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."

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 the Department of Energy (DOE), whose fi nancial support made the summer program possible. A vner Friedman Robert Gulliver v PREFACE The revolutionary progress in molecular biology within the last 30 years opens the way to full understanding of the molecular structures and mech anisms of living organisms. Interdisciplinary research in mathematics and molecular biology is driven by ever growing experimental, theoretical and computational power. The mathematical sciences accompany and support much of the progress achieved by experiment and computation as well as provide insight into geometric and topological properties of biomolecular structure and processes. This volume consists of a representative sample of the papers presented during the last two weeks of the month-long Institute for Mathematics and Its Applications Summer 1994 Program in Molecular Biology."

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 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 brain to simpler physical systems. We have witnessed during the last decade some surprising contributions of physics to the study of the brain. The most significant parallel between biological brains and many physical systems is that both are made of many tightly interacting components.

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 very same time. The traditional description of a neural network through a firing rate, the famous S-shaped curve, presupposes a wide time window of, say, at least 100 ms. It thus fails to exploit the capacity to "bind" sets of coherently firing neurons for the purpose of both scene segmentation and figure-ground segregation. Feedback is a dominant feature of the structural organization of the brain. Recurrent neural networks have been studied extensively in the physical literature, starting with the ground breaking work of John Hop field (1982)."

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 the Department of Energy (DOE), whose fi nancial support made the summer program possible. A vner Friedman Robert Gulliver v PREFACE The revolutionary progress in molecular biology within the last 30 years opens the way to full understanding of the molecular structures and mech anisms of living organisms. Interdisciplinary research in mathematics and molecular biology is driven by ever growing experimental, theoretical and computational power. The mathematical sciences accompany and support much of the progress achieved by experiment and computation as well as provide insight into geometric and topological properties of biomolecular structure and processes. This volume consists of a representative sample of the papers presented during the last two weeks of the month-long Institute for Mathematics and Its Applications Summer 1994 Program in Molecular Biology."

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."

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 very same time. The traditional description of a neural network through a firing rate, the famous S-shaped curve, presupposes a wide time window of, say, at least 100 ms. It thus fails to exploit the capacity to "bind" sets of coherently firing neurons for the purpose of both scene segmentation and figure-ground segregation. Feedback is a dominant feature of the structural organization of the brain. Recurrent neural networks have been studied extensively in the physical literature, starting with the ground breaking work of John Hop field (1982)."