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

Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

Machine learning

J. Appl. Cryst.の発刊に際して

Photosynthesis provides the primary energy source for almost all life on Earth. One of its remarkable features is the efficiency with which energy is transferred within the light harvesting complexes comprising the photosynthetic apparatus. Suspicions that quantum trickery might be involved in the energy transfer processes at the core of photosynthesis are now confirmed by a new spectroscopic study. The study reveals electronic quantum beats characteristic of wavelike energy motion within the bacteriochlorophyll complex from the green sulphur bacterium Chlorobium tepidum. This wavelike characteristic of the energy transfer process can explain the extreme efficiency of photosynthesis, in that vast areas of phase space can be sampled effectively to find the most efficient path for energy transfer. A spectroscopic study has directly monitored the quantum beating arising from remarkably long-lived electronic quantum coherence in a bacteriochlorophyll complex. This wavelike characteristic of the energy transfer process can explain the extreme efficiency of photosynthesis, in that vast areas of phase space can be sampled effectively to find the most efficient path for energy transfer. Photosynthetic complexes are exquisitely tuned to capture solar light efficiently, and then transmit the excitation energy to reaction centres, where long term energy storage is initiated. The energy transfer mechanism is often described by semiclassical models that invoke ‘hopping’ of excited-state populations along discrete energy levels1,2. Two-dimensional Fourier transform electronic spectroscopy3,4,5 has mapped6 these energy levels and their coupling in the Fenna–Matthews–Olson (FMO) bacteriochlorophyll complex, which is found in green sulphur bacteria and acts as an energy ‘wire’ connecting a large peripheral light-harvesting antenna, the chlorosome, to the reaction centre7,8,9. The spectroscopic data clearly document the dependence of the dominant energy transport pathways on the spatial properties of the excited-state wavefunctions of the whole bacteriochlorophyll complex6,10. But the intricate dynamics of quantum coherence, which has no classical analogue, was largely neglected in the analyses—even though electronic energy transfer involving oscillatory populations of donors and acceptors was first discussed more than 70 years ago11, and electronic quantum beats arising from quantum coherence in photosynthetic complexes have been predicted12,13 and indirectly observed14. Here we extend previous two-dimensional electronic spectroscopy investigations of the FMO bacteriochlorophyll complex, and obtain direct evidence for remarkably long-lived electronic quantum coherence playing an important part in energy transfer processes within this system. The quantum coherence manifests itself in characteristic, directly observable quantum beating signals among the excitons within the Chlorobium tepidum FMO complex at 77 K. This wavelike characteristic of the energy transfer within the photosynthetic complex can explain its extreme efficiency, in that it allows the complexes to sample vast areas of phase space to find the most efficient path.

Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems

Adaptive versus non-adaptive responses to drought in a non-native riparian tree / shrub, Tamarix spp

The solution of partial differential equations on adaptively generated grids play an important role in scientific computation. In this paper we compare two Poisson solvers for data on nonequispaced mesh points. A new meshless Fourier method based on NFFT is constructed in R 3 . This algorithm is compared to the well-established multigrid method working on nonequidistant meshes. Our investigations are motivated especially by simulations of the behaviour of charged particles in accelerators.

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Fast Poisson solvers on nonequispaced grids: Multigrid and Fourier methods compared

This paper is concerned with function reconstruction from samples. The sampling points used in several approaches are (1) structured points connected with fast algorithms or (2) unstructured points coming from, e.g., an initial random draw to achieve an improved information complexity. We connect both approaches and propose a subsampling of structured points in an offline step. In particular, we start with structured quadrature points (QMC), which provide stable $L_2$ reconstruction properties. The subsampling procedure consists of a computationally inexpensive random step followed by a deterministic procedure to further reduce the number of points while keeping its information. In these points functions (belonging to a RKHS of bounded functions) will be sampled and reconstructed from whilst achieving state of the art error decay. Our method is dimension-independent and is applicable as soon as we know some initial quadrature points. We apply our general findings on the $d$-dimensional torus to subsample rank-1 lattices, where it is known that full rank-1 lattices lose half the optimal order of convergence (expressed in terms of the size of the lattice). In contrast to that, our subsampled version regains the optimal rate since many of the lattice points are not needed. Moreover, we utilize fast and memory efficient Fourier algorithms in order to compute the approximation. Numerical experiments in several dimensions support our findings.

On the reconstruction of functions from values at subsampled quadrature points

In this paper we study the multivariate ANOVA decomposition for $1$-periodic functions on the torus. In particular we use the integral projection operator that leads to the classical ANOVA decomposition. Relationships between the Fourier coefficients of the function and its ANOVA terms lead to special frequency index sets and give an understanding of the decomposition working in the frequency domain. Moreover, we consider the truncated ANOVA decomposition and provide error bounds for approximation in $\mathrm{L}_\infty$ and $\mathrm{L}_2$. We present an approximation method based on the truncated decomposition with regard to a superposition dimension $d_s$.

Learning high-dimensional additive models on the torus.

In this paper, we study the error behavior of the nonequispaced fast Fourier transform (NFFT). This approximate algorithm is mainly based on the convenient choice of a compactly supported window function. So far, various window functions have been used and new window functions have recently been proposed. We present novel error estimates for NFFT with compactly supported, continuous window functions and derive rules for convenient choice from the parameters involved in NFFT. The error constant of a window function depends mainly on the oversampling factor and the truncation parameter.

Daniel Potts

Papers

Adaptive versus non-adaptive responses to drought in a non-native riparian tree / shrub, Tamarix spp

Fast Poisson solvers on nonequispaced grids: Multigrid and Fourier methods compared

On the reconstruction of functions from values at subsampled quadrature points

Learning high-dimensional additive models on the torus.

Uniform error estimates for nonequispaced fast Fourier transforms