Related papers: Can one predict DNA Transcription Start Sites by s…
Phase separation, the spontaneous segregation of density, is a ubiquitous phenomenon observed across diverse physical and biological systems. Within a crowd of motile elements, active phase separation emerges from the interplay of activity…
Cloud and bubble chambers have historically been used for particle detection, capitalizing on supersaturation and superheating, respectively. Here we present new results from a prototype snowball chamber, in which an incoming particle…
We carry out a comprehensive linear stability analysis of active Brownian particle systems around a constant homogeneous state. These scalar models, being important prototypes for the continuous description of active matter, are…
A couple of models are explained. Helicoidal PB model is studied in more details. It is shown that semi-discrete approximation yields to breather-type soliton moving along the chain. The model can explain local opening as a resonance mode.…
This paper addresses the issue of detecting change-points in multivariate time series. The proposed approach differs from existing counterparts by making only weak assumptions on both the change-points structure across series, and the…
We carry out molecular dynamics (MD) and Monte Carlo (MC) simulations to characterize nucleation in liquid clusters of 600 Lennard-Jones particles over a broad range of temperatures. We use the formalism of mean first-passage times to…
We obtain, using transfer matrix methods, the distribution function $P(R)$ of the end-to-end distance, the loop formation probability and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the…
Cryogenic liquids, particularly liquid xenon and argon, are of interest as detector media for experiments in nuclear and particle physics. Here we present a new detector diagnostic technique using piezoelectric sensors to detect bubbling of…
A novel theoretical model for bubble dynamics is established that simultaneously accounts for the liquid compressibility, phase transition, oscillation, migration, ambient flow field, etc. The bubble dynamics equations are presented in a…
The purpose of this paper is to show that it is possible to replace Monod's type model of a chemostat by a constraint based model of bacteria at the genome scale. This new model is an extension of the RBA model of bacteria developed in a…
Recent Chandra and XMM-Newton observations of galaxy cluster cooling flows have revealed X-ray emission voids of up to 30 kpc in size that have been identified with buoyant, magnetized bubbles. Motivated by these observations, we have…
A nonlocal diffuse interface model is used to study bubble assemblies in ternary systems. As model parameters vary, a large number of morphological phases appear as stable stationary states. One open question related to the polarity…
The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…
Trapping by active sites on surfaces plays important roles in various chemical and biological processes, including catalysis, enzymatic reactions, and viral entry into host cells. However, the mechanisms of these processes remain not well…
We investigate the kinetics of the DNA melting transition using modified versions of the Peyrard-Dauxois-Bishop and Poland-Scheraga models that include long and short range interactions. Using Brownian dynamics and Monte Carlo simulations,…
In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins…
Motion of chemically driven droplets is analyzed by applying a solvability condition of perturbed hydrodynamic equations affected by the adsorbate concentration. Conditions for traveling bifurcation analogous to a similar transition in…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
Turing's theory of pattern formation has been used to describe the formation of self-organised periodic patterns in many biological, chemical and physical systems. However, the use of such models is hindered by our inability to predict, in…