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.
Sample Chapter(s)
Chapter 1: Model-Free Statistical Reduction of Single-Molecule Time Series (1,819 KB)
Contents:
- Model-Free Statistical Reduction of Single-Molecule Time Series (H Yang)
- Testing Hypothesis with Single Molecules: Bayesian Approach (T Plakhotnik)
- Generating Functions for Single-Molecule Statistics (F L H Brown)
- Multipoint Correlation Functions for Photon Statistics in Single-Molecule Spectroscopy: Stochastic Dynamics in Liouville Space (F (anda & S Mukamel)
- Thermodynamics and Kinetics from Single-Molecule Force Spectroscopy (G Hummer & A Szabo)
- Theory of Photon Counting in Single-Molecule Spectroscopy (I V Gopich & A Szabo)
- Memory Effects in Single-Molecule Time Series (J-S Cao)
- Analysis of Experimental Observables and Oscillations in Single-Molecule Kinetics (M O Vlad & J Ross)
- Discrete-Stochastic Models of Single-Molecule Motor Proteins Dynamics (A B Kolomeisky)
- Unique Mechanisms from Finite Two-State Trajectories (O Flomenbom & R J Silbey)
- Weak Ergodicity Breaking in Single-Particle Dynamics (E Barkai)
Readership: Researchers, academics and industry practitioners in life sciences, material sciences, chemistry, physics and biophysics; suitable for graduate courses on single-molecule spectroscopy and microscopy.
Eli Barkai received his BSc, MSc (summa cum laude), and PhD (summa cum laude) in Physics from Tel-Aviv University. During his PhD studies, he developed a fractional kinetic framework describing anomalous transport in dynamical systems. In 1998, he joined the Chemistry department in Massachusetts Institute of Technology for his postdoctoral research, where he developed the theory of single-molecule spectroscopy. Dr Barkai joined the Physics department in Notre Dame University, Indiana, in the capacity of an Assistant Professor, in 2002. In 2004, he returned to Israel to join the Physics department at Bar-Ilan University. In 2006, he won the Krill prize for excellence in scientific research selected by the Wolf Foundation. His main research interests today are weak ergodicity breaking and photon counting statistics for single-molecule spectroscopy.
Frank L H Brown received his BS in Chemistry and BA in Applied Mathematics from UC Berkeley, and his PhD in Physical Chemistry from MIT in 1998. While at MIT, he worked with Robert Silbey on theoretical problems related to single-molecule spectroscopy in low-temperature systems. He then moved to UC San Diego to complete postdoctoral training in the labs of Kent Wilson and J Andrew McCammon, where his research focus shifted toward more biologically inspired problems. In 2001, Dr Brown joined the faculty at UC Santa Barbara. Dr Brown's current research interests include a variety of problems in physical chemistry and biophysics, mostly related to single-molecule statistics and lipid bilayer membranes.
Michel Orrit works in the field of the interaction of light with organic condensed matter. From 1979, he worked on surface excitons in molecular crystals with Ph Kottis in Bordeaux. During a post-doctoral stay in Göttingen in 1985 with H Kuhn and D Möbius, he worked on Langmuir-Blodgett films doped with dyes. Back in Bordeaux, he used spectral hole burning to study low-temperature dynamics and molecular orientation in ultrathin molecular films. With J Bernard, he observed the fluorescence of immobilized single molecules for the first time in 1990. Since then, single-molecule fluorescence has developed quickly in several groups throughout the world, in particular towards room temperature from 1993. Since then, M Orrit's group, first in Bordeaux, then in Leiden after 2001, has applied single-molecule spectroscopy to molecular photophysics, solid state dynamics, nonlinear optics, and to other single nano-objects, semiconductor nanocrystals and metal nanoparticles.
Haw Yang received his BS in Chemistry from National Taiwan University, and his PhD in Physical Chemistry from UC Berkeley in 1999. While at UC Berkeley, he worked with Charles Harris using femtosecond IR spectroscopy to probe the mechanism of chemical bond activation by organometallic compounds in solution. He then moved to Harvard University to complete postdoctoral training in Sunney Xie's lab, where he was exposed to single-molecule spectroscopy. In 2002, Yang joined the faculty at UC Berkeley. His current research interests include protein structure-function dynamics, semiconductor nanocrystals, and the physical and chemical states inside a cell.
