Volume EditorsTamiki Komatsuzaki is a Professor in the Molecule and Life Nonlinear Sciences Laboratory, Research Institute for Electronic Science at Hokkaido University in Japan. His research interests include origin of selectivity and stochasticity of reactions, single-molecule biophysics, as well as protein landscape and complexity in kinetics and dynamics. Masaru Kawakami is an Associate Professor at the Japan Advanced Institute of Science and Technology (JAIST) School of Material Science. He specializes in biophysics, single-molecule measurement, protein folding, and structural biology, and his research focuses on single-molecule dynamics of biomolecules.Satoshi Takahashi is a Professor at the Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Japan. His research focuses on protein folding and functional dynamics.Haw Yang is an Associate Professor in the Department of Chemistry at Princeton University. His current research focuses on high-resolution quantitative single-molecule protein dynamics and real-time 3D single-particle tracking spectroscopy.Robert J. Silbey is the Class of 1942 Professor of Chemistry at MIT. His research involves theoretical studies of single-molecule spectroscopy at low temperatures, energy and electron transfer and relaxation in molecular aggregates, the optical and electronic properties of conjugated oligomers and polymers, and the transport of charge in organic systems.Series EditorsStuart A. Rice received his master's and doctorate from Harvard University and was a junior fellow at Harvard for two years before joining the faculty of the University of Chicago in 1957, where he is currently the Frank P. Hixon Distinguished Service Professor Emeritus.Aaron R. Dinner received his bachelor's degree and doctorate from Harvard University, after which he conducted postdoctoral research at the University of Oxford and the University of California, Berkeley. He joined the faculty at the University of Chicago in 2003.

• Preface xiii Part One Developments on Single-Molecule ExperimentsStaring at a Protein: Ensemble and Single-Molecule Investigations on Protein-Folding Dynamics 3By Satoshi Takahashi and Kiyoto KamagataSingle-Molecule FRET of Protein-Folding Dynamics 23By Daniel Nettels and Benjamin SchulerQuantitative Analysis of Single-Molecule FRET Signals and its Application to Telomere DNA 49By Kenji Okamoto and Masahide TerazimaForce to Unbind Ligand–Receptor Complexes and the Internal Rigidity of Globular Proteins Probed by Single-Molecule Force Spectroscopy 71By Atsushi Ikai, Rehana Afrin, and Hiroshi SekiguchiRecent Advances in Single-Molecule Biophysics with the Use of Atomic Force Microscopy 89By Masaru Kawakami and Yukinori TaniguchiDynamical Single-Molecule Observations of Membrane Protein Using High-Energy Probes 133By Yuji C. SasakiSingle-Molecular Gating Dynamics for the KcsA Potassium Channel 147By Shigetoshi Oiki, Hirofumi Shimizu, Masayuki Iwamoto, and Takashi KonnoStatic and Dynamic Disorder in IN VITRO Reconstituted Receptor–Adaptor Interaction 195By Hiroaki Takagi, Miki Morimatsu, and Yasushi SakoPart Two Developments on Single-Molecule Theories and AnalysesChange-Point Localization and Wavelet Spectral Analysis of Single-Molecule Time Series 219By Haw YangTheory of Single-Molecule FRET Efficiency Histograms 245By Irina V. Gopich and Attila SzaboMultidimensional Energy Landscapes in Single-Molecule Biophysics 299By Akinori Baba and Tamiki KomatsuzakiGeneralized Michaelis–Menten Equation for Conformation Modulated Monomeric Enzymes 329By Jianlan Wu and Jianshu CaoMaking it Possible: Constructing a Reliable Mechanism from a Finite Trajectory 367By Ophir FlomenbomFree Energy Landscapes of Proteins: Insights from Mechanical Probes 395By Zu Thur Yew, Peter D. Olmsted, and Emanuele PaciMechanochemical Coupling Revealed by the Fluctuation Analysis of Different Biomolecular Motors 419By Hiroaki Takagi and Masatoshi NishikawaAuthor Index 437Subject Index 467

