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

Use of amphiphilic triblock copolymers to direct the organization of polymerizing silica species has resulted in the preparation of well-ordered hexagonal mesoporous silica structures (SBA-15) with uniform pore sizes up to approximately 300 angstroms. The SBA-15 materials are synthesized in acidic media to produce highly ordered, two-dimensional hexagonal (space group p6mm) silica-block copolymer mesophases. Calcination at 500°C gives porous structures with unusually large interlattice d spacings of 74.5 to 320 angstroms between the (100) planes, pore sizes from 46 to 300 angstroms, pore volume fractions up to 0.85, and silica wall thicknesses of 31 to 64 angstroms. SBA-15 can be readily prepared over a wide range of uniform pore sizes and pore wall thicknesses at low temperature (35° to 80°C), using a variety of poly(alkylene oxide) triblock copolymers and by the addition of cosolvent organic molecules. The block copolymer species can be recovered for reuse by solvent extraction with ethanol or removed by heating at 140°C for 3 hours, in both cases, yielding a product that is thermally stable in boiling water.

Triblock copolymer syntheses of mesoporous silica with periodic 50 to 300 angstrom pores

This paper reviews recent experimental and theoretical progress concerning many-body phenomena in dilute, ultracold gases. It focuses on effects beyond standard weak-coupling descriptions, such as the Mott-Hubbard transition in optical lattices, strongly interacting gases in one and two dimensions, or lowest-Landau-level physics in quasi-two-dimensional gases in fast rotation. Strong correlations in fermionic gases are discussed in optical lattices or near-Feshbach resonances in the BCS-BEC crossover.

/pdf/many-body-physics-with-ultracold-gases-552s10zfdn.pdf

Many-Body Physics with Ultracold Gases

We critically review dissipative particle dynamics (DPD) as a mesoscopic simulation method. We have established useful parameter ranges for simulations, and have made a link between these parameters and χ-parameters in Flory-Huggins-type models. This is possible because the equation of state of the DPD fluid is essentially quadratic in density. This link opens the way to do large scale simulations, effectively describing millions of atoms, by firstly performing simulations of molecular fragments retaining all atomistic details to derive χ-parameters, then secondly using these results as input to a DPD simulation to study the formation of micelles, networks, mesophases and so forth. As an example application, we have calculated the interfacial tension σ between homopolymer melts as a function of χ and N and have found a universal scaling collapse when σ/ρkBTχ0.4 is plotted against χN for N>1. We also discuss the use of DPD to simulate the dynamics of mesoscopic systems, and indicate a possible problem with...

https://www.physics.iitm.ac.in/~iol/lecture_notes/groot-warren.pdf

Dissipative particle dynamics : bridging the gap between atomistic and mesoscopic simulation

Using self-consistent field theory, we examine microphases of diblock copolymers and find, in addition to lamellar, hexagonal, and cubic phases, a stable gyroid phase which occurs between the lamellar and hexagonal ones. It terminates at a triple point, with a lamellar to hexagonal transition occurring in the weak-segregation limit. Other phases of experimental interest are studied, and we describe the regions in which they are most nearly stable.

Stable and unstable phases of a diblock copolymer melt

This paper presents a systematic classification of multilayer-adsorption phenomena on attractive substrates, with emphasis on the buildup of thick films. The approach is based on statistical mechanics and includes adsorption-desorption effects and the interrelation of bulk and surface behavior. The surface phase diagram depends qualitatively on the relative strengths and ranges of adatom-adatom and adatom-substrate attractions. When the adatom-substrate attraction dominates (strong substrate), the film builds up uniformly, as the bulk adatom density increases, and the excess surface density diverges at coexistence (complete wetting). The buildup proceeds via an infinite sequence of discrete layer transitions (layering) at low temperatures (below the roughening temperature ${T}_{R}$ and smoothly at higher temperatures, as originally noted by de Oliveira and Griffiths. Substrates of intermediate strength are characterized by a wetting temperature ${T}_{W}$ above which wetting at coexistence is approached. The relative values of ${T}_{W}$ and ${T}_{R}$ define three subregions: When ${T}_{W}l{T}_{R}$ layering occurs, with an infinite sequence of transitions between ${T}_{W}$ and ${T}_{R}$ when ${T}_{R}\ensuremath{\lesssim}{T}_{W}$, layer transitions have coalesced into a single thick-film\char22{}thin-film transition (prewetting); when ${T}_{R}\ensuremath{\ll}{T}_{W}$, prewetting may disappear, leaving only a critical-wetting transition on the coexistence axis. For still weaker substrates, wetting is incomplete at all temperatures; however, a variety of drying phenomena may occur on the high-density side of bulk coexistence. Specific calculations are given for a lattice-gas model at $T=0$ and in the mean-field approximation. Conclusions are informed, in addition, by certain exact results and symmetries. The last section includes a critical discussion of the relation of the lattice-gas model to the real world and a brief review of relevant experimental data.

Systematics of multilayer adsorption phenomena on attractive substrates

https://faculty.washington.edu/schick/Abstracts/aurelia45.pdf

Line Tensions, Correlation Lengths, and Critical Exponents in Lipid Membranes Near Critical Points

http://www.mrl.ucsb.edu/%7Ekatsov/pubs/pub024.pdf

Biological and synthetic membranes: What can be learned from a coarse-grained description?

Self-assembling Systems - Surfactants Lipids Fluid Mixtures - Binary and Ternary Systems Containing Amphiphile lnterfaces - Liquid-liquid Theories of Interfaces, Surface Phase Transitions Wetting Membranes.

Michael Schick

Papers

Stable and unstable phases of a diblock copolymer melt

Systematics of multilayer adsorption phenomena on attractive substrates

Line Tensions, Correlation Lengths, and Critical Exponents in Lipid Membranes Near Critical Points

Biological and synthetic membranes: What can be learned from a coarse-grained description?

Self-assembling amphiphilic systems