Related papers: Bubble relaxation dynamics in homopolymer DNA sequ…
We present molecular dynamics simulations on the slow dynamics of a mixture of big and small soft-spheres with a large size disparity. Dynamics are investigated in a broad range of temperature and mixture composition. As a consequence of…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
A cell dynamics method for domain separation of diblock copolymers (DBCPs) interacting with nanoparticles (NPs) whose diffusion coefficients depend on chain configuration is proposed for self-assembly of DBCP/NP composites. Increasing NP…
Blends of polymers of different topologies, such as ring and supercoiled, naturally occur in biology and often exhibit emergent viscoelastic properties coveted in industry. However, due to their complexity, along with the difficulty of…
In the proximity of melting transitions of artificial and biological membranes fluctuations in enthalpy, area, volume and concentration are enhanced. This results in domain formation, changes of the elastic constants, changes in…
The spherical dynamics of a bubble in a compressible liquid has been studied extensively since the early work of Gilmore. Numerical codes to study the behavior, including when large non-spherical deformations are involved, have since been…
By means of the Brownian dynamics (BD) method of simulations we have developed, we study dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE), focusing on the relevance of the `defect' concept due to de Gennes in…
We use molecular dynamics computer simulations to investigate the relaxation dynamics of a binary Lennard-Jones liquid confined in a narrow pore. We find that the average dynamics is strongly influenced by the confinement in that time…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
Relaxation processes in supercooled liquids are known to exhibit interesting as well as complex behavior. One of the hallmarks of this relaxation process observed in the measured auto correlation function is occurrence of multiple steps of…
A multi-time probing of density fluctuations is introduced to investigate hidden time scales of heterogeneous dynamics in glass-forming liquids. Molecular dynamics simulations for simple glass-forming liquids are performed, and a three-time…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
We use large-scale computer simulations to explore the non-equilibrium aging dynamics in a microscopic model for colloidal gels. We find that gelation resulting from a kinetically-arrested phase separation is accompanied by `anomalous'…
Time delays, modelling the process of intracellular gene expression, have been shown to have important impacts on the dynamics of pattern formation in reaction-diffusion systems. In particular, past work has shown that such time delays can…
Bubble-nucleation processes of a Lennard-Jones liquid are studied by molecular dynamics simulations. Waiting time, which is the lifetime of a superheated liquid, is determined for several system sizes, and the apparent finite-size effect of…
Slow dynamics in a fluid are studied in one of the most basic systems possible: polydisperse hard spheres. Monodisperse hard spheres cannot be studied as the slow down in dynamics as the density is increased is preempted by crystallisation.…
Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to…
Gene expression time delays, modelling the complex biological processes of gene transcription and translation, have been shown to play an important role in cellular dynamics. Time delays, motivated by the gene expression process, can also…
The formation and growth of helium bubbles due to self-irradiation in plutonium has been modelled by a discrete kinetic equations for the number densities of bubbles having $k$ atoms. Analysis of these equations shows that the bubble size…