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.

Chapter 5 – two dimensional and fourier transform epr

Diphthamide, the target of diphtheria toxin, is a post-translationally modified histidine residue found in archaeal and eukaryotic translation elongation factor 2 (EF2). In the first step of diphthamide biosynthesis, a [4Fe-4S] cluster-containing radical SAM enzyme, Dph1-Dph2 heterodimer in eukaryotes or Dph2 homodimer in archaea, cleaves S-adenosylmethionine and transfers the 3-amino-3-carboxypropyl group to EF2. It was demonstrated previously that for the archaeal Dph2 homodimer, only one [4Fe-4S] cluster is necessary for the in vitro activity. Here, we demonstrate that for the eukaryotic Dph1-Dph2 heterodimer, the [4Fe-4S] cluster-binding cysteine residues in each subunit are required for diphthamide biosynthesis to occur in vivo. Furthermore, our in vitro reconstitution experiments with Dph1-Dph2 mutants suggested that the Dph1 cluster serves a catalytic role, while the Dph2 cluster facilitates the reduction of the Dph1 cluster by the physiological reducing system Dph3/Cbr1/NADH. Our results reveal the asymmetric functional roles of the Dph1-Dph2 heterodimer and may help to understand how the Fe-S clusters in radical SAM enzymes are reduced in biology.

The asymmetric function of Dph1–Dph2 heterodimer in diphthamide biosynthesis

Low-density gases, in which atoms are separated by large distances, have long provided an enjoyable playground for physicists. One might suppose the pleasure of the playground would by now have been exhausted by the very simplicity of low-density gases. Recent work by a number of investigators including the author shows that this is not the case low-density gases continue to serve up a rich variety of phenomena as well as counterintuitive surprises. In particular, the macroscopic properties of a gas composed of individual hydrogen or helium atoms can under special circumstances by changed dramatically by quantum-mechanical effects. According to quantum theory, the nucleus of an atom behaves in a way similar to a rotating top, which has angular momentum about its axis of rotation; that is, the nucleus has spin, known more precisely as spin angular momentum. If the atoms of a gas are spin-polarized, so that their nuclei all have their spins pointing in the same direction, the viscosity of the gas can be changed enormously and so can its ability to conduct heat. Quantum-mechanical correlations among the nuclei called spin waves, which up to now had been observed only in certain liquids and solids such as magnets, canmore » also arise. The changes are large enough for one to say the quantum-mechanical effects have caused the gas to take on entirely new properties. In a certain sense it is amazing to think that polarizing the nuclear spins can have any effect on the macroscopic properties of the gas, since the nuclear spins are son weakly coupled to the outside world. Yet the observations are in full agreement with with theory. Moreover, because spin-polarized gases are still fairly simple systems, they can be understood in terms fundamental principles, something that is still not possible to do in the case of liquids and solids.« less

The effects of spin in gases

An extended Hueckel analysis of O/sub 2//sup -/ adsorbed on Ti ions on oxide supports is presented. The potential energy surface is obtained for deformations between the two limiting structures of the O/sub 2//sup -/ parallel to the surface and end-on. A stable conformation is found for the parallel form, consistent with recent ESR results, and there is a maximum in energy between the two limiting structures. The observed near equality of the ESR hyperfine splittings of the two O atoms is found to be consistent with a small tilting of the O/sub 2/ axis from the parallel conformation (i.e., < 10/sup 0/). A low barrier for planar rotation of O/sub 2//sup -/ about the axis perpendicular to the surface is also found, consistent with the small activation energy obtained from ESR line-shape analysis. The predicted g-tensor components allow unambiguous assignment of the ESR results, and a discussion is given on how variations in the extended Hueckel parameters improve agreement with experiment. 5 figures, 1 table.

Molecular orbital study of superoxide (O2-) adsorbed on titanium ions on oxide supports

We have developed the microscopic-order-macroscopic-disorder (MOMD) approach for studying internal mobility in polycrystalline proteins with 2H lineshape analysis. The motion itself is expressed by a diffusion tensor, R, the local spatial restraints by a potential, u, and the "local geometry" by the relative orientation of the model-related and nuclear magnetic resonance-related tensors. Here, we apply MOMD to phenyl-ring dynamics in several Αβ40-amyloid-fibrils, and the villin headpiece subdomain (HP36). Because the available data are limited in extent and sensitivity, we adjust u and R in the relevant parameter ranges, fixing the "local geometry" in accordance with standard stereochemistry. This yields a physically well-defined and consistent picture of phenyl-ring dynamics, enabling comparison between different systems. In the temperature range of 278-308 K, u has a strength of (1.7-1.8) kT and a rhombicity of (2.4-2.6) kT, and R has components of 5.0 × 102 ≤ R⊥ ≤ 2.0 × 103 s-1 and 6.3 × 105 ≤ R∥ ≤ 2.0 × 106 s-1. At 278 K, fibril hydration increases the axiality of both u and R; HP36 hydration has a similar effect at 295 K, reducing R⊥ considerably. The D23N mutation slows down the motion of the probe; Aβ40 polymorphism affects both this motion and the related local potential. The present study identifies the impact of various factors on phenyl-ring mobility in amyloid fibrils and globular proteins; the difference between the two protein forms is considerable. The distinctive impact of hydration on phenyl-ring motion and previously studied methyl-group motion is also examined. The 2H lineshapes considered here were analyzed previously with various multi-simple-mode (MSM) models, where several simple motional modes are combined. The MOMD and MSM interpretations differ in essence.

Jack H. Freed

Papers

Chapter 5 – two dimensional and fourier transform epr

The asymmetric function of Dph1–Dph2 heterodimer in diphthamide biosynthesis

The effects of spin in gases

Molecular orbital study of superoxide (O2-) adsorbed on titanium ions on oxide supports

Phenyl-Ring Dynamics in Amyloid Fibrils and Proteins: The Microscopic-Order-Macroscopic-Disorder Perspective.