Single Molecule Biophysics and Poisson Process Approach to Statistical Mechanics


Book Description

This is an overview of single molecule physics, the study of both equilibrium and non-equilibrium properties at the single molecule level. It begins with an introduction to this fascinating science and includes a chapter on how to build the most popular instrument for single molecule biophysics, the total internal reflection fluorescence (TIRF) microscope. It concludes with the Poisson process approach to statistical mechanics, explaining how to relate the process to diverse areas and see how data analysis and error bars are integral parts of science.




Introduction to the Statistics of Poisson Processes and Applications


Book Description

This book covers an extensive class of models involving inhomogeneous Poisson processes and deals with their identification, i.e. the solution of certain estimation or hypothesis testing problems based on the given dataset. These processes are mathematically easy-to-handle and appear in numerous disciplines, including astronomy, biology, ecology, geology, seismology, medicine, physics, statistical mechanics, economics, image processing, forestry, telecommunications, insurance and finance, reliability, queuing theory, wireless networks, and localisation of sources. Beginning with the definitions and properties of some fundamental notions (stochastic integral, likelihood ratio, limit theorems, etc.), the book goes on to analyse a wide class of estimators for regular and singular statistical models. Special attention is paid to problems of change-point type, and in particular cusp-type change-point models, then the focus turns to the asymptotically efficient nonparametric estimation of the mean function, the intensity function, and of some functionals. Traditional hypothesis testing, including some goodness-of-fit tests, is also discussed. The theory is then applied to three classes of problems: misspecification in regularity (MiR),corresponding to situations where the chosen change-point model and that of the real data have different regularity; optical communication with phase and frequency modulation of periodic intensity functions; and localization of a radioactive (Poisson) source on the plane using K detectors. Each chapter concludes with a series of problems, and state-of-the-art references are provided, making the book invaluable to researchers and students working in areas which actively use inhomogeneous Poisson processes.




Theory and Evaluation of Single-molecule Signals


Book Description

This book reviews recently developed theoretical and numerical approaches to deal with optical and mechanical signals from individual molecules. The character of data generated by single molecules, and more generally by single nano-objects, qualitatively differs from those obtained in conventional experiments on large ensembles of molecules. Fluctuations, randomness and irreproducibility are central to single-molecule measurements, and the specific methods required to extract reliable and statistically relevant information from them are presented here. With contributions mainly from participants of the ?Theory, Modeling and Evaluation of Single-Molecule Measurements? workshop held in Leiden, the Netherlands, on April 16-20, 2007, this book is an authoritative compendium on the subject.




Biophysics


Book Description

A physicist's guide to the phenomena of life Interactions between the fields of physics and biology reach back over a century, and some of the most significant developments in biology—from the discovery of DNA's structure to imaging of the human brain—have involved collaboration across this disciplinary boundary. For a new generation of physicists, the phenomena of life pose exciting challenges to physics itself, and biophysics has emerged as an important subfield of this discipline. Here, William Bialek provides the first graduate-level introduction to biophysics aimed at physics students. Bialek begins by exploring how photon counting in vision offers important lessons about the opportunities for quantitative, physics-style experiments on diverse biological phenomena. He draws from these lessons three general physical principles—the importance of noise, the need to understand the extraordinary performance of living systems without appealing to finely tuned parameters, and the critical role of the representation and flow of information in the business of life. Bialek then applies these principles to a broad range of phenomena, including the control of gene expression, perception and memory, protein folding, the mechanics of the inner ear, the dynamics of biochemical reactions, and pattern formation in developing embryos. Featuring numerous problems and exercises throughout, Biophysics emphasizes the unifying power of abstract physical principles to motivate new and novel experiments on biological systems. Covers a range of biological phenomena from the physicist's perspective Features 200 problems Draws on statistical mechanics, quantum mechanics, and related mathematical concepts Includes an annotated bibliography and detailed appendixes




Computational Biochemistry and Biophysics


Book Description

Covering theoretical methods and computational techniques in biomolecular research, this book focuses on approaches for the treatment of macromolecules, including proteins, nucleic acids, and bilayer membranes. It uses concepts in free energy calculations, conformational analysis, reaction rates, and transition pathways to calculate and interpret biomolecular properties gleaned from computer-generated membrane simulations. It also demonstrates comparative protein structure modeling, outlines computer-aided drug design, discusses Bayesian statistics in molecular and structural biology, and examines the RISM-SCF/MCSCF approach to chemical processes in solution.




Computational Biophysics of Membrane Proteins


Book Description

Exploring current themes in modern computational and membrane protein biophysics, this book is ideal for researchers in computational chemistry and computational biophysics.




Handbook of Single-Molecule Biophysics


Book Description

This handbook describes experimental techniques to monitor and manipulate individual biomolecules, including fluorescence detection, atomic force microscopy, and optical and magnetic trapping. It includes single-molecule studies of physical properties of biomolecules such as folding, polymer physics of protein and DNA, enzymology and biochemistry, single molecules in the membrane, and single-molecule techniques in living cells.




Single Molecule Spectroscopy


Book Description

The topics range from single molecule experiments in quantum optics and solid-state physics to analogous investigations in physical chemistry and biophysics.







Molecular and Cellular Biophysics


Book Description

Molecular and Cellular Biophysics provides advanced undergraduate and graduate students with a foundation in the basic concepts of biophysics. Students who have taken physical chemistry and calculus courses will find this book an accessible and valuable aid in learning how these concepts can be used in biological research. The text provides a rigorous treatment of the fundamental theories in biophysics and illustrates their application with examples. Conformational transitions of proteins are studied first using thermodynamics, and subsequently with kinetics. Allosteric theory is developed as the synthesis of conformational transitions and association reactions. Basic ideas of thermodynamics and kinetics are applied to topics such as protein folding, enzyme catalysis and ion channel permeation. These concepts are then used as the building blocks in a treatment of membrane excitability. Through these examples, students will gain an understanding of the general importance and broad applicability of biophysical principles to biological problems.