Related papers: Efficient methods for determining folding free ene…
We present a new computational methodology for the investigation of gel electrophoresis of polyelectrolytes. We have developed the method initially to incorporate sliding motion of tight parts of a polymer pulled by an electric field into…
We propose a model for the dynamics of a probe embedded in a living cell, where both thermal fluctuations and nonequilibrium activity coexist. The model is based on a confining harmonic potential describing the elastic cytoskeletal matrix,…
We show that, in optical pump-probe experiments on bulk samples, the statistical distribution of the intensity of ultrashort light pulses after the interaction with a nonequilibrium complex material can be used to measure the time-dependent…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
We characterize the fluctuation properties of a polymer chain under external tension and the fluctuation-induced forces between two ring molecules threaded around the chain. The problem is relevant in the context of fluctuation-induced…
We consider the random fluctuations of the free energy in the $p$-spin version of the Sherrington-Kirkpatrick model in the high temperature regime. Using the martingale approach of Comets and Neveu as used in the standard SK model combined…
The relation between thermal fluctuations and the mechanical response of a free membrane has been explored in great detail, both theoretically and experimentally. However, understanding this relationship for membranes, locally pinned by…
We measure different contributions to entropy production in a living functional epithelial tissue. We do this by extracting the functional dynamics of development while at the same time quantifying fluctuations. Using the translucent…
We present an efficient computational methodology to obtain the viscoelastic response of dilute solutions of semiflexible filaments. By considering an approach based on the fluctuation-dissipation theorem, we were able to evaluate the…
Sampling diverse, thermodynamically feasible molecular conformations plays a crucial role in predicting properties of a molecule. In this paper we propose to use GFlowNet for sampling conformations of small molecules from the Boltzmann…
The fluctuation-dissipation theorem is a cornerstone result in statistical mechanics that can be used to translate the statistics of the free natural variability of a system into information on its forced response to perturbations. By…
I investigate a disordered version of a simplified model of protein folding, with binary degrees of freedom, applied to an ideal beta-hairpin structure. Disorder is introduced by assuming that the contact energies are independent and…
We study the dynamics of a flexible fiber freely moving in a three-dimensional fully-developed turbulent field and present a phenomenological theory to describe the interaction between the fiber elasticity and the turbulent flow. This…
Quadratic trapping potentials are widely used to experimentally probe biopolymers and molecular machines and drive transitions in steered molecular-dynamics simulations. Approximating energy landscapes as locally quadratic, we design…
Fluctuations of conserved charges in a grand canonical ensemble can be calculated as derivatives of the free energy with respect to the respective chemical potential. They are directly related to experimentally available observables that…
We experimentally realize protocols that allow to extract work beyond the free energy difference from a single electron transistor at the single thermodynamic trajectory level. With two carefully designed out-of-equilibrium driving cycles…
We demonstrate a novel technique for the measurement of the charge carried by a colloidal particle. The technique uses the phenomenon of the resonance of a particle held in an optical tweezers trap and driven by a sinusoidal electric field.…
The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two…
We consider mechanically generated molecular braids composed of two molecules where long range interactions between them can be considered to be very weak. We describe a model that takes account of the thermal fluctuations of the braid,…
The free energy of inserting a protein into a membrane is determined by considering the variation in the spectrum of thermal fluctuations in response to the presence of a rigid inclusion. Both numerically and through a simple analytical…