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.

Three nitroxide spin probes of different sizes and geometrical shape were used in a 250 GHz ESR study of the probe rotational dynamics in the fragile glass former ortho-terphenyl (OTP) over a wide temperature range from 380 to 180 K. Comparative studies at 9.5 GHz have also been performed. Perdeuterated 2,2′,6,6′-tetramethyl-4-methyl aminopiperidinyl-N-oxide (MOTA), and 3,3-dimethyloxazolidinyl-N-oxy-2′,3-5α-cholestane (CSL) are, respectively, comparable in size to and larger than the OTP host molecule, whereas Perdeuterated 2,2′,6,6′-tetramethyl-4-piperidine-N-oxide (PDT) is substantially smaller. The sensitivity of 250 GHz ESR to the details of the rotational tumbling for T≳Tc (where Tc is the crossover temperature) was exploited to show that the relaxation is fit by a model that is characteristic of a homogeneous liquid. A nonlinear least-squares analysis shows that below the melting point, Tm, CSL, and MOTA dynamics are well-described by a model of dynamic cage relaxation proposed by Polimeno and Free...

A 250 GHz ESR study of o-terphenyl: Dynamic cage effects above Tc

Multifrequency electron spin resonance (ESR) spectra provide a wealth of structural and dynamic information about the local environment of the spin label and, indirectly, about the spin-labeled protein Relating the features of the observed spectra to the underlying molecular motions and interactions is, however, challenging To make progress toward a rigorous interpretation of ESR spectra, we perform extensive molecular dynamics (MD) simulations of fully solvated T4 Lysozyme, labeled with the spin label MTSSL at positions 72 and 131 These two sites have been the object of numerous experimental studies and are generally considered as prototypical solvent-exposed sites on the surfaces of alpha-helices To extend the time window afforded by the MD simulations, stochastic Markov models reflecting the dynamics of the spin label side chains in terms of their rotameric states are constructed from the trajectories The calculated multifrequency ESR spectra are in very good agreement with experiment for three different magnetic field strengths without adjusting any parameters During the trajectories, the spin labels interconvert among a fairly large number of conformations and display a propensity to form interactions with protein residues other than their nearest neighbors along the helix The detailed picture of the spin label emerging from the MD simulations provides useful insight into the molecular origins of the available spectroscopic and crystallographic data

/pdf/multifrequency-electron-spin-resonance-spectra-of-a-spin-1neikeu2h1.pdf

Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations

It is found that a very powerful method for computing slow-motional ESR (and NMR) spectra may be developed by the use of the Lanczos algorithm (LA) modified to tridiagonalize complex-symmetric matrices. It leads to at least order of magnitude reductions in computation time and in computer storage requirements than the commonly used Rutishauser algorithm. This permits the rapid analysis of spectral problems that were previously too difficult. The formal similarity of these problems to those from Fokker-Planck equations in molecular dynamics suggests that the LA should also be a very powerful method for the latter.

/pdf/efficient-computation-of-magnetic-resonance-spectra-and-16vp1ow2qt.pdf

Efficient computation of magnetic resonance spectra and related correlation functions from stochastic Liouville equations

https://www.acert.cornell.edu/PDFs/JMagnReson165_116_2003.pdf

High resolution electron spin resonance microscopy.

Viral fusogens merge viral and cell membranes during cell penetration. Their ectodomains drive fusion by undergoing large-scale refolding, but little is known about the functionally important regions located within or near the membrane. Here we report the crystal structure of full-length glycoprotein B (gB), the fusogen from herpes simplex virus, complemented by electron spin resonance measurements. The membrane-proximal (MPR), transmembrane (TMD), and cytoplasmic (CTD) domains form a uniquely folded trimeric pedestal beneath the ectodomain, which balances dynamic flexibility with extensive, stabilizing membrane interactions. The postfusion conformation of the ectodomain suggests that the CTD likewise adopted the postfusion form. However, hyperfusogenic mutations, which destabilize the prefusion state of gB, target key interfaces and structural motifs that reinforce the observed CTD structure. Thus, a similar CTD structure must stabilize gB in its prefusion state. Our data suggest a model for how this dynamic, membrane-dependent 'clamp' controls the fusogenic refolding of gB.

/pdf/structural-basis-for-membrane-anchoring-and-fusion-yqnat3wsyi.pdf

Jack H. Freed

Papers

A 250 GHz ESR study of o-terphenyl: Dynamic cage effects above Tc

Multifrequency electron spin resonance spectra of a spin-labeled protein calculated from molecular dynamics simulations

Efficient computation of magnetic resonance spectra and related correlation functions from stochastic Liouville equations

High resolution electron spin resonance microscopy.

Structural basis for membrane anchoring and fusion regulation of the Herpes Simplex Virus fusogen gB