Volume EditorsTamiki Komatsuzaki is a Professor in the Molecule and Life Nonlinear Sciences Laboratory, Research Institute for Electronic Science at Hokkaido University in Japan. His research interests include origin of selectivity and stochasticity of reactions, single-molecule biophysics, as well as protein landscape and complexity in kinetics and dynamics. Masaru Kawakami is an Associate Professor at the Japan Advanced Institute of Science and Technology (JAIST) School of Material Science. He specializes in biophysics, single-molecule measurement, protein folding, and structural biology, and his research focuses on single-molecule dynamics of biomolecules.Satoshi Takahashi is a Professor at the Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Japan. His research focuses on protein folding and functional dynamics.Haw Yang is an Associate Professor in the Department of Chemistry at Princeton University. His current research focuses on high-resolution quantitative single-molecule protein dynamics and real-time 3D single-particle tracking spectroscopy.Robert J. Silbey is the Class of 1942 Professor of Chemistry at MIT. His research involves theoretical studies of single-molecule spectroscopy at low temperatures, energy and electron transfer and relaxation in molecular aggregates, the optical and electronic properties of conjugated oligomers and polymers, and the transport of charge in organic systems.Series EditorsStuart A. Rice received his master's and doctorate from Harvard University and was a junior fellow at Harvard for two years before joining the faculty of the University of Chicago in 1957, where he is currently the Frank P. Hixon Distinguished Service Professor Emeritus.Aaron R. Dinner received his bachelor's degree and doctorate from Harvard University, after which he conducted postdoctoral research at the University of Oxford and the University of California, Berkeley. He joined the faculty at the University of Chicago in 2003.

• Preface xiii Part One Developments on Single-Molecule ExperimentsStaring at a Protein: Ensemble and Single-Molecule Investigations on Protein-Folding Dynamics 3By Satoshi Takahashi and Kiyoto KamagataSingle-Molecule FRET of Protein-Folding Dynamics 23By Daniel Nettels and Benjamin SchulerQuantitative Analysis of Single-Molecule FRET Signals and its Application to Telomere DNA 49By Kenji Okamoto and Masahide TerazimaForce to Unbind Ligand–Receptor Complexes and the Internal Rigidity of Globular Proteins Probed by Single-Molecule Force Spectroscopy 71By Atsushi Ikai, Rehana Afrin, and Hiroshi SekiguchiRecent Advances in Single-Molecule Biophysics with the Use of Atomic Force Microscopy 89By Masaru Kawakami and Yukinori TaniguchiDynamical Single-Molecule Observations of Membrane Protein Using High-Energy Probes 133By Yuji C. SasakiSingle-Molecular Gating Dynamics for the KcsA Potassium Channel 147By Shigetoshi Oiki, Hirofumi Shimizu, Masayuki Iwamoto, and Takashi KonnoStatic and Dynamic Disorder in IN VITRO Reconstituted Receptor–Adaptor Interaction 195By Hiroaki Takagi, Miki Morimatsu, and Yasushi SakoPart Two Developments on Single-Molecule Theories and AnalysesChange-Point Localization and Wavelet Spectral Analysis of Single-Molecule Time Series 219By Haw YangTheory of Single-Molecule FRET Efficiency Histograms 245By Irina V. Gopich and Attila SzaboMultidimensional Energy Landscapes in Single-Molecule Biophysics 299By Akinori Baba and Tamiki KomatsuzakiGeneralized Michaelis–Menten Equation for Conformation Modulated Monomeric Enzymes 329By Jianlan Wu and Jianshu CaoMaking it Possible: Constructing a Reliable Mechanism from a Finite Trajectory 367By Ophir FlomenbomFree Energy Landscapes of Proteins: Insights from Mechanical Probes 395By Zu Thur Yew, Peter D. Olmsted, and Emanuele PaciMechanochemical Coupling Revealed by the Fluctuation Analysis of Different Biomolecular Motors 419By Hiroaki Takagi and Masatoshi NishikawaAuthor Index 437Subject Index 467

