Stephen C. Harvey

Bio: Stephen C. Harvey is an academic researcher from Ohio University. The author has contributed to research in topics: Coaching & Physical education. The author has an hindex of 57, co-authored 273 publications receiving 12445 citations. Previous affiliations of Stephen C. Harvey include Shell Canada Limited & University of West Virginia.

Dynamics of proteins and nucleic acids

Abstract: Preface 1. Introduction 2. Structure of proteins, nucleic acids, and their solvent surroundings 3. Dynamics of proteins, nucleic acids, and their solvent surroundings 4. Theoretical methods 5. Short time dynamics 6. Local structural transitions 7. Global structural changes 8. Dynamics of molecular associations 9. Recent developments and future directions Appendices References Index.

The flying ice cube: Velocity rescaling in molecular dynamics leads to violation of energy equipartition

Abstract: This article describes an unexpected phenomenon encountered during MD simulations: velocity rescaling using standard protocols can systematically change the proportion of total kinetic energy (KE) found in motions associated with the various degrees of freedom. Under these conditions, the simulation violates the principle of equipartition of energy, which requires a mean kinetic energy of RT/2 in each degree of freedom. A particularly pathological form of this problem occurs if one does not periodically remove the net translation of (and rotation about) the center of mass. In this case, almost all of the kinetic energy is converted into these two kinds of motion, producing a system with almost no kinetic energy associated with the internal degrees of freedom. We call this phenomenon “the flying ice cube.” We present a mathematical analysis of a simple diatomic system with two degrees of freedom, to document the origin of the problem. We then present examples from three kinds of MD simulations, one being an in vacuo simulation on a diatomic system, one involving a low resolution model of DNA in vacuo, and the third using a traditional all-atom DNA model with full solvation, periodic boundary conditions, and the particle mesh Ewald method for treating long-range electrostatics. Finally, we discuss methods for avoiding the problem. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 726–740, 1998

Fast parallel algorithms for short-range molecular dynamics

Abstract: 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.

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

Abstract: 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。

Using Multivariate Statistics

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Scalable molecular dynamics with NAMD

Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.