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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

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GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

From the Publisher: 
The accessible presentation of this book gives both a general view of the entire computer vision enterprise and also offers sufficient detail to be able to build useful applications. Users learn techniques that have proven to be useful by first-hand experience and a wide range of mathematical methods. A CD-ROM with every copy of the text contains source code for programming practice, color images, and illustrative movies. Comprehensive and up-to-date, this book includes essential topics that either reflect practical significance or are of theoretical importance. Topics are discussed in substantial and increasing depth. Application surveys describe numerous important application areas such as image based rendering and digital libraries. Many important algorithms broken down and illustrated in pseudo code. Appropriate for use by engineers as a comprehensive reference to the computer vision enterprise.

Computer vision : a modern approach = 计算机视觉 : 一种现代的方法

IEEE Transactions on Pattern Analysis and Machine Intelligence

We have carried out a comprehensive computational study of the structures and 
properties of a series of iron-bearing minerals under various conditions using grid 
technologies developed within the eMinerals project. The work has enabled by a close 
collaboration between computational scientists from different institutions across the UK, 
as well as the involvement of computer and grid scientists in a true team effort. We show 
here that our new approach for scientific research is only feasible with the use of the 
eMinerals minigrid. Prior to the eMinerals project, such an approach would have been 
almost impossible within the timescale available. The new approach allows us to achieve 
our goals in a much quicker, more comprehensive and detailed way. Preliminary 
scientific results of an investigation of the transport and immobilization of arsenic 
species in the environment are presented in the paper.

A virtual research organization enabled by eMinerals minigrid: an integrated study of the transport and immobilisation of arsenic species in the environment

In the late 1970s, the embryonic UK research community in molecular simulation – physicists and physical chemists – organised itself around CCP5, one of a set of Collaborative Computational Projects in different fields. CCP5 acted to develop and use the software required by an evolving and expanding scientific agenda, to exploit quickly and efficiently the revolution in computing hardware and to educate and nurture the careers of future generations of researchers in the field. This collaboration formally began in 1980, and is still fully active now, 40 years later. Today, molecular simulation techniques, many of them pioneered by CCP5, are now used very widely, including in several other CCPs in the UK’s current family of Collaborative Computational Projects. This article tells the story of molecular simulation in the UK, with CCP5 itself at centre stage, using the written records in the CCP archives. The authors were, or are, all personally involved in this story.

Molecular simulation and the collaborative computational projects

In this paper, we draw on ideas from the field of statistical shape analysis to construct shape-spaces that span facial expressions and gender, and use the resulting shape-model to perform face recognition under varying expression and gender. Our novel contribution is to show how to construct shape-spaces over fields of surface normals rather than Cartesian landmark points. According to this model face needle-maps (or fields of surface normals) are points in a high-dimensional manifold referred to as a shape-space. We compute geodesic distances to compare the similarity between faces and gender difference.

Facial Shape Spaces from Surface Normals

This paper describes how surface shape, and in particular facial shape, can be modeled using a statistical model that captures variations in surface normal direction. To construct this model we make use of the azimuthal equidistant projection to map surface normals from the unit sphere to points on a local tangent plane. The variations in surface normal direction are captured using the covariance matrix for the projected point positions. This allows us to model variations in surface shape using a standard point distribution model. We show how this model can be trained using surface normal data acquired from range images. We fit the model to intensity data using constraints on the surface normal direction provided by Lambert's law. We demonstrate the utility of the method on the recovery of 3D surface shape from 2D images.

Modelling surface normal distribution using the azimuthal equidistant projection

When rendering the 3D graphics object in the computer vision and graphics fields, the parameter values, such as the surface roughness, refractive index, and light absorption are used for modeling realistic light scattering rendering behavior of a material. Most of these values were usually obtained from different literature or online sources. In general, a specific measuring tool is needed when acquiring the measurement, but, what if we could use an alternative method of measuring when the tools are not available? The idea is to use the light scattering model to estimate the parameter measurement values of material by doing the inverse rendering of the capture polarization image of the object’s light scattering. In this paper, we investigate whether we can estimate four different measurements, using ARLLS model. We captured the object’s degree of polarization (DOP) to be fitted and compare with the model to investigate the relationship between the two by doing the correlation test between the object measurement DOP and the model parameters to see whether the estimations are in agreement with each other (e.g. by reference or by the practical characteristics of the object). Furthermore, the test will be conducted using materials with varying degree of properties (e.g. very rough surface; highly chromatic).

William A. P. Smith

Papers

A virtual research organization enabled by eMinerals minigrid: an integrated study of the transport and immobilisation of arsenic species in the environment

Molecular simulation and the collaborative computational projects

Facial Shape Spaces from Surface Normals

Modelling surface normal distribution using the azimuthal equidistant projection

Estimating Material Parameters Using Light Scattering Model and Polarization