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.

/pdf/nonlinear-least-squares-analysis-of-slow-motion-epr-spectra-4bi7fsmovk.pdf

Nonlinear-least-squares analysis of slow-motion EPR spectra in one and two dimensions using a modified levenberg-marquardt algorithm

A general theory of the linewidths in the electron spin resonance spectra of dilute solutions of free radicals has been developed in terms of the relaxation‐matrix theory of Bloch, Redfield, and Ayant. In contrast to previous theories, it is shown that a composite line arising from a set of degenerate nuclear‐spin states should, in general, consist of a sum of superimposed lines of Lorentzian shape with different widths rather than a single line with an over‐all Lorentzian shape. A single Lorentzian line is still obtained, however, as a limiting case when the variation of the widths of the different components of a composite line is small compared to the average width. Although the non‐Lorentzian shape of a composite line is often difficult to observe experimentally, a number of other observable properties are predicted by the present development that are outside the scope of the previous theories. For example, linewidth effects resulting from differences in the widths of the separate components of a composite line are predicted that explain the alternation in the linewidths from one hyperfine line to another recently observed in the ESR spectra in certain free radicals. The detailed form of the relaxation matrix is presented for intramolecular anisotropic and isotropic electron—nuclear dipolar interactions, quadrupole interactions, and g‐tensor relaxations. Modulations of the spin density and hyperfine splittings are included, as are internal motions, and a number of cross terms between the different relaxation mechanisms arise. In general the relaxation matrix of a composite line contains significant off‐diagonal elements, and the determination of the linewidths requires the evaluation of the eigenvalues of the matrix. Problems involving rapid chemical exchange, or modulation by jumps to a small number of sites, can be treated by the relaxation‐matrix theory and, under special restrictions, by either the modified Bloch equations or the Anderson theory of motional narrowing. When applicable, these latter procedures can be used over the entire range of exchange rates, while the relaxation‐matrix theory is limited to fast rates only.

Theory of Linewidths in Electron Spin Resonance Spectra

It is shown how the equilibrium pair correlation function between spin‐bearing molecules in liquids may be incorporated as an effective force in the relative diffusion expressions, and how one may solve for the resulting time correlation functions and spectral densities needed for studies of spin relaxation by translational diffusion. The use of finite difference methods permits the solution no matter how complex the form of the pair correlation function (pcf) utilized. In particular, a Percus–Yevick pcf as well as one corrected from computer dynamics, both for hard spheres, are utilized. Good agreement with the experiments of Harmon and Muller on dipolar relaxation in liquid ethane is obtained from this analysis. Effects of ionic interactions in electrolyte solutions upon dipolar relaxation are also obtained in terms of Debye–Huckel theory for the pcf. Analytic solutions are given which are appropriate for the proper boundary‐value problem for the relative diffusion of molecules (i.e., a distance of mini...

Dynamic effects of pair correlation functions on spin relaxation by translational diffusion in liquids

Hwang and Freed have previously given solutions for the relative diffusion of molecules that include the proper boundary condition (i.e., an excluded volume due to a distance of minimum approach) which has usually been neglected in spin relaxation theories. In this work their results are extended to include effects of (1) one type of spin that is rapidly relaxing, (2) diffusion by jumps of finite size, and (3) frequency‐dependent diffusion coefficients in the theory of spin relaxation by intermolecular dipolar interactions. These results are mathematically simpler and sounder than those commonly employed. In particular, it is shown that for case (2) measurements of J (O), the zero‐frequency spectral density cannot solely be used to determine the jump size, in constrast to the Torrey theory, which did not consider the boundary‐value problem.

Dynamic effects of pair correlation functions on spin relaxation by translational diffusion in liquids. II. Finite jumps and independent T1 processes

https://www.acert.cornell.edu/PDFs/JMagnReson172_279_2005.pdf

Jack H. Freed

Papers

Nonlinear-least-squares analysis of slow-motion EPR spectra in one and two dimensions using a modified levenberg-marquardt algorithm

Theory of Linewidths in Electron Spin Resonance Spectra

Dynamic effects of pair correlation functions on spin relaxation by translational diffusion in liquids

Dynamic effects of pair correlation functions on spin relaxation by translational diffusion in liquids. II. Finite jumps and independent T1 processes

The determination of pair distance distributions by pulsed ESR using Tikhonov regularization.