Related papers: Mesoscopic modeling for nucleic acid chain dynamic…
The granular microstructure of metals evolves significantly during thermomechanical processing through viscoplastic deformation and recrystallization. Microstructural features such as grain boundaries (GBs), subgrains, localized deformation…
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…
The one solitary boson exchange potential (OSBEP) is used to evaluate observables of NN elastic scattering below pion threshold. In this approach, we use a nonlinear model of self-interacting mesons as a substitution for the commonly used…
We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of…
Molecular motor proteins form the basis of cellular dynamics. Recently, notable efforts have led to the creation of their DNA-based mimics, which can carry out complex nanoscale motion. However, such functional analogues have not yet been…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
Nucleosomes form the basic unit of compaction within eukaryotic genomes and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
Liquid crystals establish a nearly unique combination of thermodynamic, hydrodynamic, and topological behavior. This poses a challenge to their theoretical understanding and modeling. The arena where these effects come together is the…
We use an off - lattice bead - spring model of a self - avoiding polymer chain immersed in a 3-dimensional quenched random medium to study chain dynamics by means of a Monte - Carlo (MC) simulation. The chain center of mass mean-squared…
In this article, we report a fully ab initio variational Monte Carlo study of the linear, and periodic chain of Hydrogen atoms, a prototype system providing the simplest example of strong electronic correlation in low dimensions. In…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we…
We introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…
Atomistic simulations provide valuable insights into the physical processes governing material behavior. However, their applicability is fundamentally constrained by the limited time scales accessible to brute-force simulations. This…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. They are (i) it is a reversible hydrogel or (ii) it is a…
All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy…
DNA torsion dynamics is essential in the transcription process; a simple model for it, in reasonable agreement with experimental observations, has been proposed by Yakushevich (Y) and developed by several authors; in this, the DNA subunits…
Semiflexible polymers in concentrated lyotropic solution are studied within a bead-spring model by molecular dynamics simulations, focusing on the emergence of a smectic A phase and its properties. We systematically vary the density of the…
Neural activity patterns related to behavior occur at many scales in time and space from the atomic and molecular to the whole brain. Here we explore the feasibility of interpreting neurophysiological data in the context of many-body…