Related papers: Dynamical versus statistical mesoscopic models for…
We present and analyze a new derivation of the meso-level behavior of a discrete microscopic model of heat transfer. This construction is based on the principle of dynamic consistency. Our work reproduces and corrects, when needed, all the…
We revisit the mesoscopic hydrodynamic description of the dynamics of sessile partially wetting compound drops, i.e., of drops that consist of two immiscible nonvolatile partially wetting liquids and are situated on a smooth rigid solid…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
Models for the microstructure evolution during hot rolling are reviewed. The basic macroscopic phenomena related to recrystallization are summarized. Constitutive models based on semi empirical equations are compared to more sophisticated…
A continuum evolutionary model for micromagnetics is presented that, beside the standard magnetic balance laws, includes thermo-magnetic coupling. To allow conceptually efficient computer implementation, inspired by relaxation method of…
We consider the links between nonlinear dynamics and thermodynamics in the framework of a simple nonlinear model for DNA. Two analyses of the phase transition, either with the transfer integral approach or by considering the instability of…
The paper discusses dynamics of quantum measurements in mesoscopic solid-state systems. The aim is to show how the general ideas of the quantum measurement theory play out in the realistic models of actual mesoscopic detectors. The two…
Nucleation, commonly associated with discontinuous transformations between metastable and stable phases, is crucial in fields as diverse as atmospheric science and nanoscale electronics. Traditionally, it is considered a microscopic process…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
We study the metastability, internal frequencies, activation mechanism, energy transfer, and the collective base-flipping in a mesoscopic DNA via resonance with specific electric fields. Our new mesoscopic DNA model takes into account not…
Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA -- subject to the earlier found unusual, frustrated…
A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
We study the dynamical melting of "hot" one-dimensional many-body localized systems. As disorder is weakened below a critical value these non-thermal quantum glasses melt via a continuous dynamical phase transition into classical thermal…
We used the Transfer-Integral method to compute, with an uncertainty smaller than 5%, the six fundamental characteristic exponents of two dynamical models for DNA thermal denaturation and investigate the validity of the scaling laws. Doubts…
We propose two different macroscopic dynamics to describe the decay of metastable phases in many-particle systems with local interactions. These dynamics depend on the macroscopic order parameter $m$ through the restricted free energy…