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

Structure and nanostructure in ionic liquids.

We introduce density functional theory and review recent progress in its application to transition metal chemistry. Topics covered include local, meta, hybrid, hybrid meta, and range-separated functionals, band theory, software, validation tests, and applications to spin states, magnetic exchange coupling, spectra, structure, reactivity, and catalysis, including molecules, clusters, nanoparticles, surfaces, and solids.

Density functional theory for transition metals and transition metal chemistry

Pulsed electron-electron double resonance techniques such as the four-pulse double electron-electron resonance experiment measure a dipolar evolution function of the sample. For a sample consisting of spin-carrying nanoobjects, this function is the product of a form factor, corresponding to the internal structure of the nanoobject, and a background factor, corresponding to the distribution of nanoobjects in space. The form factor contains information on the spin-to-spin distance distribution within the nanoobject and on the average number of spins per nanoobject, while the background factor depends on constraints, such as a confinement of the nanoobjects to a two-dimensional layer. Separation of the dipolar evolution function into these two contributions and extraction of the spin-to-spin distance distribution require numerically stable mathematical algorithms that can handle data for different classes of samples, e.g., spin-labelled biomacromolecules and synthetic materials. Furthermore, experimental imperfections such as the limited excitation bandwidth of microwave pulses need to be considered. The software package DeerAnalysis2006 provides access to a comprehensive set of tools for such data analysis within a common user interface. This interface allows for several tests of the reliability and precision of the extracted information. User-supplied models for the spin-to-spin distance distribution within a certain class of nanoobjects can be added to an existing library and be fitted with a universal algorithm.

DeerAnalysis2006 - a comprehensive software package for analyzing pulsed ELDOR data

Effect of Ionic Liquids on the Solution Structure of Human Serum Albumin

Despite these efforts,a molecular-scale picture of what happens when thermores-ponsive polymers start to dehydrate at a certain temperature,subsequently collapse, and then assemble to mesoglobules,does not exist. This absence severely hampers rationalmaterials design.In an exploratory research effort aimed at detectingunusual properties of dendronized polymers,

EPR Spectroscopic Characterization of Local Nanoscopic Heterogeneities during the Thermal Collapse of Thermoresponsive Dendronized Polymers

Intrinsically disordered proteins (IDPs) constitute a class of biologically active proteins that lack defined tertiary and often secondary structure. The IDP Osteopontin (OPN), a cytokine involved in metastasis of several types of cancer, is shown to simultaneously sample extended, random coil-like conformations and stable, cooperatively folded conformations. By a combination of two magnetic resonance methods, electron paramagnetic resonance and nuclear magnetic resonance spectroscopy, we demonstrate that the OPN ensemble exhibits not only characteristics of an extended and flexible polypeptide, as expected for an IDP, but also simultaneously those of globular proteins, in particular sigmoidal structural denaturation profiles. Both types of states, extended and cooperatively folded, are populated simultaneously by OPN in its apo state. The heterogeneity of the structural properties of IDPs is thus shown to even involve cooperative folding and unfolding events.

https://pubs.acs.org/doi/pdf/10.1021/bi400502c

Cooperative unfolding of compact conformations of the intrinsically disordered protein osteopontin.

The dynamic and chemical behavior of solute molecules inside new thermoresponsive hydrogels (photocrosslinked poly(N-isopropylacrylamide) (pNiPAAm) copolymers) is studied by continuous-wave electron paramagnetic resonance spectroscopy. Via addition of paramagnetic tracer molecules (so-called spin probes) a picture is obtained of the thermally induced collapse on the molecular scale, which proceeds over a substantially broader temperature range than indicated by the sharp macroscopic volume transition. The sampling of hydrophilic and hydrophobic environments suggests a discontinuous collapse mechanism with a coexistence of collapsed and expanded network regions. These structural inhomogeneities on the nanoscale also lead to an inhomogeneity in chemical reactivity. The hydrophilic regions form nanoreactors, which strongly accelerate the reaction while the hydrophobic regions act as nanoshelters, in which enclosed spin probes are protected from the decay. The results show that the system consisting of a statistical binary or tertiary copolymer displays remarkably complex behavior that mimics spatial and chemical inhomogeneities observed in functional biopolymers such as enzymes.

EPR spectroscopy reveals nanoinhomogeneities in the structure and reactivity of thermoresponsive hydrogels.

We present experimental evidence for the significant effect that water can have on the functional structure of proteins in solution. Human (HSA) and Bovine Serum Albumin (BSA) have an amino acid sequence identity of 75.52% and are chosen as model proteins. We employ EPR-based nanoscale distance measurements using double electron-electron resonance (DEER) spectroscopy and both albumins loaded with long chain fatty acids (FAs) in solution to globally (yet indirectly) characterize the tertiary protein structures from the bound ligands’ points of view. The complete primary structures and crystal structures of HSA and as of recently also BSA are available. We complement the picture as we have recently determined the DEER-derived solution structure of HSA and here present the corresponding BSA solution structure. The characteristic asymmetric FA distribution in the crystal structure of HSA can surprisingly be observed by DEER in BSA in solution. This indicates that the BSA conformational ensemble in solution seems to be narrow and close to the crystal structure of HSA. In contrast, for HSA in solution a much more symmetric FA distribution was found. Thus, conformational adaptability and flexibility dominate in the HSA solution structure while BSA seems to lack these properties. We further show that differences in amino acid hydropathies of specific structural regions in both proteins can be used to correlate the observed difference in the global (tertiary) solution structures with the differences on the primary structure level.

/pdf/evidence-for-water-tuned-structural-differences-in-proteins-3saa4e64gd.pdf

Dariush Hinderberger

Papers

Effect of Ionic Liquids on the Solution Structure of Human Serum Albumin

EPR Spectroscopic Characterization of Local Nanoscopic Heterogeneities during the Thermal Collapse of Thermoresponsive Dendronized Polymers

Cooperative unfolding of compact conformations of the intrinsically disordered protein osteopontin.

EPR spectroscopy reveals nanoinhomogeneities in the structure and reactivity of thermoresponsive hydrogels.

Evidence for Water-Tuned Structural Differences in Proteins: An Approach Emphasizing Variations in Local Hydrophilicity