Related papers: Two-State Migration of DNA in a structured Microch…
We study the structural transition from `B' form of DNA to 'A' form of DNA using group theoretic methods. The transition is not of the order-disorder type and hence to construct a Landau kind of theory for the transition we define a higher…
We show that the evolution of two-component particles governed by a two-dimensional spin-orbit lattice Hamiltonian can reveal transitions between topological phases. A kink in the mean width of the particle distribution signals the closing…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
We investigate the transient nonequilibrium dynamics of a molecular junction biased by a finite voltage and strongly coupled to internal vibrational degrees of freedom. Using two different, numerical exact techniques, diagrammatic Monte…
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…
We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness…
Time-dependent perturbations can drive a trivial two-dimensional band insulator into a quantum Hall-like phase, with protected nonequilibrium states bound to its edges. We propose an experiment to probe the existence of these topological…
Simulations show that when a phase-separated binary AB fluid is driven to flow past chemically patterned substrates in a microchannel, the fluid exhibits unique morphological instabilities. For the pattern studied, these instabilities give…
We propose that semiflexible polymers in poor solvent collapse in two stages. The first stage is the well known formation of a dense toroidal aggregate. However, if the solvent is sufficiently poor, the condensate will undergo a second…
Nonlinear dynamics of two biomolecules is studied. These are a microtubule and DNA molecule. Two mathematical procedures are explained, yielding to three kinds of solitary waves moving through the systems. These waves are kinks, modulated…
The zero-temperature transmission rate spectrum of a double-chain tight-binding model for real DNA is calculated. It is shown that a band of extended-like states exists only for finite chain length with strong inter-chain coupling. While…
As a generic model for transport of interacting fermions through a barrier or interstitials in a lattice, quantum Brownian motion in a periodic potential is studied. There is a duality transformation between the continuous coordinate or…
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.…
We consider anomalous non-Markovian transport of Brownian particles in viscoelastic fluid-like media with very large but finite macroscopic viscosity under the influence of a constant force field F. The viscoelastic properties of the medium…
We investigated the translation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compared the mobilities with those obtained from previous coarse-grained equilibrium…
Cell migration is a fundamental process involved in physiological phenomena such as the immune response and morphogenesis, but also in pathological processes, such as the development of tumor metastasis. These functions are effectively…
In this paper, we report a Brownian dynamics simulation of the mobility-induced phase separation which occurs in a two-dimensional binary mixture of active soft Brownian particles, whose interactions are modeled by non-additive…
Random walks are studied on disordered cellular networks in 2-and 3-dimensional spaces with arbitrary curvature. The coefficients of the evolution equation are calculated in term of the structural properties of the cellular system. The…
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…
The macroscopic curvature induced in double helical B-DNA by regularly repeated adenine tracts (A-tracts) is a long known, but still unexplained phenomenon. This effect plays a key role in DNA studies because it is unique in the amount and…