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Microstructural evolution in structural materials is known to occur in response to mechanical loading and can often accommodate substantial plastic deformation through the coupled motion of grain boundaries (GBs). This can produce desirable…
The intermittent transition between slow growth and rapid shrinkage in polymeric assemblies is termed dynamic instability, a feature observed in a variety of biochemically distinct assemblies including microtubules, actin and their…
Molecular dynamics simulations are performed to study spatially heterogeneous dynamics in a model of viscous silica above and below the critical temperature of the mode coupling theory, $T_{MCT}$. Specifically, we follow the evolution of…
The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide…
We have studied a random walk model based on majority rule. At a given instant, the moving direction of a cargo is determined by motor coordination mediated by a tug-of-war mechanism between two kinds of competing motor proteins. We have…
Collective cell motions underlie structure formation during embryonic development. Tissues exhibit emergent multicellular characteristics such as jamming, rigidity transitions, and glassy dynamics, but there remain questions about how those…
The adaptive learning capabilities seen in biological neural networks are largely a product of the self-modifying behavior emerging from online plastic changes in synaptic connectivity. Current methods in Reinforcement Learning (RL) only…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
Multispeckle x-ray photon correlation spectroscopy was employed to characterize the slow dynamics of a colloidal suspension formed by highly-charged, nanometer-sized disks. At scattering wave vectors $q$ corresponding to interparticle…
Stick-slip motion, a common phenomenon observed during crawling of cells, is found to be strongly sensitive to the substrate stiffness. Stick-slip behaviours have previously been investigated typically using purely elastic substrates. For a…
The evolutionary state of blue supergiants is still unknown. Stellar wind mass loss is one of the dominant processes determining the evolution of massive stars, and it may provide clues on the evolutionary properties of blue supergiants. As…
We develop a framework to study the role of variability in transport across a streamline of a reference flow. Two complementary schemes are presented: a graphical approach for individual cases, and an analytical approach for general…
The main objective of this work is to numerically investigate the effect of geometric imperfections on the macroscopic response and domain formation in soft biological composites that exhibit plasticity in the stiff (fiber) phase.This work…
Experimental investigations of the biosynthesis of a number of proteins have pointed out that part of the native structure can be acquired already during translation. We carried out a comprehensive statistical analysis of some average…
When an amorphous solid is deformed homogeneously, the response exhibits heterogeneous plastic instabilities with localized cooperative rearrangement of cluster of particles. The heterogeneous behavior plays an important role in deciding…
Surface roughness emerges naturally during mechanical removal of material, fracture, chemical deposition, plastic deformation, indentation, and other processes. Here, we use continuum simulations to show how roughness which is neither…
Evolution in changing environments is an important, but little studied aspect of the theory of evolution. The idea of adaptive walks in fitness landscapes has triggered a vast amount of research and has led to many important insights about…
We study the folding dynamics of polyalanine (Ala$_{20}$), a protein fragment with 20 residues whose native state is a single alpha helix. We use the CSAW model (conditioned self-avoiding walk), which treats the protein molecule as a chain…
In this study, we use discrete dislocation dynamics (DDD) simulation to investigate the effect of heterogeneous dislocation density on the transition between quasi-elastic deformation and plastic flow in face-centered cubic single crystals.…
Polyampholytes (PA) are charged polymers composed of positively and negatively charged monomers along their backbone. The sequence of the charged monomers and the bending of the chain significantly influence the conformation and dynamical…