相关论文: Energy Localization in the Peyrard-Bishop DNA mode…

Two models for energy and charge transport and storage in biomolecules are considered. A model based on the discrete nonlinear Schrodinger equation with long-range dispersive interactions (LRI's) between base pairs of DNA is offered for the…

DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force…

We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…

The estimation of rare event probabilities plays a pivotal role in diverse fields. Our aim is to determine the probability of a hazard or system failure occurring when a quantity of interest exceeds a critical value. In our approach, the…

Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…

In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins…

In this first of two papers, we present a new method for searching for oscillatory features in the primordial power spectrum. A wide variety of models predict these features in one of two different flavors: logarithmically spaced…

We examine quantum percolation on a square lattice with random dilution up to $q=38%$ and energy $0.001 \le E \le 1.6$ (measured in units of the hopping matrix element), using numerical calculations of the transmission coefficient at a much…

The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…

The response of a semiflexible polyelectrolyte chain to stretching in the regimes of moderate and weak screening is studied theoretically, with a special focus on DNA experiments. By using the nonlinear Poisson--Boltzmann description of…

We propose a new scheme for constraining the dark energy equation of state parameter/parameters based on the study of the evolution of the configuration entropy. We analyze a set of one parameter and two parameter dynamical dark energy…

This work examines the impact of energy over-minimization on an ensemble of biological molecules subjected to the potential energy minimization procedure in vacuum. In the studied structures, long potential energy minimization stage leads…

We introduce the Hierarchically Interacting Particle Neural Network (HIP-NN) to model molecular properties from datasets of quantum calculations. Inspired by a many-body expansion, HIP-NN decomposes properties, such as energy, as a sum over…

We demonstrate that period-doubled discrete breathers appear from the anti-continuum limit of the driven Peyrard-Bishop-Dauxois model of DNA. These novel breathers result from a stability overlap between sub-harmonic solutions of the driven…

Low-energy electrons offer a unique possibility for long exposure imaging of individual biomolecules without significant radiation damage. In addition, low-energy electrons exhibit high sensitivity to local potentials and thus can be…

We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…

The impact of various types of external potentials to the Peyrard-Bishop DNA denaturation is investigated through statistical mechanics approach. The partition function is obtained using transfer integral method, and further the stretching…

In the present paper we study the impact of dispersion and nonlinearity on DNA dynamics. We rely on the helicoidal Peyrard-Bishop model and use the fact that nonlinear DNA dynamics represents an interplay between nonlinearity and…

The formation of polaron and its migration in a DNA chain are studied within a semiclassical Peyrard-Biship-Holstein polaron model. Comparing the energetics of the polaron system found from the quantum chemical and semiclassical…

Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations:…