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

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

“Bioinformatics” 특집을 내면서

We describe a global optimization technique using “basin-hopping” in which the potential energy surface is transformed into a collection of interpenetrating staircases. This method has been designed to exploit the features that recent work suggests must be present in an energy landscape for efficient relaxation to the global minimum. The transformation associates any point in configuration space with the local minimum obtained by a geometry optimization started from that point, effectively removing transition state regions from the problem. However, unlike other methods based upon hypersurface deformation, this transformation does not change the global minimum. The lowest known structures are located for all Lennard-Jones clusters up to 110 atoms, including a number that have never been found before in unbiased searches.

/pdf/global-optimization-by-basin-hopping-and-the-lowest-energy-2s1wxtsj18.pdf

Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms

Theoretical studies of icosahedral C60 and some related species

Finding the optimal solution to a complex optimization problem is of great importance in many fields, ranging from protein structure prediction to the design of microprocessor circuitry. Some recent progress in finding the global minima of potential energy functions is described, focusing on applications of the simple "basin-hopping" approach to atomic and molecular clusters and more complicated hypersurface deformation techniques for crystals and biomolecules. These methods have produced promising results and should enable larger and more complex systems to be treated in the future.

/pdf/global-optimization-of-clusters-crystals-and-biomolecules-2ehy01ydei.pdf

Global optimization of clusters, crystals, and biomolecules

Energy landscapes hold the key to understanding a wide range of molecular phenomena. The problem of how a denatured protein re-folds to its active state (Levinthal's parado1) has been addressed in terms of the underlying energy landscape2,3,4,5,6,7, as has the widely used ‘strong’ and ‘fragile’ classification of liquids8,9. Here we show how three archetypal energy landscapes for clusters of atoms or molecules can be characterized in terms of the disconnectivity graphs10 of their energy minima—that is, in terms of the pathways that connect minima at different threshold energies. First we consider a cluster of 38 Lennard–Jones particles, whose energy landscape is a ‘double funnel’ on which relaxation to the global minimum is diverted into a set of competing structures. Then we characterize the energy landscape associated with the annealing of C60 cages to buckministerfullerene, and show that it provides experimentally accessible clues to the relaxation pathway. Finally we show a very different landscape morphology, that of a model water cluster (H2O)20, and show how it exhibits features expected for a ‘strong’ liquid. These three examples do not exhaust the possibilities, and might constitute substructures of still more complex landscapes.

Archetypal energy landscapes

The study of energy landscapes holds the key to resolving some of the most important contemporary problems in chemical physics. Many groups are now attempting to understand the properties of clusters, glasses and proteins in terms of the underlying potential energy surface. The aim of this book is to define and unify the field of energy landscapes in a reasonably self-contained exposition. This is the first book to cover this active field. The book begins with an overview of each area in an attempt to make the subject matter accessible to workers in different disciplines. The basic theoretical groundwork for describing and exploring energy landscapes is then introduced followed by applications to clusters, biomolecules and glasses in the final chapters. Beautifully illustrated in full colour throughout, this book is aimed at graduate students and workers in the field.

David J. Wales

Papers

Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms

Theoretical studies of icosahedral C60 and some related species

Global optimization of clusters, crystals, and biomolecules

Archetypal energy landscapes

Energy Landscapes: Applications to Clusters, Biomolecules and Glasses