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

The nonequilibrium activity taking place in a living cell can be monitored with a tracer embedded in the medium. While microrheology experiments based on optical manipulation of such probes have become increasingly standard, we put forward a number of experiments with alternative protocols that, we claim, will provide new insight into the energetics of active fluctuations. These are based on either performing thermodynamic--like cycles in control-parameter space, or on determ...

The existence of fluctuations of temperature has been a somewhat controversial topic in thermodynamics but nowadays it is recognized that they must be taken into account in small, finite systems. Although for nonequilibrium steady states superstatistics is becoming the \textit{de facto} framework for expressing such temperature fluctuations, some recent results put into question the idea of temperature as a phase space observable. In this work we present and explore the stati...

In the past decades, advances in microscopy have made it possible to study the dynamics of individual biomolecules in vitro and resolve intramolecular kinetics that would otherwise be hidden in ensemble averages. More recently, single-molecule methods have been used to image, localize and track individually labeled macromolecules in the cytoplasm of living cells, allowing investigations of intermolecular kinetics under physiologically relevant conditions. In this review, we i...

One of the important challenges facing high resolution molecular dynamics calculations is to reproduce biological functions that occur in the macroscopic world and involve macroscopic variables. Some of these functions can be well described by reduced models, with few parameters, over a wide range of conditions, even though the functions are complex. We are all eager to see how molecular dynamics will accurately estimate the thermodynamic variables that define and control so ...

Here, we discuss a collection of cutting-edge techniques and applications in use today by some of the leading experts in the field of correlative approaches in single-molecule biophysics. A key difference in emphasis, compared with traditional single-molecule biophysics approaches detailed previously, is on the emphasis of the development and use of complex methods which explicitly combine multiple approaches to increase biological insights at the single-molecule level. These...

The esteemed physicist Erwin Schroedinger, whose name is associated with the most notorious equation of quantum mechanics, also wrote a brief essay entitled 'What is Life?', asking: 'How can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?' The 60+ years following this seminal work have seen enormous developments in our understanding of biology on the molecular scale, physics playing a ke...

Molecular machines transduce free energy between different forms throughout all living organisms. While truly machines in their own right, unlike their macroscopic counterparts molecular machines are characterized by stochastic fluctuations, overdamped dynamics, and soft components, and operate far from thermodynamic equilibrium. In addition, information is a relevant free-energy resource for molecular machines, leading to new modes of operation for nanoscale engines. Towards...

Information transmission in cells occurs quite accurately even when concentration changes are "read" by individual target molecules. In this Letter we study molecule number fluctuations when molecules diffuse and react. We show that, for immobile binding sites, fluctuations in the number of bound molecules are averaged out on a relatively fast timescale due to correlations. This result can explain the observed co-existence of highly fluctuating instantaneous transcriptional a...

Living things avoid equilibrium using molecular machines. Such microscopic soft-matter objects encounter relatively large friction and fluctuations. We discuss design principles for effective molecular machine operation in this unfamiliar context.

Small systems in a thermodynamic medium --- like colloids in a suspension or the molecular machinery in living cells --- are strongly affected by the thermal fluctuations of their environment. Physicists model such systems by means of stochastic processes. Stochastic Thermodynamics (ST) defines entropy changes and other thermodynamic notions for individual realizations of such processes. It applies to situations far from equilibrium and provides a unified approach to stochast...