Related papers: Statistical physics and mesoscopic modeling to int…
Conventional analysis of in vitro assays of motor proteins rests on the assumption that all proteins with the same chemical composition function identically; however molecule-to-molecule variation is often seen even in well-controlled…
We use Stokesian Dynamics simulations to study the microscopic motion of particles suspended in fluids passing through porous media. We construct model porous media with fixed spherical particles, and allow mobile ones to move through this…
In the so-called "microscopic" models of vehicular traffic, attention is paid explicitly to each individual vehicle each of which is represented by a "particle"; the nature of the "interactions" among these particles is determined by the…
Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent…
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…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
It is well established that gene expression can be modeled as a Markovian stochastic process and hence proper observables might be subjected to large fluctuations and rare events. Since dynamics is often more than statics, one can work with…
Particle tracking velocimetry in 3D is becoming an increasingly important imaging tool in the study of fluid dynamics, combustion as well as plasmas. We introduce a dynamic discrete tomography algorithm for reconstructing particle…
The aim of this review is to provide a concise overview of some of the generic approaches that have been developed to deal with the statistical description of large systems of interacting dissipative 'units'. The latter notion includes,…
Stochastic modelling provides an indispensable tool for understanding how random events at the molecular level influence cellular functions. In practice, the common challenge is to calibrate a large number of model parameters against the…
The convergence of statistical learning and molecular physics is transforming our approach to modeling biomolecular systems. Physics-informed machine learning (PIML) offers a systematic framework that integrates data-driven inference with…
Single-molecule stretching experiments on DNA, RNA, and other biological macromolecules opened up the possibility of an impressive progress in many fields of Life and Medical sciences. The reliability of such experiments may be crucially…
The observation of light super-partners from a supersymmetric extension to the Standard Model is an intensely sought-after experimental outcome, providing an explanation for the stabilization of the electroweak scale and indicating the…
The dynamics of particles moving in a medium defined by its relativistically invariant stochastic properties is investigated. For this aim, the force exerted on the particles by the medium is defined by a stationary random variable as a…
DNA microarrays are a relatively new technology that can simultaneously measure the expression level of thousands of genes. They have become an important tool for a wide variety of biological experiments. One of the most common goals of DNA…
Mouse-tracking recording techniques are becoming very attractive in experimental psychology. They provide an effective means of enhancing the measurement of some real-time cognitive processes involved in categorization, decision-making, and…
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…
We consider the problem of reconstructing the paths of a set of points over time, where, at each of a finite set of moments in time the current positions of points in space are only accessible through some small number of their X-rays. This…
A two level model of a single molecule undergoing spectral diffusion dynamics and interacting with a sequence of two short laser pulses is investigated. Analytical solution for the probability of n=0,1,2 photon emission events for the…
Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected…