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.

Recent studies on model and biological membranes by two-dimensional (2-D) electronelectron double resonance (ELDOR) are reviewed and discussed The studies include (1) the phase behavior of dispersions of phospholipid-cholesterol membrane vesicles; (2) the effect of the ion-channel-forming peptide gramicidin A on the lipid membrane; and (3) the effects of stimulation by antigen of the immunoglobulin E receptors in plasma membrane vesicles upon the lipid structure In the first studies it is shown that the 2-D ELDOR spectra enable clear distinctions amongst the different phases, and this leads to a reliable temperature and composition-dependent phase diagram In the second studies it is possible to distinguish bulk and boundary lipids and to describe their different dynamic structures In the third studies we could distinguish both liquid-ordered and liquid-disordered spectral components, and one finds that the fraction of the latter increases as a result of stimulation Emphasis is placed on the new “full Sc — method” of processing the 2-D ELDOR data to significantly enhance spectral resolution, which is particularly important in studying the spectra from coexisting phases or components In the full Sc — method, one utilizes both the real and imaginary parts of the signal, instead of their magnitude; the needed phase corrections are obtained as part of the nonlinear least-squares fitting of the 2-D ELDOR data

Two-dimensional ELDOR in the study of model and biological membranes

Two-dimensional electron-electron double resonance (2D-ELDOR) is a technique that is sensitive to the dynamical processes affecting spin labels in complex fluid environments. In ordered fluids, such as membrane vesicles, the 2D-ELDOR experiment is affected by the molecular tumbling in the locally ordered environment. This motion occurs on two different time scales, the faster molecular motion relative to the local director, and the slower collective fluctuations of the director field. In the experimental study of Patyal, Crepeau, and Freed (Biophys. J. 1997, 73, 2201), it was found that the widths of the autopeaks of the 2D-ELDOR spectrum increased as a function of the mixing time. In the present work, a theory is developed for the effects of director fluctuations on the autopeaks in the 2D-ELDOR experiment by employing an analytical solution of the stochastic Liouville equation for which the director field is treated as a multidimensional Gaussian process, as previously developed by Frezzato, Kothe, and Moro (J. Phys. Chem. B 2001, 105, 1281 and J. Phys. Chem. B 2004, 108, 9505). Good agreement is found between theory and experiment, notably the only adjustable parameter is , the bending elastic modulus of the membrane. The values of ) 11 10 -20 J for 1,2dipalmitoyl-sn-glycero-phosphatidylcholine (DPPC) vesicles and ) 15 10 -20 J for DPPC/gramicidin A (5:1) vesicles, both at 45 °C, were found from the analysis and agree well with previous related measurements by other physical techniques. This establishes 2D-ELDOR as a useful technique to study the elastic properties of biological membranes. Electron spin resonance (ESR) is a versatile spectroscopic technique that provides a wealth of information on the molecular structure of various paramagnetic systems. In addition, it can be used to characterize the dynamics of spin probes embedded in diamagnetic systems provided that the rotational motions modulate the magnetic interactions. This application, however, requires suitable theoretical tools for interpreting the effects of the molecular motions on the spectroscopic observables. The simplest situation is certainly that of a fast tumbling spin probe in an isotropic liquid, where the spectral line widths can be analyzed according to motional narrowing theory 1,2 based on a separate treatment of the reorientational motions and the dynamics of the spin degrees of freedom. A quite different approach is required in the absence of a time scale separation between the magnetic anisotropies (in frequency units) and the reorientational rates. In this case, a slow motion theory has to be employed involving a solution of the stochastic Liouville equation (SLE), 3-6 which describes the coupled evolution of the spin degrees of freedom and the stochastic variables for the probe orientation. This ensures a rather general treatment of the magnetization dynamics, albeit analytical solutions for the direct interpretation of experimental observables are not available. The standard solution procedure is based on a matrix representation of the SLE evolution operator to be generated by using a suitable basis for both the spin degrees of freedom and the functional dependence on the stochastic variables. 7 An algebraic solution can then be achieved by employing efficient algorithms to diagonalize this matrix. 8

/pdf/collective-fluctuations-in-ordered-fluids-investigated-by-xdw2vwyvg9.pdf

Collective fluctuations in ordered fluids investigated by two-dimensional electron-electron double resonance spectroscopy.

https://www.acert.cornell.edu/PDFs/JMagnReson188_231_2007.pdf

2D-ELDOR using full S(c-) fitting and absorption lineshapes.

