相关论文: Recovery of free energy branches in single molecul…
Recent advances in non-equilibrium statistical mechanics and single molecule technologies make it possible to extract free energy differences from irreversible work measurements in pulling experiments. To date, free energy recovery has been…
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…
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…
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…
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…
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 investigate the work dissipated during the irreversible unfolding of single molecules by mechanical force, using the simplest model necessary to represent experimental data. The model consists of two levels (folded and unfolded states)…
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…
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…
In this report I discuss fluctuation theorems and transient violations of the second law of thermodynamics in small systems. Special emphasis is placed on free-energy recovery methods in the framework of non-equilibrium single-molecule…
We theoretically investigate the extractable work in single molecule unfolding-folding experiments with applied feedback. Using a simple two-state model, we obtain a description of the full work distribution, from discrete to continuous…
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non covalent bonding in drug receptor systems. I show that most of the pitfalls and entanglements for the…
We used the atomic force microscope to manipulate and unfold individual molecules of the titin I27 domain and reconstructed its free energy surface using Jarzynski's equality. The free energy surface for both stretching and unfolding was…
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…
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…
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…
Non-equilibrium path integral methods for computing quantum free energy differences are applied to a quantum particle trapped in a harmonic well of uniformly changing strength with the purpose of establishing the convergence properties of…
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…
The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is investigated by using atomic force microscopy. Exploiting a fluctuation relation, the equilibrium free energy as a function of the molecule elongation is…