Related papers: Rebinding kinetics from single-molecule force spec…
Motivation: Measurements of gene expression over time enable the reconstruction of transcriptional networks. However, Bayesian networks and many other current reconstruction methods rely on assumptions that conflict with the differential…
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 present a spectral-theoretic approach to time-average statistical mechanics for general, non-equilibrium initial conditions. We consider the statistics of bounded, local additive functionals of reversible as well as irreversible ergodic…
Motivated by a recent work on the metabolism of carbohydrates in bacteria, we study the kinetics and thermodynamics of two classic models for reversible polymerization, one preserving the total polymer concentration and the other one not.…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
Quasiparticle dynamics in relativistic plasmas associated with hot, weakly-coupled gauge theories (such as QCD at asymptotically high temperature $T$) can be described by an effective kinetic theory, valid on sufficiently large time and…
We develop a theory of reversible diffusion-controlled reactions with generalized binding/unbinding kinetics. In this framework, a diffusing particle can bind to the reactive substrate after a random number of arrivals onto it, with a given…
A local equilibrium approach for the kinetics of a simplified protein folding model, whose equilibrium thermodynamics is exactly solvable, was developed in [M. Zamparo and A. Pelizzola, Phys. Rev. Lett. 97, 068106 (2006)]. Important…
Based on the Bell theorem, it has been believed that a theoretical computation of the Bell correlation requires explicit use of an entangled state. Such a physical superposition of light waves occurs in the downconverter sources used in…
Electronic-vibrational coupling in single-molecule junctions may result in current-induced bond rupture and is thus an important mechanism for the stability of molecular junctions. We use the hierarchical quantum master equation (HQME)…
We examine the thermally-induced fracture of an unstrained polymer chain of discrete segments coupled by an anharmonic potential by means of Molecular Dynamics simulation with a Langevin thermostat. Cases of both under- and over-damped…
We investigate the effective interaction between two like-charged rods in the regime of large electrostatic coupling parameters using both Molecular Dynamics simulation techniques and the recently introduced strong-coupling theory. We…
A systematic study for a single-specie lattice Boltzmann model with frustrated-short range attractive and mid/long-range repulsive-interactions is presented. The equilibrium analysis is performed along the guidelines proposed by [X. Shan,…
We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with…
We show how spectral submanifold theory can be used to provide analytic predictions for the response of periodically forced multi-degree-of-freedom mechanical systems. These predictions include an explicit criterion for the existence of…
The rates at which a user can generate device-independent quantum random numbers from a Bell-type experiment depend on the measurements that he performs. By numerically optimising over these measurements, we present lower bounds on the…
In this paper we study aggregation kinetics in systems of particles functionalised by complementary linkers. Most of the coarse-grained models currently employed to study large-scale self-assembly of these systems rely on effective…
We develop inference procedures robust to general forms of weak dependence. The procedures utilize test statistics constructed by resampling in a manner that does not depend on the unknown correlation structure of the data. We prove that…
Mechanically induced protein unfolding in the force-clamp apparatus is shown, in a coarse-grained model of ubiquitin, to have lognormal statistics above a treshold force and exponential below it. Correspondingly, the mean unfolding time is…