Related papers: Thermodynamics of DNA loops with long-range correl…
A coarse-grained molecular dynamics model of linear polyethylene-like polymer chain system was built to investigate the responds of structure and mechanical properties during uniaxial deformation. The influence of chain length, temperature,…
We numerically investigate the dynamics and linear rheology of disordered systems made of patchy particles, focussing on the role of valence, temperature and bonding mechanism. We demonstrate that the dynamics is enslaved to bonding, giving…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
Correlation-driven phenomena in molecular periodic systems are challenging to predict computationally not only because such systems are periodically infinite but also because they are typically strongly correlated. Here we generalize the…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
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…
In this work, we study long-time wave transport in correlated and uncorrelated disordered 2D arrays. When a separation of dimensions is applied to the model, we find that the predicted 1D random dimer phenomenology also appears in so-called…
The linear response to temperature changes is derived for systems with overdamped stochastic dynamics. Holding both in transient and steady state conditions, the results allow to compute nonequilibrium thermal susceptibilities from…
We observe regular patterns emerging across multiple length scales with high-concentration DNA solutions in microfluidic pillar arrays at low Reynolds numbers and high Deborah. Interacting vortices between pillars lead to long-range order…
We study quenched disorder in strongly correlated systems via holography, focusing on the thermodynamic effects of mild electric disorder. Disorder is introduced through a random potential which is assumed to self-average on macroscopic…
Under sufficiently high electric field gradients, electron behaviour within exactly perpendicular shocks is unstable to the so-called trajectory instability. We extend previous work paying special attention to shortiscale, high amplitude…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
We investigate long-range correlations (LRCs) induced by shear flow using the molecular dynamics (MD) simulation. We observe the LRCs by comparing the MD results with the linearized fluctuating hydrodynamics (LFH). We find that the MD…
The effect of a thermal environment on electron (or hole) transfer through molecular bridges and on the electron conduction properties of such bridges is studied. Our steady state formalism based on an extension of the Redfield theory (D.…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
Localization property in the disordered few-chain DNA systems with a long-range correlation is numerically investigated. We apply the chain system with the correlated disorder in the interchain and/or intrachain hoppings to the simple model…
Statistics and thermally activated dynamics of crack nucleation and propagation in a two-dimensional heterogeneous material containing quenched randomly distributed defects are studied theoretically. Using the generalized Griffith criterion…
The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this…
DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…
Based on classical statistical thermodynamics, we develop a theoretical approach that provides new insight into how macroscopic and microscopic physical properties are bridged via crystal lattice for condensed mat- ters. We find that in…