Related papers: Facilitated diffusion on mobile DNA: configuration…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
DNA looping participates in transcriptional regulation, for instance, by allowing distal binding sites to act synergistically. Here we study this process and compare different regulatory mechanisms based on repression with and without…
Diffusive transport of particles or, more generally, small objects is a ubiquitous feature of physical and chemical reaction systems. In configurations containing confining walls or constrictions transport is controlled both by the…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as…
Fluorescence microscopy has led to impressive quantitative models and new insights gained from richer sets of biomedical imagery. However, there is a dearth of rigorous and established bioimaging strategies for modeling spatiotemporal…
We investigate the obstructed motion of tracer (test) particles in crowded environments by carrying simulations of two-dimensional Gaussian random walk in model fibrinogen monolayers of different orientational ordering. The fibrinogen…
We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…
Confined thin structures are ubiquitous in nature. Spatial and length constraints have led to a number of novel packing strategies at both the micro-scale, as when DNA packages inside a capsid, and the macro-scale, seen in plant root…
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…
Tracer diffusion in crowded environments is central to many biological and soft matter systems, but quantitative frameworks for linking tracer motion to environmental structure remain limited. Here, we study the transport of rigid tracers…
n this work, we propose a latent molecular diffusion model that can make the generated 3D molecules rich in diversity and maintain rich geometric features. The model captures the information of the forces and local constraints between atoms…
We study how double-stranded DNA translocates through graphene nanogaps. Nanogaps are fabricated with a novel capillary-force induced graphene nanogap formation technique. DNA translocation signatures for nanogaps are qualitatively…
Metagenomic binning aims to cluster DNA fragments from mixed microbial samples into their respective genomes, a critical step for downstream analyses of microbial communities. Existing methods rely on deterministic representations, such as…
The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
We study the search process of a target on a rapidly folding polymer (`DNA') by an ensemble of particles (`proteins'), whose search combines 1D diffusion along the chain, Levy type diffusion mediated by chain looping, and volume exchange. A…
We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences.…
A model for diffusion on a cubic lattice with a random distribution of traps is developed. The traps are redistributed at certain time intervals. Such models are useful for describing systems showing dynamic disorder, such as ion-conducting…