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

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

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

We will review some of the major results in random graphs and some of the more challenging open problems. We will cover algorithmic and structural questions. We will touch on newer models, including those related to the WWW.

Random graphs

Planning algorithms are impacting technical disciplines and industries around the world, including robotics, computer-aided design, manufacturing, computer graphics, aerospace applications, drug design, and protein folding. This coherent and comprehensive book unifies material from several sources, including robotics, control theory, artificial intelligence, and algorithms. The treatment is centered on robot motion planning but integrates material on planning in discrete spaces. A major part of the book is devoted to planning under uncertainty, including decision theory, Markov decision processes, and information spaces, which are the “configuration spaces” of all sensor-based planning problems. The last part of the book delves into planning under differential constraints that arise when automating the motions of virtually any mechanical system. Developed from courses taught by the author, the book is intended for students, engineers, and researchers in robotics, artificial intelligence, and control theory as well as computer graphics, algorithms, and computational biology.

Planning Algorithms: Introductory Material

Motion planning for spatially constrained robots is difficult due to additional constraints placed on the robot, such as closure constraints for closed chains or requirements on end-effector placement for articulated linkages. It is usually computationally too expensive to apply sampling-based planners to these problems since it is difficult to generate valid configurations. We overcome this challenge by redefining the robotâs degrees of freedom and constraints into a new set of parameters, called reachable distance space (RD-space), in which all configurations lie in the set of constraint-satisfying subspaces. This enables us to directly sample the constrained subspaces with complexity linear in the number of the robotâs degrees of freedom. In addition to supporting efficient sampling of configurations, we show that the RD-space formulation naturally supports planning and, in particular, we design a local planner suitable for use by sampling-based planners. We demonstrate the effectiveness and efficiency of our approach for several systems including closed chain planning with multiple loops, restricted end-effector sampling, and on-line planning for drawing/sculpting. We can sample single-loop closed chain systems with 1,000 links in time comparable to open chain sampling, and we can generate samples for 1,000-link multi-loop systems of varying topologies in less than a second.

Reachable Distance Space: Efficient Sampling-Based Planning for Spatially Constrained Systems

Provably optimal parallel transport sweeps on semi-structured grids

The problem addressed is the distributed reconfiguration of a metamorphic robot system composed of any number of two dimensional robots (modules) front specific initial to specific goal configurations. The initial configuration we consider is a straight chain of modules, while the goal configuration satisfies a simple admissibility condition. Reconfiguration of the modules depends on finding a contiguous path of cells, called a substrate path, that spans the goal configuration. Modules fill in this substrate path and then move along the path to fill in the remainder of the goal without collision or deadlock. In this paper, we examine the problem of finding the substrate path most likely to result in fast parallel reconfiguration, drawing on results from our previous papers (2000, 2001). Admissible goal configurations are represented as directed acyclic graphs (DAGs). We present a combination graph traversal-weighting algorithm that traverses all paths in the rooted DAG and use this algorithm to determine the best substrate path. We extend our definition of admissible substrate paths to consider admissible obstacle surfaces for reconfiguration when obstacles are present in the environment.

Choosing good paths for fast distributed reconfiguration of hexagonal metamorphic robots

This research supported in part by NSF awards CNS-0551685, CCF-0833199, CCF-0830753, IIS-0916053, IIS-0917266, EFRI-1240483, RI-1217991, by NIH NCI R25 CA090301-11, by Chevron, IBM, Intel, Oracle/Sun and by Award KUS-C1-016-04, made by King Abdullah University of Science and Technology (KAUST).

Sampling-based motion planning with reachable volumes: Theoretical foundations

In this paper we present a heuristic approach to planning in an environment with moving obstacles. Our approach assumes that the robot has no knowledge of the future trajectory of the moving objects. Our framework also distinguishes between two types of moving objects in the environment: hard and soft objects. We distinguish between the two types of objects in the environment as varying application domains could allow for some collision between some types of moving objects. For example, a robot planning a path in an environment with people could have the people modeled as circular disks with a safe zone surrounding each person. Although the robot may try to stay out of each safe zone, violating that criteria would not necessarily result in planning failure. We will show the effectiveness of our planner in general dynamic environments with the soft objects having varying behaviors.

/pdf/a-framework-for-planning-motion-in-environments-with-moving-52a9bfv8n6.pdf

Nancy M. Amato

Papers

Reachable Distance Space: Efficient Sampling-Based Planning for Spatially Constrained Systems

Provably optimal parallel transport sweeps on semi-structured grids

Choosing good paths for fast distributed reconfiguration of hexagonal metamorphic robots

Sampling-based motion planning with reachable volumes: Theoretical foundations

A framework for planning motion in environments with moving obstacles