Related papers: Mesoscopic modeling for nucleic acid chain dynamic…
Mesoscopic molecular dynamics simulations are used to determine the large scale structure of several binary polymer mixtures of various chemical architecture, concentration, and thermodynamic conditions. By implementing an analytical…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
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,…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
Posttranslational modification of proteins is key in transmission of signals in cells. Many signaling pathways contain several layers of modification cycles that mediate and change the signal through the pathway. Here, we study a simple…
The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…
A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
The nuclear spin, being much more isolated from the environment than its electronic counterpart, enables quantum experiments with prolonged coherence times and presents a gateway towards uncovering the intricate dynamics within an atom.…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
We describe a complete methodology to bridge the scales between nanoscale Molecular Dynamics and (micrometer) mesoscale Monte Carlo simulations in lipid membranes and vesicles undergoing phase separation, in which curving molecular species…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
Accurate identification of protein nucleic-acid-binding residues poses a significant challenge with important implications for various biological processes and drug design. Many typical computational methods for protein analysis rely on a…
One aim of the equal load sharing fiber bundle model is to describe the critical behavior of failure events. One way of accomplishing this, is through a discrete recursive dynamics. We introduce a continuous mesoscopic equation catching the…