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.

https://www.acert.cornell.edu/PDFs/BiophysJ84_3364_2003.pdf

Lipid-gramicidin interactions: Dynamic structure of the boundary lipid by 2D-ELDOR

Two-dimensional Fourier transform (2D-FT) and CW-ESR experiments at X-band frequencies were performed over a broad range of temperatures covering the solid and melt states of a liquid crystalline (LC) polymer. The CW-ESR experiments were analyzed by conventional motional models. The nematic phase was macroscopically aligned in the dc magnetic field, whereas the solid state showed microscopic order but macroscopic disorder (MOMD). An end-label on the polymer showed smaller ordering and larger reorientational rates than that of the cholestane (CSL) spin probe dissolved in the same polymer, since the former can reorient by local internal chain modes. It was demonstrated that the 2D-FT-ESR experiments provide greatly enhanced resolution to the ordering and dynamics of the end-label, especially when performed as 2D-ELDOR (electron−electron double resonance) experiments as a function of mixing time. The conventional model of Brownian reorientation in an orienting potential was unsuccessful in interpreting these...

Molecular Dynamics of a Liquid Crystalline Polymer Studied by Two-Dimensional Fourier Transform and CW ESR

A coupled system of two molecules bearing spins of 1/2, which are allowed to diffuse relative to each other, is considered. By using a symmetry-adapted basis operator set, the overall density matrix equation is decoupled into two equations for the time-resolved isochromat components, the sum of which yields the observed signal. The appropriate stochastic Liouville equation is solved by a combination of eigenfunction expansion and finite-differences for the angular and radial relative motions, respectively. A full range of spectra from classic Pake patterns in the rigid limit to motionally narrowed Lorentzians is recovered. As an extension of the above approach, the solid-echo experiment is described in terms of the ensemble-averaged isochromats. Homogeneous transverse relaxation times (T2) as a function of the translational diffusion coefficient (DT) are obtained from simulating SECSY (spin-echo correlation spectroscopy) signals, which show distinct T2 minima vs DT. The present method of separating the qu...

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Spin relaxation by dipolar coupling: From motional narrowing to the rigid limit

The ESR relaxation of a weakly aligned spin probe dissolved in N-[$p$-methoxybenzylidine]-$p$-butylaniline has been studied near ${T}_{c}$, the isotropic-nematic transition. Spin relaxation due to critical orientational fluctuations is observed on either side of ${T}_{c}$ and is characterized by a symmetry about ${T}_{c}$ that is rather well explained by simple Landaude Gennes mean-field theory for the weak first-order transition.

Symmetry of Orientational Order Fluctuations about the Nematic-Isotropic Phase Transition: An ESR Study

A relatively simple method is developed whereby the many‐body features of a typical generalized Fokker–Planck equation (GFPE) for a diffusing molecule are first replaced by stochastic bath variables that are assumed to be Markovian. Then the combined molecular and bath variables are characterized as a multidimensional Markov process obeying a stochastic–Liouville equation, which is, in general, incomplete, because it ignores the back reaction of the molecule on the bath variables. In the final step, the equation is completed by subjecting it to the appropriate constraints required for detailed balance. In this form the augmented Fokker–Planck equation (AFPE) properly describes relaxation to thermal equilibrium, and, for the appropriate limiting conditions, it reduces to the classical Fokker–Planck equation. This procedure for stochastic modeling of GFPE is both an improvement on and a generalization of a method previously outlined by Hwang, Mason, Hwang, and Freed (HMHF). Detailed illustrations of AFPE’s ...

Jack H. Freed

Papers

Lipid-gramicidin interactions: Dynamic structure of the boundary lipid by 2D-ELDOR

Molecular Dynamics of a Liquid Crystalline Polymer Studied by Two-Dimensional Fourier Transform and CW ESR

Spin relaxation by dipolar coupling: From motional narrowing to the rigid limit

Symmetry of Orientational Order Fluctuations about the Nematic-Isotropic Phase Transition: An ESR Study

Stochastic modeling of generalized Fokker-Planck equations. I.