相关论文: Calibration of Tethered Particle Motion Experiment…

The extension of DNA confined to nanochannels has been studied intensively and in detail. Yet quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined…

We investigate DNA breathing dynamics by suggesting and examining several different Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base…

Optical tweezers setup is often used to probe the motion of individual tracer particle, which promotes the study of relaxation dynamics of a generic process confined in a harmonic potential. We uncover the dependence of ensemble- and…

The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling $G$ between twisting and bending, known to arise from…

The non-equilibrium structural and dynamical properties of a flexible polymer tethered to a reflecting wall and subject to oscillatory linear flow are studied by numerical simulations. Polymer is confined in two dimensions and is modeled as…

Cells and tissues are constantly exposed to various chemical and physical signals that intricately regulate various physiological and pathological processes. This study explores the integration of two biophysical methods, Traction Force…

Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…

Many structures inside the cell such as nucleosomes and protein-mediated DNA loops contain sharply bent double-stranded (ds) DNA. Therefore, the energetics of strong dsDNA bending constitutes an essential part of cellular thermodynamics.…

Previous work shows that a net directed motion arises from a system of individual particles undergoing run-and-tumble dynamics in the presence of an array of asymmetric barriers. Here, we show that when the individual particle is replaced…

2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…

For biologically relevant macromolecules such as intrinsically disordered proteins, internal degrees of freedom that allow for shape changes have a large influence on both the motion and function of the compound. A detailed understanding of…

Ensuring the stability of the AuNP-gene complex until it reaches the target sites is a crucial factor for the success of gene therapy. Though different AuNP sizes and AuNP-to-DNA ratios are investigated for specific therapeutic needs, their…

We present experimental evidence for a long-range protein-protein interaction in purple membrane (PM). The interprotein dynamics were quantified by measuring the spectrum of the acoustic phonons in the 2D bacteriorhodopsin (BR) protein…

Microelectromechanical systems (MEMS) that require contact of moving parts to implement complex functions exhibit limits to their performance and reliability. Here, we advance our particle tracking method to measure MEMS motion in operando…

Recently, it has been shown that entropy can be used to sort Brownian particles according to their size. In particular, a combination of a static and a time-dependent force applied on differently sized particles which are confined in an…

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…

Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…

We introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…

We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…

Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three…