Related papers: Experimental free energy measurements of kinetic m…
We present a method for determining the free energy of coexisting states from irreversible work measurements. Our approach is based on a fluctuation relation that is valid for dissipative transformations in partially equilibrated systems.…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…
We present two examples of how single-molecule experimental techniques applied to biological systems can give insight into problems within the scope of equilibrium and nonequilibrium mesoscopic thermodynamics. The first example is the…
Brownian dynamics simulations are used to study the detachment of a particle from a substrate. Although the model is simple and generic, we attempt to map its energy, length and time scales onto a specific experimental system, namely a bead…
We derive the optimal estimates of the free energies of an arbitrary number of thermodynamic states from nonequilibrium work measurements; the work data are collected from forward and reverse switching processes and obey a fluctuation…
The description of nonequilibrium processes in nano-sized objects, where the typical energies involved are a few times, is increasingly becoming central to disciplines as diverse as condensed-matter physics, materials science, and…
In this note we review recent progress about fluctuation relations and their applicability to free energy recovery in single molecule experiments. We underline the importance of the operational definition for the mechanical work and the…
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…
The Jarzynski equality and the fluctuation theorem relate equilibrium free energy differences to non-equilibrium measurements of the work. These relations extend to single-molecule experiments that have probed the finite-time thermodynamics…
A main goal of single-molecule experiments is to evaluate equilibrium free energy differences by applying fluctuation relations to repeated work measurements along irreversible processes. We quantify the error that is made in a free energy…
Fluctuation relations (FRs) are among the few existing general results in non-equilibrium systems. Their verification requires the measurement of the total work (or entropy production) performed on a system. Nevertheless in many cases only…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
Recent developments in statistical mechanics have allowed the estimation of equilibrium free energies from the statistics of work measurements during processes that drive the system out of equilibrium. Here a different class of processes is…
Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…
Thermodynamic bulk measurements of binding reactions critically rely on the validity of the law of mass action and the assumption of a dilute solution. Yet important biological systems such as allosteric ligand-receptor binding,…
Fluctuation theorems have become an important tool in single molecule biophysics to measure free energy differences from non-equilibrium experiments. When significant coarse-graining or noise affect the measurements, the determination of…
Fluctuation relations allow for the computation of equilibrium properties, like free energy, from an ensemble of non-equilibrium dynamics simulations. Computing them for quantum systems, however, can be difficult, as performing dynamic…
Understanding design principles of biomolecular recognition is a key question of molecular biology. Yet the enormous complexity and diversity of biological molecules hamper the efforts to gain a predictive ability for the free energy of…