Related papers: Conformations and diffusion of flexibly linked col…
Shape changes resulting from segmental flexibility are ubiquitous in molecular and biological systems, and are expected to affect both the diffusive motion and (biological) function of dispersed objects. The recent development of colloidal…
Ring, or cyclic, polymers have unique properties compared to linear polymers, due to their topologically closed structure that has no beginning or end. Experimental measurements on molecular ring polymers are challenging due to their…
Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…
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…
In this paper, we present a theory to efficiently deal with mechanical properties of heterogeneous polymer chain in free space and the central problem is to evaluate the diffusion equation and orientation-orientation correlation function,…
We investigate the chain conformation of ring polymers confined to a cylindrical nanochannel using both theoretical analysis and three dimensional Langevin dynamics simulations. We predict that the longitudinal size of a ring polymer scales…
Polymer chains dissolved in a solvent take random conformations due to large internal degrees of freedom and are characterized geometrically by their average shape and size. The diffusive dynamics of such large macromolecules play an…
We study the swelling of a flexible linear chain composed of active particles by analytical theory and computer simulation. Three different situations are considered: a free chain, a chain confined to an external harmonic trap, and a chain…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
Colloidal molecules are ideal model systems for mimicking real molecules and can serve as versatile building blocks for the bottom-up self-assembly of flexible and smart materials. While most colloidal molecules are rigid objects, the…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
A simple phenomenological model for describing the conformational dynamics of biological macromolecules via the nonlinearity-induced instabilities is proposed. It is shown that the interaction between charges and bending degrees of freedom…
A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the…
Polymer chains immersed in different solvent molecules exhibit diverse properties due to multiple spatiotemporal scales and complex interactions. Using molecular dynamics simulations, we study the conformational and static properties of…
Active processes in living systems generate nonequilibrium forces that deform embedded passive macromolecules. To understand how such dynamics influence polymer conformation, we study a flexible passive chain in an active nematic fluid.…
The non-equilibrium structural and dynamical properties of a flexible polymer tethered to a reflecting wall and subject to oscillatory linear flow are studied by numerical simulations. Polymer is confined in two dimensions and is modeled as…
Complex fluids containing low concentrations of slender colloidal rods can display a high viscosity, while little flow is needed to thin the fluid. This feature makes slender rods essential constituents in industrial applications and…
Turing patterns are fundamental in biophysics, emerging from short-range activation and long-range inhibition processes. However, their paradigm is based on diffusive transport processes, which yields Turing patters that are less sharp than…
An important goal of self-assembly is to achieve a preprogrammed structure with high fidelity. Here, we control the valence of DNA-functionalized emulsions to make linear and branched model polymers, or `colloidomers'. The distribution of…