The third volume in the series on Computer Simulation of Biomolecular Systems continues with the format introduced in the first volume [1] and elaborated in the second volume [2]. The primary emphasis is on the methodological aspects of simulations, although there are some chapters that present the results obtained for specific systems of biological interest. The focus of this volume has changed somewhat since there are several chapters devoted to structure-based ligand design, which had only a single chapter in the second volume. It seems useful to set the stage for this volume by quoting from my preface to Volume 2 [2]. "The long-range 'goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last fifty years great progress has been made in applying the equations representing the underlying physical laws to chemical problems involv ing the structures and reactions of small molecules. Corresponding studies of mesoscopic systems have been undertaken much more recently. Molecular dynamics simulations, which are the primary focus of this volume, represent the most important theoretical approach to macromolecules of biological interest." ...

Provides critical experimental studies and state-of-the-art theoretical analyses of organic reactions in which the role of the aqueous environment is particularly clear. Examines equilibrium and nonequilibrium solvent effects for a variety of chemical processes. Provides an overview of the scope and utility of the present broad array of modeling techniques for mimicking aqueous solution. Includes detailed studies of the hydrophobic effect as it influences protein folding and organic reactivity. Examines the effect of aqueous solvation on biological macromolecules and interfaces.

This practical reference explores computer modeling of enzyme reations--techniques that help chemists, biochemists and pharmaceutical researchers understand drug and enzyme action.

Modeling Chemical Systems using Cellular Automata provides a practical introduction to an exciting modeling paradigm for complex systems. The book first discusses the nature of scientific inquiry using models and simulations, and then describes the nature of cellular automata models. It then gives detailed descriptions, with examples and exercises, of how cellular automata models can be used in the study of a wide variety chemical, physical, and biochemical phenomena. Topics covered include models of water itself, solution phenomena, solution interactions with stationary systems, first- and second-order kinetic phenomena, enzyme kinetics, vapor-liquid equilibrium, and atomic and molecular excited-state kinetics. The student experiences these systems through hands-on examples and guided studies. This book is the first of its kind: a textbook and a laboratory manual about cellular automata modeling of common systems in chemistry. The book is designed to be used as a text in undergraduate courses dealing with complex systems and/or as a computational supplement to laboratory courses taught at the undergraduate level. The book includes: - Compact descriptions of a large variety of physical and chemical phenomena - Illustrative examples of simulations, with exercises for further study - An instructor's manual for use of the program The book will be of great value in undergraduate courses in chemistry, physics, biology, applied mathematics, and bioinformatics, and as a supplement for laboratory courses in introductory chemistry, organic chemistry, physical chemistry, medicinal chemistry, chemical engineering and other courses dealing with statistical and dynamic systems. It allows the exploration of a wide range of dynamic phenomena, many of which are not normally accessible within conventional laboratory settings due to limitations of time, cost, and experimental equipment. The book is both a textbook on applied Cellular Automata and a lab manual for chemistry (physics, engineering) courses with lab activity. It would supplement other lab work and be an additonal book the students would use in the course. The authors have assessed the emerging need for this kind of activity in science labs because of the cost of the practical activitites and the frequent failure of some exercises leading to lost didactic value of some experiments. This book is pioneering an alternative that will grow in use. There are no course directors who would use Cellular Automata exclusively. The authors see an emerging interest in this kind of work in courses that contain lab exercises. One such course is the graduate course that Lemont Kier gives in Life Sciences about complexity. He uses many examples and studies from Cellular Automata in the latter part of this course.

VOLUME 12 REVIEWS IN COMPUTATIONAL CHEMISTRY Kenny B. Lipkowitz and Donald B. Boyd HOW DOES ONE COMPUTE FREE ENERGY AND ENTROPY FROM MOLECULAR SIMULATIONS? WHAT HAPPENS WHEN SIMULATIONS ARE RUN WITH CONSTRAINTS? HOW SHOULD SIMULATIONS BE PERFORMED TO MODEL INTERFACIAL PHENOMENA? HOW IS DENSITY FUNCTIONAL THEORY USED TO SIMULATE MATERIALS? WHAT QUANTUM MECHANICAL METHODS SHOULD BE USED TO COMPUTE NONLINEAR OPTICAL PROPERTIES OF MATERIALS? WHICH PARAMETERS ARE MOST INFLUENTIAL IN A MOLECULAR SIMULATION? HOW CAN CRYSTAL STRUCTURES BE PREDICTED? TUTORIALS PROVIDING ANSWERS TO THESE QUESTIONS ARE THE FOCUS OF THIS BOOK. FROM REVIEWS OF THE SERIES "The series continues to be one of the most useful information sources." -JOURNAL OF THE AMERICAN CHEMICAL SOCIETY