Related papers: Single-molecule force spectroscopy: Practical limi…
We propose an approach for estimating the probability that a given small target, among many, will be the first to be reached in a molecular dynamics simulation. Reaching small targets out of a vast number of possible configurations…
Single-molecule biophysics has transformed our understanding of the fundamental molecular processes involved in living biological systems, but also of the fascinating physics of life. Far more exotic than a collection of exemplars of soft…
The dynamics of active particles is of interest at many levels and is the focus of theoretical and experimental research. There have been many attempts to describe the dynamics of particles affected by random active forces in terms of an…
Studying the effects of one-way variation of any number of parameters on any number of output probabilities quickly becomes infeasible in practice, especially if various evidence profiles are to be taken into consideration. To provide for…
Rare transitions between long-lived metastable states underlie a great variety of physical, chemical and biological processes. Our quantitative understanding of reactive mechanisms has been driven forward by the insights of transition state…
The problem of estimating multiple loss parameters of an optical system using the most general ancilla-assisted parallel strategy is solved under energy constraints. An upper bound on the quantum Fisher information matrix is derived…
We investigate the escape rate of an overdamped, self-propelled spherical Brownian particle on a surface from a metastable potential well. Within a modeling in terms of a 1D constant speed of the particle's active dynamics we consider the…
This paper investigates a function of macroscopic variables known as the singular potential, building on previous work by Ball and Majumdar. The singular potential is a function of the admissible statistical averages of probability…
Many processes in chemistry, physics, and biology involve rare events in which the system escapes from a metastable state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation events…
Quantum experiments are observed as probability density functions. We often encounter multi-peaked densities which we model in this paper by a metastable dynamical system. The dynamics can be regarded in a thought experiment where a mouse…
We review the leading momentum, frequency and temperature dependences of the single particle self-energy and the corresponding term in the entropy of a two dimensional Fermi liquid (FL) with a free particle spectrum. We calculate the…
Cells and other soft particles are often forced to flow in confined geometries in both laboratory and natural environments, where the elastic deformation induces an additional drag and pressure drop across the particle. In contrast with…
The Social Force Model of pedestrian dynamics is formulated in a way that a) most of its parameters do not have an immediate interpretation, b) often one single parameter has an impact on many aspects of walking behavior and c) a certain…
Thermally activated escape of an over-damped particle from a metastable well under the action of a time-ramped force is studied. We express the mean first passage time (MFPT) as the solution to a partial differential equation, which we…
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…
Forced detachment of a single polymer chain, strongly-adsorbed on a solid substrate, is investigated by two complementary methods: a coarse-grained analytical dynamical model, based on the Onsager stochastic equation, and Molecular Dynamics…
Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious…
Motion of particles (bodies) in presence of random effects can be considered stochastic process. However, application of widely known stochastic processes used for description of particle motion is reduced to relatively small class of…
The kinetics of two (2D) and three (3D) dimensional diffusion-assisted escaping of Brownian particles from a potential well in the presence of an external force is analyzed in detail. The kinetics is studied within the two-state model (TSM)…