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

1. Introduction 20642. Synthesis of Magnetic Nanoparticles 20662.1. Classical Synthesis by Coprecipitation 20662.2. Reactions in Constrained Environments 20682.3. Hydrothermal and High-TemperatureReactions20692.4. Sol-Gel Reactions 20702.5. Polyol Methods 20712.6. Flow Injection Syntheses 20712.7. Electrochemical Methods 20712.8. Aerosol/Vapor Methods 20712.9. Sonolysis 20723. Stabilization of Magnetic Particles 20723.1. Monomeric Stabilizers 20723.1.1. Carboxylates 20733.1.2. Phosphates 20733.2. Inorganic Materials 20733.2.1. Silica 20733.2.2. Gold 20743.3. Polymer Stabilizers 20743.3.1. Dextran 20743.3.2. Polyethylene Glycol (PEG) 20753.3.3. Polyvinyl Alcohol (PVA) 20753.3.4. Alginate 20753.3.5. Chitosan 20753.3.6. Other Polymers 20753.4. Other Strategies for Stabilization 20764. Methods of Vectorization of the Particles 20765. Structural and Physicochemical Characterization 20785.1. Size, Polydispersity, Shape, and SurfaceCharacterization20795.2. Structure of Ferro- or FerrimagneticNanoparticles20805.2.1. Ferro- and Ferrimagnetic Nanoparticles 20805.3. Use of Nanoparticles as Contrast Agents forMRI20825.3.1. High Anisotropy Model 20845.3.2. Small Crystal and Low Anisotropy EnergyLimit20855.3.3. Practical Interests of Magnetic NuclearRelaxation for the Characterization ofSuperparamagnetic Colloid20855.3.4. Relaxation of Agglomerated Systems 20856. Applications 20866.1. MRI: Cellular Labeling, Molecular Imaging(Inﬂammation, Apoptose, etc.)20866.2.

Magnetic Iron Oxide Nanoparticles: Synthesis, Stabilization, Vectorization, Physicochemical Characterizations, and Biological Applications

The endoplasmic reticulum (ER) responds to the accumulation of unfolded proteins in its lumen (ER stress) by activating intracellular signal transduction pathways - cumulatively called the unfolded protein response (UPR). Together, at least three mechanistically distinct arms of the UPR regulate the expression of numerous genes that function within the secretory pathway but also affect broad aspects of cell fate and the metabolism of proteins, amino acids and lipids. The arms of the UPR are integrated to provide a response that remodels the secretory apparatus and aligns cellular physiology to the demands imposed by ER stress.

Signal integration in the endoplasmic reticulum unfolded protein response

https://easyspin.org/pubs/easyspin_jmr06.pdf

EasySpin, a comprehensive software package for spectral simulation and analysis in EPR.

Author response: Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments

High-field EPR spectroscopy at 250 and 170 GHz was used to study polyaniline (PA) in the 100-300 K temperature range. Splitting of the EPR spectrum was observed which depended linearly on the magnetic field strength. The line shape for a PA sample was found to depend on the temperature. The spectra were simulated using the dynamic model of spin exchange.

The high-frequency EPR spectra of polyaniline : Line narrowing due to the spin exchange

We start with the time rate of change of the spin density matrix for a single spin system: 

$$\dot \sigma \left( {\rm{t}} \right) = - {\rm{i}}\left[ {H,\sigma } \right] \equiv - {\rm{i}}{H^ \times }\sigma $$

(1)

where H = H 0 + H 1 (t), and we use the Kubo2,3 notation for super-operators: A×, such that A×B = [A, B] We define an interaction representation by: 

$${\sigma ^\ddag }\left( {\rm{t}} \right) = {{\rm{e}}^{{\rm{i}}H_0^ \times {\rm{t}}}}\sigma = {{\rm{e}}^{{\rm{i}}{H_0}{\rm{t}}}}\sigma {{\rm{e}}^{ - {\rm{i}}{H_0}{\rm{t}}}}$$

(3)

and 

$$H_1^\ddag \left( {\rm{t}} \right) = {{\rm{e}}^{{\rm{i}}H_0^ \times {{\rm{t}}_{{H_1}}}}}\left( {\rm{t}} \right) = {{\rm{e}}^{{\rm{i}}{H_0}{{\rm{t}}_{{H_1}}}}}\left( {\rm{t}} \right){{\rm{e}}^{ - {\rm{i}}{H_0}{\rm{t}}}}$$

(4)

ESR Relaxation and Lineshapes from the Generalized Cumulant and Relaxation Matrix Viewpoint

aS 2 Suppl

A general overview of molecular dynamics in liquid crystals is presented, which will serve as the basis for our discussion of ESR experiments.

Jack H. Freed

Papers

Author response: Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments

The high-frequency EPR spectra of polyaniline : Line narrowing due to the spin exchange

ESR Relaxation and Lineshapes from the Generalized Cumulant and Relaxation Matrix Viewpoint

aS 2 Suppl

ESR And Liquid Crystals: Statistical Mechanics and Generalised Smoluchowski Equations