Related papers: Theoretical investigation of finite size effects a…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
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…
A model of self avoiding walks with suitable constraint has been developed to study the effect of temperature on a single stranded DNA (ssDNA) in the constant force ensemble. Our exact calculations for small chains show that the extension…
We perform a systematic analytical study of finite size effects in separable recurrent neural network models with sequential dynamics, away from saturation. We find two types of finite size effects: thermal fluctuations, and…
The thermodynamics of phase transitions between phases that are size-mismatched but coherent differs from conventional stress-free thermodynamics. Most notably, in open systems such phase transitions are always associated with hysteresis.…
We study the thermodynamic properties of a superconductor/normal metal/superconductor Josephson junction {in the short limit}. Owing to the proximity effect, such a junction constitutes a thermodynamic system where {phase difference},…
We consider an isolated point defect embedded in a homogeneous crystalline solid. We show that, in the harmonic approximation, a periodic supercell approximation of the formation free energy as well as of the transition rate between two…
In this paper we report direct measurement of large low frequency temperature fluctuations in double stranded (ds) DNA when it undergoes thermal denaturation transition. The fluctuation, which occurs only in the temperature range where the…
We analyze large deviations of the time-averaged activity in the one dimensional Fredrickson-Andersen model, both numerically and analytically. The model exhibits a dynamical phase transition, which appears as a singularity in the large…
Defect concentrations in semiconductors are strongly influenced by thermal history during growth and cooldown, yet most defect calculations assume either instantaneous quenching from high temperature or that full-equilibrium is maintained -…
We investigate the effect of thermal fluctuations on the (mean-field) Abrikosov phase. The lower critical dimension of the superconducting phase is three, indicating the absence of the Abrikosov phase for dimensions d<3. Within the d=3…
The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent…
We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the…
We present simulation data of first-order isotropic-to-nematic transitions in lattice models of liquid crystals and locate the thermodynamic limit inverse transition temperature $\epsilon_\infty$ via finite-size scaling. We observe that the…
A hallmark of a thermodynamic phase transition is the qualitative change of system thermodynamic properties such as energy and heat capacity. On the other hand, no phase transition is thought to operate in the supercritical state of matter…
We present a finite-size scaling analysis of the droplet condensation-evaporation transition of a lattice gas (in two and three dimensions) and a Lennard-Jones gas (in three dimensions) at fixed density. Parallel multicanonical simulations…
Many thermodynamic instabilities in one dimension (e.g. DNA thermal denaturation, wetting of interfaces) can be described in terms of simple models involving harmonic coupling between nearest neighbors and an asymmetric on-site potential…
We discuss the effects of external stress on the thermal denaturation of homogeneous DNA. Pulling double-stranded DNA at each end exerts a profound effect on the thermal denaturation, or melting, of a long segment of this molecule. We…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
Quantum phase transitions typically result in a broadened critical or crossover region at nonzero temperature. Josephson arrays are a model of this phenomenon, exhibiting a superconductor-insulator transition at a critical wave impedance,…