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Simulations are used to examine the microscopic origins of strain hardening in polymer glasses. While stress-strain curves for a wide range of temperature can be fit to the functional form predicted by entropic network models, many other…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
We report on an extensive study of craze formation in glassy polymers. Molecular dynamics simulations of a coarse-grained bead-spring model were employed to investigate the molecular level processes during craze nucleation, widening, and…
Mass conservation in chemical species appears in a broad class of reaction-diffusion systems (RDs) and is known to bring about coarsening of the pattern in chemical concentration. Recent theoretical studies on RDs with mass conservation…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Simulations are used to examine the microscopic origins of strain hardening in polymer glasses. While traditional entropic network models can be fit to the total stress, their underlying assumptions are inconsistent with simulation results.…
Experiments are conducted in a two-dimensional mono-layer vibrofluidized bed of glass beads, with a goal to understand the transition scenario and the underlying microstructure and dynamics in different patterned-states. At small shaking…
Tension-compression asymmetry is a notable feature of plasticity in bcc single crystals. Recent experiments reveal striking differences in the plasticity of bcc nanopillars for tension and compression. Here we present results from molecular…
An adhesively stressed thin film of a soft hydrogel confined between two rigid flat substrates auto-roughens with its dominant wavelength exhibiting pronounced dependence on the film thickness (H). A linear stability analysis confirmed that…
We investigate the microtubule polymerization dynamics with catastrophe and rescue events for three different confinement scenarios, which mimic typical cellular environments: (i) The microtubule is confined by rigid and fixed walls, (ii)…
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 study equilibrium shapes and shape transformations of a confined semiflexible chain inside a soft lipid tubule using simulations and continuum theories. The deformed tubular shapes and chain conformations depend on the relative magnitude…
We have carried out a quantitative analysis of the chain packing in polymeric melts using molecular dynamics simulations. The analysis involves constructing Voronoi tessellations in the equilibrated configurations of the polymeric melts. In…
Sacrificial bonds and hidden length (SBHL) in structural molecules provide a mechanism for energy dissipation at the nanoscale. It is hypothesized that their presence leads to greater fracture toughness than what is observed in materials…
Macromolecules can form regular structures on inert surfaces. We have developed a combined empirical and modeling approach to derive the bonding. From experimental scanning tunneling microscopy (STM) images of structures formed on Au(111)…
Ionic microgels are soft colloidal particles, composed of crosslinked polymer networks, that ionize and swell when dispersed in a good solvent. Swelling of these permeable, compressible particles involves a balance of electrostatic,…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
The early planetesimal growth proceeds through a sequence of sticking collisions of dust agglomerates. Very uncertain is still the relative velocity regime in which growth rather than destruction can take place. The outcome of a collision…
We develop a stochastic kinetic model of a pre-formed attachment of a mictrotuble (MT) with a cell cortex, in which the MT is tethered to the cell by a group of active motor proteins. Such an attachment is a particularly unique case of…
Bacterial colonies growing on surfaces are shaped by mechanical stresses transmitted through the community, governed by the balance between cell growth and steric and cell-substrate interactions. Using overdamped dynamics simulations of…