Related papers: Mesoscopic modeling for nucleic acid chain dynamic…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
Nonlinear vibrations in strained monoatomic carbon chains are studied with the aid of ab initio methods based on the density functional theory. An unexpected phenomenon of structural transformation at the atomic level above a certain value…
Past models of stress-strain response under cyclic loading mainly rely on macroscopic equations which consider microstructure evolution indirectly or simply discard microstructure information. Modern materials science, on the other hand,…
Nuclear magnetic resonance (NMR) is a powerful method for determining the structure of molecules and proteins. While conventional NMR requires averaging over large ensembles, recent progress with single-spin quantum sensors has created the…
Bacterial chromosome replication occurs in the absence of a canonical spindle apparatus; yet it reliably produces organised and segregated genomes. While both passive and active mechanisms have been investigated, DNA replication itself is a…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
The phase transition kinetics in three phase systems was investigated using the numerically efficient cell dynamics method. A phasefield model with a simple analytical free energy and single order parameter was used to study the kinetics…
Molecular dynamics simulations are used to study the spreading of binary polymer nanodroplets in a cylindrical geometry. The polymers, described by the bead-spring model, spread on a flat surface with a surface-coupled Langevin thermostat…
A kinetic Monte Carlo approach is applied to study physical mechanisms responsible for the breakup of nanowires with the diamond cubic crystal structure into a chain of nanoparticles discovered in preceding experiments on Silicon nanowires.…
We compare a newly developed hybrid simulation method which combines classical molecular dynamics (MD) and computational fluid dynamics (CFD) to a simulation consisting only of molecular dynamics. The hybrid code is composed of three…
We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical and thermodynamic properties of RNA,…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
Codon usage bias has a crucial impact on the translation efficiency and co-translational folding of proteins, necessitating the algorithmic development of codon optimization/harmonization methods, particularly for heterologous recombinant…
A rigorous mathematical framework for analyzing the chemical master equation (CME) with bistability, based on the theory of large deviation, is proposed. Using a simple phosphorylation-dephosphorylation cycle with feedback as an example, we…
We introduce a machine learning approach to determine the transition dynamics of silicon atoms on a single layer of carbon atoms, when stimulated by the electron beam of a scanning transmission electron microscope (STEM). Our method is…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Computer modeling of multicellular systems has been a valuable tool for interpreting and guiding in vitro experiments relevant to embryonic morphogenesis, tumor growth, angiogenesis and, lately, structure formation following the printing of…
Cell-cell adhesion plays a vital role in the development and maintenance of multicellular organisms. One of its functions is regulation of cell migration, such as occurs, e.g. during embryogenesis or in cancer. In this work, we develop a…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…