Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems

What is the major difference between large and small systems? At small length-scales the dynamics is dominated by fluctuations, whereas at large scales fluctuations are irrelevant. Therefore, any thermodynamically consistent description of quantum systems necessitates a thorough understanding of the nature and consequences of fluctuations. In this chapter, we outline two closely related fields of research that are commonly considered separately -- fluctuation forces and fluct...

A method is presented that, when used in conjunction with single molecule experimental techniques, allows for the extraction of rates and mechanical properties of a biomolecule undergoing transitions between mechanically distinct states. This analysis enables the exploration of systems where the lifetimes of survival are of order of the intrinsic time constant of the experimental apparatus; permitting the study of kinetic events whose transition rates are an order of magnitud...

We discuss the possibility of existence of entanglement in biological systems. Our arguments centre on the fact that biological systems are thermodynamic open driven systems far from equilibrium. In such systems error correction can occur which may maintain entanglement despite high levels of de-coherence. We also discuss the possibility of cooling (classical or quantum) at molecular level.

Nonequilibrium energetics of single molecule translational motor kinesin was investigated by measuring heat dissipation from the violation of the fluctuation-response relation of a probe attached to the motor using optical tweezers. The sum of the dissipation and work did not amount to the input free energy change, indicating large hidden dissipation exists. Possible sources of the hidden dissipation were explored by analyzing the Langevin dynamics of the probe, which incorpo...

In the last ten years, a number of ``Conventional Fluctuation Theorems'' have been derived for systems with deterministic or stochastic dynamics, in a transient or in a non-equilibrium stationary state. These theorems gave explicit expressions for the ratio of the probability to find the system with a certain value of entropy (or heat) production to that of finding the opposite value. A similar theorem for the fluctuations of the work done on a system has recently been demons...

We review a series of experimental studies of the thermodynamics of nonequilibrium processes at the microscale. In particular, in these experiments we studied the fluctuations of the thermodynamic properties of a single optically-trapped microparticle immersed in water and in the presence of external random forces. In equilibrium, the fluctuations of the position of the particle can be described by an effective temperature that can be tuned up to thousands of Kelvins. Isother...

Biologically driven non-equilibrium fluctuations are often characterized by their non-Gaussianity or by an "effective temperature", which is frequency dependent and higher than the ambient temperature. We address these two measures theoretically by examining a randomly kicked "particle", with a variable number of kicking "motors", and show how these two indicators of non-equilibrium behavior can contradict. Our results are compared with new experiments on shape fluctuations o...

We demonstrate with an experiment how molecules are a natural test-bed for probing fundamental quantum thermodynamics. Single-molecule spectroscopy has undergone transformative change in the past decade with the advent of techniques permitting individual molecules to be distinguished and probed. By considering the time-resolved emission spectrum of organic molecules as arising from quantum jumps between states, we demonstrate that the quantum Jarzynski equality is satisfied i...

It has been shown recently that Bose Gase with weak pair (enough well) interaction is non ergodic system. But Bose Gase with weak pair interaction is so general system that it is evident that the majority of statistical mechanics systems are non ergodic too. It is also has been shown that it is possible to generalize the scheme of standard statistical mechanics and thermodynamics to take into account non ergodicity. This generalization is called a generalized thermodynamics. ...

We review methods of data analysis for biophysical data with a special emphasis on single molecule applications. Our review is intended for anyone, from student to established researcher. For someone just getting started, we focus on exposing the logic, strength and limitations of each method and cite, as appropriate, the relevant literature for implementation details. We review traditional frequentist and Bayesian parametric approaches to data analysis and subsequently exten...