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.

A general and detailed analysis is given of the phenomenon of chemically‐induced dynamic electron polarization (CIDEP) by means of the stochastic‐Liouville method in accordance with the earlier preliminary report. The finite‐difference technique employed permits rapid and convergent solutions without requiring any untoward assumptions on the nature of the models. The dependence of the polarization on the exchange interactionJ(r), the Larmor frequency differences between the interacting pair of radicals, diffusion rates, and rates of spin‐selective chemical reactions are given in detail. It is shown that models in which J(r) is taken to decay exponentially with r, the radical‐separation distance of the radical pair, yield results which are distinctly different from those for a contact exchange model, when J 0 [the value of J(r) when r is at the distance of closest approach] is appreciable. The former, more realistic model yields substantial polarizations asymptotically independent of J 0, but larger the slower the decrease of J(r) with r; the contact exchange model, however, rapidly goes to zero with increasing J 0. These asymptotic values of polarization are predicted to be as high as 10–40 times the equilibrium polarizations (P eq) for sensible values of the relevant parameters, while for values of J 0 yielding maximum polarizations (generated at the formative reaction), they can be greater than 100 P eq. These results are of the correct order for agreement with recent experiments. The polarizations have been related to the CIDEP intensities that one may observe for typical schemes of radical production, reaction, and relaxation in order to allow a comparison of the theoretical predictions with experiment.

Theory of chemically induced dynamic electron polarization. I

It is shown how the analysis of Freed et al. for ESR lineshapes in the slow tumbling region may be generalized to include anisotropic liquids. Particular emphasis is given to the case of nitroxide radicals in liquid crystal environments with cylindrically symmetric restoring potentials U (β). It is found that when |U(β)|≲ kT, spectral appearances are qualitatively (but not quantitatively) similar to those for isotropic liquids. In particular, the spectra are sensitive to the model of reorientation. They are also predicted to be a very sensitive indicator of effects of anisotropic viscosity. The analysis given for the motional narrowing region yields analytic expressions for the needed spectral densities, where previously only numerical results had been obtained. The analytic expressions are valid when |U(β)|≲ kT. Analytic solutions to the rotational diffusion equation appropriate for |U(β)|≫kT are given and it is outlined how they may be applied to magnetic resonance.

ESR line shapes in the slow‐motional region: Anisotropic liquids

Analysis of protein-lipid interactions based on model simulations of electron spin resonance spectra

The effects of internal rotations of methyl groups on ESR hyperfine lines are analyzed in terms of a quantum‐mechanical description of the motion. The classical description of rotational averaging is replaced by (1) spin—rotational coupling from a hyperfine operator, and (2) rotational relaxation by thermal collisions. In the absence of collisions, the effects of (1) lead to a static set of splittings whose values depend upon the relative magnitudes of the hyperfine‐versus‐tunneling frequencies. In the presence of frequent collisions, represented by a strong‐collision model, the effects of (1) lead to line broadening, the detailed nature of which also depends on the hyperfine‐versus‐tunneling frequencies. In general, results predicted from a classical treatment of the motion are obtained when the hyperfine frequency is significantly greater, while quantum effects become important for relatively larger tunneling frequencies. The results are illustrated by application to relevant experimental observations. In the Appendix, the strong‐collision relaxation theory is generalized to apply to the present case where the spin—rotational coupling connects states of different nuclear spin symmetry.

Quantum Effects of Methyl-Group Rotations in Magnetic Resonance: ESR Splittings and Linewidths

A new method is presented to denoise 1-D experimental signals using wavelet transforms. Although the state-of-the-art wavelet denoising methods perform better than other denoising methods, they are not very effective for experimental signals. Unlike images and other signals, experimental signals in chemical and biophysical applications, for example, are less tolerant to signal distortion and under-denoising caused by the standard wavelet denoising methods. The new method: 1) provides a method to select the number of decomposition levels to denoise; 2) uses a new formula to calculate noise thresholds that does not require noise estimation; 3) uses separate noise thresholds for positive and negative wavelet coefficients; 4) applies denoising to the approximation component; and 5) allows the flexibility to adjust the noise thresholds. The new method is applied to continuous wave electron spin resonance spectra and it is found that it increases the signal-to-noise ratio (SNR) by more than 32 dB without distorting the signal, whereas standard denoising methods improve the SNR by less than 10 dB and with some distortion. In addition, its computation time is more than six times faster.

Jack H. Freed

Papers

Theory of chemically induced dynamic electron polarization. I

ESR line shapes in the slow‐motional region: Anisotropic liquids

Analysis of protein-lipid interactions based on model simulations of electron spin resonance spectra

Quantum Effects of Methyl-Group Rotations in Magnetic Resonance: ESR Splittings and Linewidths

A New Wavelet Denoising Method for Selecting Decomposition Levels and Noise Thresholds