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Mathematical Approaches to Biomolecular Structure and Dynamics
This IMA Volume in Mathematics and its Applications MATHEMATICAL APPROACHES TO BIOMOLECULAR STRUCTURE AND DYNAMICS is one of the two volumes based on the proceedings of the 1994 IMA Sum mer Program on "Molecular Biology" and comprises Weeks 3 and 4 of the four-week program. Weeks 1 and 2 appeared as Volume 81: Genetic Mapping and DNA Sequencing. We thank Jill P. Mesirov, Klaus Schulten, and De Witt Sumners for organizing Weeks 3 and 4 of the workshop and for editing the proceedings. We also take this opportunity to thank the National Institutes of Health (NIH) (National Center for Human Genome Research), the National Science Foundation (NSF) (Biological Instrumen tation and Resources), and t...
Models of Neural Networks
Since the appearance of Vol. 1 of Models of Neural Networks in 1991, the theory of neural nets has focused on two paradigms: information coding through coherent firing of the neurons and functional feedback. Information coding through coherent neuronal firing exploits time as a cardinal degree of freedom. This capacity of a neural network rests on the fact that the neuronal action potential is a short, say 1 ms, spike, localized in space and time. Spatial as well as temporal correlations of activity may represent different states of a network. In particular, temporal correlations of activity may express that neurons process the same "object" of, for example, a visual scene by spiking at the ...
Innovations in Biomolecular Modeling and Simulations
This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts.
Quantum Effects in Biology
Explores the role of quantum mechanics in biology for advanced undergraduate and graduate students in physics, biology and chemistry.
Models of Neural Networks I
One of the great intellectual challenges for the next few decades is the question of brain organization. What is the basic mechanism for storage of memory? What are the processes that serve as the interphase between the basically chemical processes of the body and the very specific and nonstatistical operations in the brain? Above all, how is concept formation achieved in the human brain? I wonder whether the spirit of the physics that will be involved in these studies will not be akin to that which moved the founders of the "rational foundation of thermodynamics". C. N. Yang! 10 The human brain is said to have roughly 10 neurons connected through about 14 10 synapses. Each neuron is itself ...
Models of Neural Networks
One of the great inteJlectual cha1lenges for the next few decades is the question of brain organization. What is the basic mechanism for storage of memory? What are the processes that serve as the interphase between the basically chemical processes of the body and the very specific and nonstatistical operations in the brain? Above all. how is concept formation achieved in the human brain? I wonder whether the spirit of the physics that will be involved in these studies will not be akin to that which moved the founders of the ''rational foundation of thermodynamics". CN. Yangl 10 The human brain is said 10 have roughly 10 neurons connected through about 14 10 synapses. Each neuron is itself a complex device which compares and integrates incoming electrical signals and relays a nonlinear response to other neurons. The brain certainly exceeds in complexity any system which physicists have studied in the past. Nevertheless, there do exist many analogies of the We have witnessed during the last decade brain to simpler physical systems.
Molecular Simulations and Biomembranes
The need for information in the understanding of membrane systems has been caused by three things - an increase in computer power; methodological developments and the recent expansion in the number of researchers working on it worldwide. However, there has been no up-to-date book that covers the application of simulation methods to membrane systems directly and this book fills an important void in the market. It provides a much needed update on the current methods and applications as well as highlighting recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The objectives are to show how simulation methods can provide an important cont...
Kohonen Maps
The Self-Organizing Map, or Kohonen Map, is one of the most widely used neural network algorithms, with thousands of applications covered in the literature. It was one of the strong underlying factors in the popularity of neural networks starting in the early 80's. Currently this method has been included in a large number of commercial and public domain software packages. In this book, top experts on the SOM method take a look at the state of the art and the future of this computing paradigm. The 30 chapters of this book cover the current status of SOM theory, such as connections of SOM to clustering, classification, probabilistic models, and energy functions. Many applications of the SOM are given, with data mining and exploratory data analysis the central topic, applied to large databases of financial data, medical data, free-form text documents, digital images, speech, and process measurements. Biological models related to the SOM are also discussed.
Parallel and Distributed Processing
This book constitutes the refereed proceedings of 11 IPPS/SPDP '98 Workshops held in conjunction with the 13th International Parallel Processing Symposium and the 10th Symposium on Parallel and Distributed Processing in San Juan, Puerto Rico, USA in April 1999. The 126 revised papers presented were carefully selected from a wealth of papers submitted. The papers are organised in topical sections on biologically inspired solutions to parallel processing problems: High-Level Parallel Programming Models and Supportive Environments; Biologically Inspired Solutions to Parallel Processing; Parallel and Distributed Real-Time Systems; Run-Time Systems for Parallel Programming; Reconfigurable Architectures; Java for Parallel and Distributed Computing; Optics and Computer Science; Solving Irregularly Structured Problems in Parallel; Personal Computer Based Workstation Networks; Formal Methods for Parallel Programming; Embedded HPC Systems and Applications.
Models of Neural Networks III
One of the most challenging and fascinating problems of the theory of neural nets is that of asymptotic behavior, of how a system behaves as time proceeds. This is of particular relevance to many practical applications. Here we focus on association, generalization, and representation. We turn to the last topic first. The introductory chapter, "Global Analysis of Recurrent Neural Net works," by Andreas Herz presents an in-depth analysis of how to construct a Lyapunov function for various types of dynamics and neural coding. It includes a review of the recent work with John Hopfield on integrate-and fire neurons with local interactions. The chapter, "Receptive Fields and Maps in the Visual Cortex: Models of Ocular Dominance and Orientation Columns" by Ken Miller, explains how the primary visual cortex may asymptotically gain its specific structure through a self-organization process based on Hebbian learning. His argu ment since has been shown to be rather susceptible to generalization.