Volume EditorsTamiki Komatsuzaki is a Professor in the Molecule and Life Nonlinear Sciences Laboratory, Research Institute for Electronic Science at Hokkaido University in Japan. His research interests include origin of selectivity and stochasticity of reactions, single-molecule biophysics, as well as protein landscape and complexity in kinetics and dynamics. Masaru Kawakami is an Associate Professor at the Japan Advanced Institute of Science and Technology (JAIST) School of Material Science. He specializes in biophysics, single-molecule measurement, protein folding, and structural biology, and his research focuses on single-molecule dynamics of biomolecules.Satoshi Takahashi is a Professor at the Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Japan. His research focuses on protein folding and functional dynamics.Haw Yang is an Associate Professor in the Department of Chemistry at Princeton University. His current research focuses on high-resolution quantitative single-molecule protein dynamics and real-time 3D single-particle tracking spectroscopy.Robert J. Silbey is the Class of 1942 Professor of Chemistry at MIT. His research involves theoretical studies of single-molecule spectroscopy at low temperatures, energy and electron transfer and relaxation in molecular aggregates, the optical and electronic properties of conjugated oligomers and polymers, and the transport of charge in organic systems.Series EditorsStuart A. Rice received his master's and doctorate from Harvard University and was a junior fellow at Harvard for two years before joining the faculty of the University of Chicago in 1957, where he is currently the Frank P. Hixon Distinguished Service Professor Emeritus.Aaron R. Dinner received his bachelor's degree and doctorate from Harvard University, after which he conducted postdoctoral research at the University of Oxford and the University of California, Berkeley. He joined the faculty at the University of Chicago in 2003.

• Preface xiii Part One Developments on Single-Molecule ExperimentsStaring at a Protein: Ensemble and Single-Molecule Investigations on Protein-Folding Dynamics 3By Satoshi Takahashi and Kiyoto KamagataSingle-Molecule FRET of Protein-Folding Dynamics 23By Daniel Nettels and Benjamin SchulerQuantitative Analysis of Single-Molecule FRET Signals and its Application to Telomere DNA 49By Kenji Okamoto and Masahide TerazimaForce to Unbind Ligand–Receptor Complexes and the Internal Rigidity of Globular Proteins Probed by Single-Molecule Force Spectroscopy 71By Atsushi Ikai, Rehana Afrin, and Hiroshi SekiguchiRecent Advances in Single-Molecule Biophysics with the Use of Atomic Force Microscopy 89By Masaru Kawakami and Yukinori TaniguchiDynamical Single-Molecule Observations of Membrane Protein Using High-Energy Probes 133By Yuji C. SasakiSingle-Molecular Gating Dynamics for the KcsA Potassium Channel 147By Shigetoshi Oiki, Hirofumi Shimizu, Masayuki Iwamoto, and Takashi KonnoStatic and Dynamic Disorder in IN VITRO Reconstituted Receptor–Adaptor Interaction 195By Hiroaki Takagi, Miki Morimatsu, and Yasushi SakoPart Two Developments on Single-Molecule Theories and AnalysesChange-Point Localization and Wavelet Spectral Analysis of Single-Molecule Time Series 219By Haw YangTheory of Single-Molecule FRET Efficiency Histograms 245By Irina V. Gopich and Attila SzaboMultidimensional Energy Landscapes in Single-Molecule Biophysics 299By Akinori Baba and Tamiki KomatsuzakiGeneralized Michaelis–Menten Equation for Conformation Modulated Monomeric Enzymes 329By Jianlan Wu and Jianshu CaoMaking it Possible: Constructing a Reliable Mechanism from a Finite Trajectory 367By Ophir FlomenbomFree Energy Landscapes of Proteins: Insights from Mechanical Probes 395By Zu Thur Yew, Peter D. Olmsted, and Emanuele PaciMechanochemical Coupling Revealed by the Fluctuation Analysis of Different Biomolecular Motors 419By Hiroaki Takagi and Masatoshi NishikawaAuthor Index 437Subject Index 467