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 formulation is presented for calculating double quantum two dimensional electron spin resonance (DQ-2D ESR) spectra in the rigid limit that correspond to recent experimental DQ-2D ESR spectra obtained from a nitroxide biradical. The theory includes the dipolar interaction between the nitroxide moieties as well as the fully asymmetric g and hyperfine tensors and the angular geometry of the biradical. The effects of arbitrary pulses (strong but not truly nonselective pulses) are included by adapting the recently introduced split Hamiltonian theory for numerical simulations. It is shown how arbitrary pulses in magnetic resonance create “forbidden” coherence pathways, and their role in DQ-2D ESR is delineated. The high sensitivity of these DQ-2D ESR signals to the strength of the dipolar interaction is demonstrated and rationalized in terms of the orientational selectivity of the “forbidden” pathways. It is further shown that this selectivity also provides constraints on the structural geometry (i.e., the orientations of the nitroxide moieties) of the biradicals. The theory is applied to the recent double quantum modulation (DQM) experiment on an end-labeled poly-proline peptide biradical. A distance of 18.5 A between the ends is found for this biradical. A new two pulse double quantum experiment is proposed (by analogy to recent NMR experiments), and its feasibility for the ESR case is theoretically explored.

https://www.acert.cornell.edu/PDFs/JChemPhys107_1317_1997.pdf

Theory of double quantum two-dimensional electron spin resonance with application to distance measurements

Motional effects can easily be incorporated into calculated spin echo decay envelopes by idealizing the effects of the pulses and by using the stochastic Liouville equation (SLE) to govern the time dependence of the density matrix between pulses. The spectral representation of the 90°‐τ‐180°‐τ envelope is: Σl,mal,mexp[−(Λl+Λ*m)τ], where Λl is the lth eigenvalue of the SLE matrix, and al,m are products of relevant components of eigenvectors. The long time (large τ) phase memory time T∞m is equal to (Re Λ1)−1, where Λ1 is the smallest eigenvalue. For an axially symmetric g‐tensor case in the slow motional region, T∞m/τR≂ 3‖FτR‖−1/2, 2‖FτR‖−1/3, and 1, for Brownian, free, and jump diffusion models, respectively, with F≡2βeH0(g∥−g⊥)/3ℏ and τR the rotational correlation time. Analogous results hold for nitroxides having nuclear hyperfine tensors. The echo results are compared with simple methods of measuring τR from cw spectra. The overall shape of the echo envelopes in the slow motional region is exp(−bF2τ3/τ...

Analysis of electron spin echoes by spectral representation of the stochastic Liouville equation

We have observed narrow, distinct resonances in the NMR spectrum of dilute spinpolarized atomic hydrogen gas ($n\ensuremath{\sim}{10}^{16}$ atoms/${\mathrm{cm}}^{3}$). The dependence of the observed spectra on temperature, density, polarization, and magnetic field gradient is consistent with theoretical predictions for spin-wave excitations damped by diffusion. We have measured the parameter $\ensuremath{\mu}$, which is a measure of the importance of exchange effects in spin-transport processes, and the diffusion coefficient ${D}_{0}$, both of which are in reasonable agreement with theory.

/pdf/observation-of-nuclear-spin-waves-in-spin-polarized-atomic-6uj75fzyxk.pdf

Observation of Nuclear Spin Waves in Spin-Polarized Atomic Hydrogen Gas

We describe our pulsed two‐dimensional Fourier transform ESR experiment and demonstrate its applicabilty for the double resonance of motionally narrowed nitroxides. Multiple pulse irradiation of the entire nitroxide spectrum enables the correlation of two precessional periods, allowing observation of cross correlations between hyperfine lines introduced by magnetization transfer in the case of a three‐pulse experiment (2D ELDOR), or coherence transfer in the case of a two‐pulse experiment (COSY). Cross correlations are revealed by the presence of cross peaks which connect the autocorrelation lines appearing along the diagonal ω1=ω2. The amplitudes of these cross peaks are determined by the rates of magnetization transfer in the 2D ELDOR experiment. The density operator theory for the experiment is outlined and applied to the determination of Heisenberg exchange (HE) rates in 2,2,6,6‐tetramethyl‐4‐piperidone‐N‐oxyl‐d15 (PD‐tempone) dissolved in toluene‐d8. The quantitative accuracy of this experiment is established by comparison with the HE rate measured from the dependence of the spin echo T2 on nitroxide concentration.

Two‐dimensional Fourier transform ESR correlation spectroscopy

We demonstrate the use of pulsed ESR spectroscopy to measure intramolecular distances in the Parkinson's disease-associated protein alpha-synuclein bound to detergent and lysophospholipid micelles We show that the inter-helical separation between the two helices formed upon binding to micelles is dependent on micelle composition, with micelles formed from longer acyl chains leading to an increased splaying of the two helices Our data suggest that the topology of alpha-synuclein is not strongly constrained by the linker region between the two helices and instead depends on the geometry of the surface to which the protein is bound

Jack H. Freed

Papers

Theory of double quantum two-dimensional electron spin resonance with application to distance measurements

Analysis of electron spin echoes by spectral representation of the stochastic Liouville equation

Observation of Nuclear Spin Waves in Spin-Polarized Atomic Hydrogen Gas

Two‐dimensional Fourier transform ESR correlation spectroscopy

Inter-Helix Distances in Lysophospholipid Micelle-Bound α-Synuclein from Pulsed ESR Measurements