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Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
Elastomers saturated with gas at high pressure suffer from cavity nucleation, inflation, and deflation upon rapid or explosive de-compression. Although this process often results in undetectable changes in appearance, it causes internal…
We demonstrate the use of multiscale polymer modelling to quantitatively predict DNA linear dichroism (LD) in shear flow. LD is the difference in absorption of light polarised along two perpendicular axes, and has long been applied to study…
Motivated by single molecule experiments on biopolymers we explore equilibrium morphologies and force-extension behavior of copolymers with hydrophobic segments using Langevin dynamics simulations. We find that the interplay between…
The dynamic behavior of semi-dilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semi-dilute solutions are characterized by large fluctuations in concentration,…
Shear flow is known to induce huge density fluctuations in otherwise clear and uniform polymer solutions. This effect is rooted in the elasticity of the entangled polymer network, and can span distances over a thousand chains wide. It has…
We investigate extensional viscosity and polymer conformation in dilute polymer solutions under uniaxial extensional flow using dissipative particle dynamics simulations. At high extension rates, polymers are significantly stretched by…
We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise…
The nucleation process of polyethylene under quiescent and shear flow conditions are comparatively studied with all_atom molecular dynamical simulations. At both conditions, nucleation are demonstrated to be two_step processes, which,…
Understanding how polymer topology influences melt extrudability is critical for advancing material design in extrusion-based additive manufacturing. In this work, we develop a bottom-up, cross-scale modeling framework that integrates…
Polymers in nonuniform flows undergo strong deformation, which in the presence of persistent stretching can result in the coil-stretch transition. This phenomenon has been characterized by using the formalism of nonequilibrium statistical…
Polymer composites are ubiquitous in biology and industry alike, owing to their emergent desirable mechanical properties not attainable in single-species systems. At the same time, polymer topology has been shown to play a key role in…
We investigate the effects of topological constraints (entanglements) on two dimensional polymer loops in the dense phase, and at the collapse transition (Theta point). Previous studies have shown that in the dilute phase the entangled…
DNA translocation through nanopores is one of the most promising strategies for the next-generation sequencing technologies. Most part of experimental and numerical works has focused on polymer translocation biased by electrophoresis, where…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
Tumor spheroids are in vitro three-dimensional, cellular collectives consisting of cancerous cells. Embedding these spheroids in an in vitro fibrous environment, such as a collagen network, to mimic the extracellular matrix (ECM) provides…
This study investigates the impact of elasticity and plasticity on two-dimensional flow past a circular cylinder at Reynolds number $Re = 100$. Ten direct numerical simulations were performed using the Saramito-Herschel-Bulkley model to…
DNA looping is important in DNA condensation and regulation. One method for forming a DNA loop, thought to be used by the condensing agent protamine, is bind-and-bend. In bind-and-bend, molecules bind all along the DNA, each creating a bend…
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…
Transport networks, such as vasculature or river networks, provide key functions in organisms and the environment. They usually contain loops whose significance for the stability and robustness of the network is well documented. However,…