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

In this paper we study the nonuniform fast Fourier transform with nonequispaced spatial and frequency data (NNFFT) and the fast sinc transform as its application. The computation of NNFFT is mainly based on the nonuniform fast Fourier transform with nonequispaced spatial nodes and equispaced frequencies (NFFT). The NNFFT employs two compactly supported, continuous window functions. For fixed nonharmonic bandwidth, it is shown that the error of the NNFFT with two sinh-type window functions has an exponential decay with respect to the truncation parameters of the used window functions. As an important application of the NNFFT, we present the fast sinc transform. The error of the fast sinc transform is estimated, too.

Nonuniform fast Fourier transforms with nonequispaced spatial and frequency data and fast sinc transforms.

This chapter is concerned with Chebyshev methods and fast algorithms for the discrete cosine transform (DCT). Chebyshev methods are fundamental for the approximation and integration of real-valued functions defined on a compact interval. In Sect. 6.1, we introduce the Chebyshev polynomials of first kind and study their properties. Further, we consider the close connection between Chebyshev expansions and Fourier expansions of even 2π-periodic functions, the convergence of Chebyshev series, and the properties of Chebyshev coefficients. Section 6.2 addresses the efficient evaluation of polynomials, which are given in the orthogonal basis of Chebyshev polynomials. We present fast DCT algorithms in Sect. 6.3. These fast DCT algorithms are based either on the FFT or on the orthogonal factorization of the related cosine matrix.

Chebyshev Methods and Fast DCT Algorithms

Modelling vegetation succession in post-industrial ecosystems using vegetation classification in aerial photographs, Buffalo, New York

This paper describes an extension of Fourier approximation methods for multivariate functions defined on the torus $\mathbb{T}^d$ to functions in a weighted Hilbert space $L_{2}(\mathbb{R}^d, \omega)$ via a multivariate change of variables $\psi:\left(-\frac{1}{2},\frac{1}{2}\right)^d\to\mathbb{R}^d$. We establish sufficient conditions on $\psi$ and $\omega$ such that the composition of a function in such a weighted Hilbert space with $\psi$ yields a function in the Sobolev space $H_{\mathrm{mix}}^{m}(\mathbb{T}^d)$ of functions on the torus with mixed smoothness of natural order $m \in \mathbb{N}_{0}$. In this approach we adapt algorithms for the evaluation and reconstruction of multivariate trigonometric polynomials on the torus $\mathbb{T}^d$ based on single and multiple reconstructing rank-$1$ lattices. Since in applications it may be difficult to choose a related function space, we make use of dimension incremental construction methods for sparse frequency sets. Various numerical tests confirm obtained theoretical results for the transformed methods.

Transformed rank-1 lattices for high-dimensional approximation

The paper presents a general strategy to solve ordinary differential equations (ODE), where some coefficient depend on the spatial variable and on additional random variables. The approach is based on the application of a recently developed dimension-incremental sparse fast Fourier transform. Since such algorithms require periodic signals, we discuss periodization strategies and associated necessary deperiodization modifications within the occuring solution steps. 
The computed approximate solutions of the ODE depend on the spatial variable and on the random variables as well. Certainly, one of the crucial challenges of the high dimensional approximation process is to rate the influence of each variable on the solution as well as the determination of the relations and couplings within the set of variables. The suggested approach meets these challenges in a full automatic manner with reasonable computational costs, i.e., in contrast to already existing approaches, one does not need to seriously restrict the used set of ansatz functions in advance.

Daniel Potts

Papers

Nonuniform fast Fourier transforms with nonequispaced spatial and frequency data and fast sinc transforms.

Chebyshev Methods and Fast DCT Algorithms

Modelling vegetation succession in post-industrial ecosystems using vegetation classification in aerial photographs, Buffalo, New York

Transformed rank-1 lattices for high-dimensional approximation

A sparse FFT approach for ODE with random coefficients