Related papers: Mesoscopic helical models for DNA
The article proposes an algorithm to model the collision between arbitrary ellipsoids in viscous fluid. It is composed of several steps, each improving upon the standard procedure employed in the current literature. First, an efficient…
We introduce a mesoscopic three-dimensional Lattice Boltzmann Model which attempts to mimick the physical features associated with cage effects in dynamically heterogeneous fluids. To this purpose, we extend the standard Lattice Boltzmann…
A semicalssical method based on surface-hopping techniques is developed to model the dynamics of radiative association with electronic transitions in arbitrary polyatomic systems. It can be proven that our method is an extension of the…
To understand mesoscopic scaling in networks, we study the hierarchical configuration model (HCM), a random graph model with community structure. The connections between the communities are formed as in a configuration model. We study the…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
Coarse-grained, mesoscale simulations are invaluable for studying soft condensed matter because of their ability to model systems in which a background solvent plays a significant role but is not the primary interest. Such methods generally…
We introduce a mesoscopic model of dynamic Tetra-PEG hydrogel networks based on a hybrid Dissipative Particle Dynamics/Monte Carlo (DPD/MC) approach. Polymer chains are described by Finite Extensible Nonlinear Elastic (FENE) potential,…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
In this work we report the study of conformation dependent electronic transport properties of DNA double-helix within tight-binding framework including its helical symmetry. We have studied the changes in localization properties of DNA as…
One-neutron halo nuclei, composed by a weakly-bound particle coupled to a core nucleus, are studied within a particle-plus-core model. A semi-microscopic method to generate the two-body Hamiltonian of such a system, including core…
Mesoscopic density functional theory for inhomogeneous mixtures of sperical particles is developed in terms of mesoscopic volume fractions by a systematic coarse-graining procedure starting form microscopic theory. Approximate expressions…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
Proteins are regularly described with some general indices (mass fractal dimension, surface fractal dimension, entropy, enthalpy, free energies, hydrophobicity, denaturation temperature etc..), which are inherently statistical in nature.…
Hybrid particle-field molecular dynamics combines standard molecular potentials with density-field models into a computationally efficient methodology that is well-adapted for the study of mesoscale soft matter systems. Here, we introduce a…
The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of…
While analyzing the persistence length of DNA atomistic simulations Wu et al. [J. Chem. Phys. 142, 125103 (2015)] introduced an empirical formula to account for the observed length-dependence. In particular they found that the persistence…
We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
A quantum field model of helical MHD stochastically forced by gaussian hydrodynamic, magnetic and mixed noices is investigated. These helical noises lead to an exponential increase of magnetic fluctuations in the large scale range.…