo experiments. However, additional features have to be taken into account for simulating microvascular flow, e.g., the endothelial glycocalyx. The developed model is able to capture blood flow properties and provides a computational framework at the mesoscopic level for obtaining realistic predictions of blood flow in microcirculation under normal and pathological conditions.

/pdf/blood-flow-and-cell-free-layer-in-microvessels-2sbrl6uuf9.pdf

Bruce Caswell

Papers

A Multiscale Red Blood Cell Model with Accurate Mechanics, Rheology, and Dynamics

Predicting human blood viscosity in silico

The solution of viscous incompressible jet and free-surface flows using finite-element methods

Systematic coarse-graining of spectrin-level red blood cell models

Blood Flow and Cell-Free Layer in Microvessels