cover

Contents

Cover

Editorial Board

Title Page

Copyright

Preface to the Series

Contributors to Volume 149

Chapter 1: Quantum Dynamical Resonances in Chemical Reactions: From A + BC to Polyatomic Systems

I. Introduction

II. A Few Basic Concepts

III. Experimental Approaches

IV. The Benchmark F + HD Reaction

V. An Obvious Extension: F + Methane

VI. A Less-Obvious Reaction: Cl + Methane

VII. Summary and Outlook

Acknowledgments

Chapter 2: The Multiscale Coarse-Graining Method

I. Introduction

II. Methodology

III. Results

IV. Conclusion

Acknowledgments

Chapter 3: Molecular Solvation Dynamics from Inelastic X-Ray Scattering Measurements

I. Introduction

II. Review of High-Resolution Inelastic X-Ray Scattering on Liquid Water: Theory and Experiment

III. Green's Function Imaging of Dynamics with Femtosecond Temporal and Angstrom Spatial Resolution

IV. An excluded volume implementation for Green's Function Imaging of Dynamics

V. Conclusions and Outlook

Chapter 4: Polymers Under Confinement

I. Introduction

II. Models of a Polymer Chain

III. Anisotropic Confinement

IV. Confinement in Spherical Cavities

V. Confinement in Cylindrical Cavities

VI. Confinement in Slab-Like Geometries

VII. Conclusions

Acknowledgments

Chapter 5: Computational Studies Of The Properties Of Dna-Linked Nanomaterials

1. Introduction

II. Optical Properties of DNA-Au NPs

III. Melting Properties of DNA-Au NPs

IV. Structural Properties of the Self-Assembled Materials

V. Conformation of DNA

VI. Conclusion

Chapter 6: Nanopores: Single-Molecule Sensors of Nucleic Acid-Based Complexes

I. Introduction

II. DNA Capture and Translocation Processes

III. Probing DNA/Small Molecule Interactions

IV. Nanopore-Based Genomic Profiling Using Sequence-Specific Probes

V. Summary

Author Index

Subject Index

Editorial Board

Moungi G. Bawendi Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

Kurt Binder Condensed Matter Theory Group, Institut für Physik, Johannes Gutenberg-Universität Mainz, Mainz, Germany

William T. Coffey Department of Electronics and Electrical Engineering, Trinity College, University of Dublin, Dublin, Ireland

Karl F. Freed Department of Chemistry, James Franck Institute, University of Chicago, Chicago, Illinois, USA

Daan Frenkel Department of Chemistry, Trinity College, University of Cambridge, Cambridge, United Kingdom

Pierre Gaspard Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles, Brussels, Belgium

Martin Gruebele School of Chemical Sciences and Beckman Institute, Director of Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA

Jean-Pierre Hansen Department of Chemistry, University of Cambridge, Cambridge, United Kingdom

Gerhard Hummer, Chief Theoretical Biophysics Section, NIDDK-National Institutes of Health, Bethesda, Maryland, USA

Ronnie Kosloff Department of Physical Chemistry, Institute of Chemistry and Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Israel

Ka Yee Lee Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois, USA

Todd J. Martinez Department of Chemistry, Stanford University, Stanford, California, USA

Shaul Mukamel Department of Chemistry, University of California at Irvine, Irvine, California, USA

Jose Onuchic Department of Physics, Co-Director Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California, USA

Steven Quake Department of Physics, Stanford University, Stanford, California, USA

Mark Ratner Department of Chemistry, Northwestern University, Evanston, Illinois, USA

David Reichmann Department of Chemistry, Columbia University, New York, New York, USA

George Schatz Department of Chemistry, Northwestern University, Evanston, Illinois, USA

Norbert Scherer Department of Chemistry, James Franck Institute, University of Chicago, Chicago, Illinois, USA

Steven J. Sibener Department of Chemistry, James Franck Institute, University of Chicago, Chicago, Illinois, USA

Andrei Tokmakoff Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

Donald G. Truhlar Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, USA

John C. Tully Department of Chemistry, Yale University, New Haven, Connecticut, USA

Title Page

Preface to the Series

Advances in science often involve initial development of individual specialized fields of study within traditional disciplines, followed by broadening and overlapping, or even merging, of those specialized fields, leading to a blurring of the lines between traditional disciplines. The pace of that blurring has accelerated in the last few decades, and much of the important and exciting research carried out today seeks to synthesize elements from different fields of knowledge. Examples of such research areas include biophysics and studies of nanostructured materials. As the study of the forces that govern the structure and dynamics of molecular systems, chemical physics encompasses these and many other emerging research directions. Unfortunately, the flood of scientific literature has been accompanied by losses in the shared vocabulary and approaches of the traditional disciplines, and there is much pressure from scientific journals to be ever more concise in the descriptions of studies, to the point that much valuable experience, if recorded at all, is hidden in supplements and dissipated with time. These trends in science and publishing make this series, Advances in Chemical Physics, a much needed resource.

The Advances in Chemical Physics is devoted to helping the reader obtain general information about a wide variety of topics in chemical physics, a field that we interpret very broadly. Our intent is to have experts present comprehensive analyses of subjects of interest and to encourage the expression of individual points of view. We hope that this approach to the presentation of an overview of a subject will both stimulate new research and serve as a personalized learning text for beginners in a field.

Stuart A. Rice

Aaron R. Dinner

Contributors to Volume 149

R. H. Coridan, Department of Bioengineering and California NanoSystems Institute, University of California, Los Angeles, CA 90024, USA

One-Sun Lee, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA

Kopin Liu, Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, P. O. Box 23-166, Taipei 10617, Taiwan; Department of Physics, National Taiwan University, Taipei 10617, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan

Lanyuan Lu, Computation Institute, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA

Amit Meller, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA

M. Muthukumar, Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA 01003, USA

George C. Schatz,} {Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA

Gregory A. Voth, Department of Chemistry, James Franck and Computation Institutes, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL 60637, USA

G. C. L. Wong, Department of Bioengineering and California NanoSystems Institute, University of California, Los Angeles, CA 90024, USA