The well-known result from the steady-state (s.s.) solution of the Bloch Equations is that the absorption is given by the y-component of magnetization ${{\rm{\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\smile$}}\over M} }}_{\rm{y}}}$ in the rotating frame: 

$${{\rm{\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\smile$}}\over M} }}_{\rm{y}}} = {{{\rm{\gamma }}{{\rm{H}}_1}{{\rm{T}}_2}} \over {1 + {{\left( {{{\rm{T}}_2}\Delta {\rm{\omega }}} \right)}^2} + {{\rm{\gamma }}^2}{\rm{H}}_1^2{{\rm{T}}_1}{{\rm{T}}_2}}}{{\rm{M}}_{\rm{0}}}$$

(1)

with M0 the equilibrium magnetization. When we switch to a quantum mechanical description, we can calculate: 

$${{\rm{M}}_ \pm } = {{\rm{M}}_{\rm{X}}} \pm {\rm{i}}{{\rm{M}}_{\rm{y}}} = \left( {{{{\rm{\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\smile$}}\over M} }}}_{\rm{x}}}{\rm{i}}{{{\rm{\mathord{\buildrel{\lower3pt\hbox{$\scriptscriptstyle\smile$}}\over M} }}}_{\rm{y}}}} \right){{\rm{e}}^{ \pm {\rm{i\omega t}}}}$$

(2)

statistically from its associated quantum mechanical operator 

$${{\rm{m}}_ \pm } = \Re {\rm{ }}{{\rm{Y}}_{\rm{e}}}{\rm{S}}{{\rm{ }}_ \pm }$$

(3)

where ℜ is the concentration of electron spins, by taking a trace of the spin density matrix σ(t) with the spin operator S±: 

$${{\rm{M}}_ \pm }\left( {\rm{t}} \right) = \Re {{\rm{Y}}_{\rm{e}}}{\rm{ Tr}}\left[ {{\rm{\sigma }}\left( {\rm{t}} \right){{\rm{S}}_ \pm }} \right]$$

(4)

The trace is invariant to a choice of zero-order basis states. The equation of motion for σ(t) is taken to be the relaxation matrix form given by Eq. VIII-20, and we shall neglect effects of higher order than R(2).

ESR Saturation and Double Resonance in Liquids

Exchange processes which include conformational change, protonation/deprotonation, and binding equilibria are routinely studied by 2D exchange NMR techniques, where information about the exchange of nuclei between environments with different NMR shifts is obtained from the development of cross-peaks. Whereas 2D NMR enables the real time study of millisecond and slower exchange processes, 2D ESR in the form of 2D-ELDOR (two-dimensional electron-electron double resonance) has the potential for such studies over the nanosecond to microsecond real time scales. Cross-peak development due to chemical exchange has been seen previously for semiquinones in ESR, but this is not possible for most common ESR probes, such as nitroxides, studied at typical ESR frequencies because, unlike NMR, the exchanging states yield ESR signals that are not resolved from each other within their respective line widths. But at 95 GHz, it becomes possible to resolve them in many cases because of the increased g-factor resolution. The 95 GHz instrumental developments occurring at ACERT now enable such studies. We demonstrate these new capabilities in two studies: (A) the protonation/deprotonation process for a pH-sensitive imidazoline spin label in aqueous solution where the exchange rate and the population ratio of the exchanging states are controlled by the concentration and pH of the buffer solution, respectively, and (B) a nitroxide radical partitioning between polar (aqueous) and nonpolar (phospholipid) environments in multilamellar lipid vesicles, where the cross-peak development arises from the exchange of the nitroxide between the two phases. This work represents the first example of the observation and analysis of cross-peaks arising from chemical exchange processes involving nitroxide spin labels.

Jack H. Freed

Papers

Two-dimensional ELDOR in the study of model and biological membranes

Collective fluctuations in ordered fluids investigated by two-dimensional electron-electron double resonance spectroscopy.

2D-ELDOR using full S(c-) fitting and absorption lineshapes.

ESR Saturation and Double Resonance in Liquids

Microsecond Exchange Processes Studied by Two-Dimensional ESR at 95 GHz.