相关论文: Two-State Migration of DNA in a structured Microch…
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,…
T cells use sophisticated shape dynamics (morphodynamics) to migrate towards and neutralise infected and cancerous cells. However, there is limited quantitative understanding of the migration process in 3D extracellular matrices (ECMs) and…
We study the dynamics of the passage of a stiff chain through a pore into a cell containing particles that bind reversibly to it. Using Brownian Molecular Dynamics simulations we investigate the mean-first-passage time as a function of the…
Intermediate filaments form an essential structural network, spread throughout the cytoplasm and play a key role in cell mechanics, intracellular organization and molecular signaling. The maintenance of the network and its adaptation to the…
In this letter, we study the structure-transport property relationships of small ligand intercalated DNA molecules using a multiscale modelling approach where extensive ab-initio calculations are performed on numerous MD-simulated…
We study an intermediate quantum coherent-incoherent charge transport mechanism in metal-molecule-metal junctions using B\"uttiker's probe technique. This tool allows us to include incoherent effects in a controlled manner, and thus to…
Diffusion of tracer particles in the cytoplasm of mammalian cells is often anomalous with a marked heterogeneity even within individual particle trajectories. Despite considerable efforts, the mechanisms behind these observations have…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
By means of the Brownian dynamics (BD) method of simulations we have developed, we study dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE), focusing on the relevance of the `defect' concept due to de Gennes in…
Active transport of biomolecular condensates and cell migration in collectives are fundamental to development, homeostasis, and processes such as cancer progression, wound healing, and infection response. Yet how these assemblies are…
Electron transport experiments on two lateral quantum dots coupled in series are reviewed. An introduction to the charge stability diagram is given in terms of the electrochemical potentials of both dots. Resonant tunneling experiments show…
We provide a rigorous solution to the problem of constructing a structural evolution for a network of coupled identical dynamical units that switches between specified topologies without constraints on their structure. The evolution of the…
The transport behavior of a system of gravitationally driven colloidal particles is investigated. The particle interactions are determined by the superparamagnetic behavior of the particles. They can thus be arranged in a crystalline order…
We study the Grain Boundary (GB) migration based on the underlying disconnection structure and mechanism. Disconnections are line defects that lie solely within a GB and are characterized by both a Burgers vector and a step height, as set…
We perform a spatially resolved simulation study of an AND gate based on DNA strand displacement using several lengths of the toehold and the adjacent domains. DNA strands are modelled using a coarse-grained dynamic bonding model {[}C.…
T cells undergo large shape changes (morphodynamics) when migrating. While progress has been made elucidating the molecular basis of cell migration, statistical characterization of morphodynamics and migration has been limited, particularly…
We study the topological configurations and dynamics of individual point defect vacancies and interstitials in a two-dimensional colloidal crystal. Our Brownian dynamics simulations show that the diffusion mechanism for vacancy defects…
Literature data on the properties of DNA open states are reviewed and analyzed. These states are formed as a result of strong DNA fluctuations and have a great impact on a number of biochemical processes; among them is charge transfer in…
The long time dynamics of the conformational transition from B-DNA to Z-DNA is shown to undergo a dynamic phase transition. We obtained the dynamic phase diagram for the stability of the front separating B and Z. The instability in this…
Stochastic Resonance in single voltage-dependent ion channels is investigated within a three state non-Markovian modeling of the ion channel conformational dynamics. In contrast to a two-state description one assumes the presence of an…