Related papers: DNA confined in a two-dimensional strip geometry
We study the quench dynamics of a two dimensional superconductor in a lattice of size up to $200\times 200$ employing the self-consistent time dependent Bogoliubov-de Gennes (BdG) formalism. In the clean limit, the dynamics of the order…
Single-molecule force-extension experiments have allowed quantitative measurements of the mechanical responses of biomolecules to applied forces explaining their roles in key biological functions. Electrophoretic stretching of charged…
The conformational states of a semiflexible polymer enclosed in a volume $V:=\ell^{3}$ are studied as stochastic realizations of paths using the stochastic curvature approach developed in [Rev. E 100, 012503 (2019)], in the regime whenever…
The transport of nanoparticles (NPs) in polymer networks, as a typical simplified model describing various structures in living systems, is profoundly important in biomedical engineering and nanotechnology. Predicting the effective…
We report on nano-infrared (IR) imaging studies of confined plasmon modes inside patterned graphene nanoribbons (GNRs) fabricated with high-quality chemical-vapor-deposited (CVD) graphene on Al2O3 substrates. The confined geometry of these…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The cellular cytoplasm is organized into compartments. Phase separation is a simple manner to create membrane-less compartments in order to confine and localize particles like proteins. In many cases these particles are bound to fluctuating…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
We study the electronic structure within a system of phase-decoupled one-dimensional superconductors coexisting with stripe spin and charge density wave order. This system has a nodal Fermi surface (Fermi arc) in the form of a hole pocket…
We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude $F$ and frequency $\nu$ and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis…
Diffusion properties of a self-avoiding polymer embedded in regularly distributed obstacles with spacing a=20 and confined in two dimensions is studied numerically using the extended bond fluctuation method which we have developed recently.…
Using molecular dynamics simulation of a standard bead-spring model we investigate the density crossover scaling of strictly two-dimensional self-avoiding polymer chains focusing on properties related to the contact exponent set by the…
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…
Strain-inducing deformations in graphene alter charge distributions and provide a new method to design specific features in the band structure and transport properties. Novel approaches implement engineered substrates to induce specifically…
When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension…
We consider the lattice model for an ideal-linear polymer chain to mimic the conformations of the semi-flexible homo-polymer chain. The polymer chain is assumed to confine in the fairly small area, such that the flexible chain conformations…
A theory is presented of DNA hairpins enclosed in a nanochannel. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The free energy of the hairpin computed…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
In these lecture notes, which are based on the mini-course given at 2013 Prague School on Mathematical Statistical Physics, we discuss ballistic phase of quenched and annealed stretched polymers in random environment on ${\mathbb Z}^d$ with…
We present a critique and extension of the mean-field approach to the mechanical pulling transition in bound polymer systems. Our model is motivated by the theoretically and experimentally important examples of adsorbed polymers and…