Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are `discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.

/pdf/features-and-development-of-coot-5al5bhwkg1.pdf

Features and development of Coot.

This paper provides a theoretical framework for analysis of consensus algorithms for multi-agent networked systems with an emphasis on the role of directed information flow, robustness to changes in network topology due to link/node failures, time-delays, and performance guarantees. An overview of basic concepts of information consensus in networks and methods of convergence and performance analysis for the algorithms are provided. Our analysis framework is based on tools from matrix theory, algebraic graph theory, and control theory. We discuss the connections between consensus problems in networked dynamic systems and diverse applications including synchronization of coupled oscillators, flocking, formation control, fast consensus in small-world networks, Markov processes and gossip-based algorithms, load balancing in networks, rendezvous in space, distributed sensor fusion in sensor networks, and belief propagation. We establish direct connections between spectral and structural properties of complex networks and the speed of information diffusion of consensus algorithms. A brief introduction is provided on networked systems with nonlocal information flow that are considerably faster than distributed systems with lattice-type nearest neighbor interactions. Simulation results are presented that demonstrate the role of small-world effects on the speed of consensus algorithms and cooperative control of multivehicle formations

/pdf/consensus-and-cooperation-in-networked-multi-agent-systems-5ame7z72ny.pdf

Consensus and Cooperation in Networked Multi-Agent Systems

In this article we discuss our experience designing and implementing a statistical computing language. In developing this new language, we sought to combine what we felt were useful features from two existing computer languages. We feel that the new language provides advantages in the areas of portability, computational efficiency, memory management, and scoping.

R: A Language for Data Analysis and Graphics

In this paper we present a new data structure for representing Boolean functions and an associated set of manipulation algorithms. Functions are represented by directed, acyclic graphs in a manner similar to the representations introduced by Lee [1] and Akers [2], but with further restrictions on the ordering of decision variables in the graph. Although a function requires, in the worst case, a graph of size exponential in the number of arguments, many of the functions encountered in typical applications have a more reasonable representation. Our algorithms have time complexity proportional to the sizes of the graphs being operated on, and hence are quite efficient as long as the graphs do not grow too large. We present experimental results from applying these algorithms to problems in logic design verification that demonstrate the practicality of our approach.

/pdf/graph-based-algorithms-for-boolean-function-manipulation-2u3osq5jc0.pdf

Graph-Based Algorithms for Boolean Function Manipulation

The primary purpose of a programming language is to assist the programmer in the practice of her art. Each language is either designed for a class of problems or supports a different style of programming. In other words, a programming language turns the computer into a ‘virtual machine’ whose features and capabilities are unlimited. In this article, we illustrate these aspects through a language similar tologo. Programs are developed to draw geometric pictures using this language.

Introduction to algorithms: 4. Turtle graphics

: The objective of this research is to create the architectural, algorithmic, and technological foundations for exploiting programmable materials. These are materials that incorporate vast numbers of programmable elements that react to each other and to their environment. Such materials can be fabricated economically, provided that the computing elements are amassed in bulk without arranging for precision interconnect and testing. In order to exploit programmable materials we must identify engineering principles for organizing and instructing myriad programmable entities to cooperate to robustly achieve pre-established goals, even though the individual entities are unreliable and interconnected in unknown, irregular, and time-varying ways. Progress in microfabrication and in bioengineering will make it possible to assemble such amorphous systems at almost no cost, provided that (1) the units need not all work correctly; (2) the units are identically programmed; and (3) there is no need to manufacture precise geometrical arrangements of the units or precise interconnections among them.

http://www.ai.mit.edu/research/abstracts/abstracts2002/artificial-life/01abelson.pdf

Amorphous and Cellular Computing

Am Anfang dieses Buches haben wir uns mit Prozessen befast und sie mit Hilfe von Lisp-Prozeduren beschrieben. Die Bedeutung dieser Prozeduren haben wir mit einer Reihe von Auswertungsmodellen erlautert: dem Substitutionsmodell in Kapitel 1, dem Umgebungsmodell in Kapitel 3 und dem metazirkularen Evaluator in Kapitel 4. Insbesondere durch die Beschaftigung mit dem metazirkularen Evaluator wurde das Geheimnis weitgehend geluftet, das die Interpretation von Lispahnlichen Sprachen umgab. Aber auch der metazirkulare Evaluator last wichtige Fragen unbeantwortet, weil mit ihm die Steuerungsmechanismen in einem Lisp-System nicht erhellt werden konnen. Mit dem Evaluator last sich zum Beispiel nicht erklaren, wie nach der Auswertung eines Teilausdrucks ein Wert an den Ausdruck geliefert werden kann, in dem dieser Wert dann verwendet wird; noch last sich mit dem Evaluator erklaren, warum manche Prozeduren iterative Prozesse erzeugen (das heist, mit konstantem Speicherbedarf ausgewertet werden), wahrend andere Prozeduren rekursive Prozesse erzeugen. Diese Fragen bleiben unbeantwortet, weil der metazirkulare Evaluator selbst ein Lisp-Programm ist und daher die Steuerungsstruktur des zugrundeliegenden Lisp-Systems ubernimmt. Um eine vollstandigere Beschreibung der Steuerungsstruktur des Lisp-Evaluators zu erhalten, mussen wir uns auf eine elementarere Ebene begeben als Lisp.

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OTHERBOOKS RECEIVED All books received are listed here. Some ofthem will be reviewed at a later date. Reliability Theory and ModelsmStochastic Failure Models, Optimal Maintenance Policies, Life Testing, and

Harold Abelson

Papers

Amorphous and Cellular Computing

Rechnen mit Registermaschinen

OTHERBOOKS RECEIVED All books received are listed here. Some ofthem will be reviewed at a later date. Reliability Theory and ModelsmStochastic Failure Models, Optimal Maintenance Policies, Life Testing, and