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The mechanical response of intrinsically disordered proteins (IDPs) and polyampholyte (PA) chains is vital for understanding their biological functions and designing functional materials. We investigate the force-extension behavior of a PA…
We present a set of molecular dynamics (MD) simulations of strongly charged, flexible polyelectrolyte chains under poor solvent conditions in a salt free solution. Structural properties of the chains and of the solutions are reported. By…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
Polyelectrolyte (PE) hydrogels can dynamically respond to external stimuli, such as changes in pH and temperature, which benefits their use for smart materials and nanodevices with tunable properties. We investigate equilibrium…
Using numerical simulations we study the pinning and dynamics of interacting colloids on periodic one-dimensional substrates. As a function of colloid density, temperature, and substrate strength, we find a variety of pinned and dynamic…
We investigate the crystallization mechanism of a single, flexible homopolymer chain with short range attractions. For a sufficiently narrow attractive well, the system undergoes a first-order like freezing transition from an expanded…
Recent experiments have identified peptides with adhesion affinity for GaAs and Si surfaces. Here we use all-atom Monte Carlo (MC) simulations with implicit solvent to investigate the behavior in aqueous solution of four such peptides, all…
We present a minimal model for simulating dynamics of assorted lipid assemblies in a computationally efficient manner. Our model is particle-based and consists of coarse-grained beads put together on a modular platform to give generic…
Active polymers possess numerous unique properties that are quite different from those observed in the system of small active molecule due to the intricate interplay between their activity and topological constraints. This study focuses on…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Electrostatic interactions play a fundamental role in the structure and function of proteins. Due to ionizable amino acid residues present on the solvent-exposed surfaces of proteins, the protein charge is not constant but varies with the…
Conformation of single polyelectrolytes in tetravalent salt solutions is investigated under the framework of a coarse-grained model, using Langevin dynamics simulations. The chain size, studied by the radius of gyration, shows three…
We propose a highly coarse-grained simulation model for crystalline polymer solids with crystalline lamellar structures. The mechanical properties of a crystalline polymer solid are mainly determined by the crystalline lamellar structures.…
We analyze the effect of an external electric field on the electronic structure of molecules which have been recently studied as molecular wires or diodes. We use a self-consistent tight binding technique which provides results in good…
The extension elasticity of rod-coil mutliblock copolymers is analyzed for two experimentally accessible situations. In the quenched case, when the architecture is fixed by the synthesis, the force law is distinguished by a sharp change in…
Microgels are soft colloids that, in virtue of their polymeric nature, can react to external stimuli such as temperature or pH by changing their size. The resulting swelling/deswelling transition can be exploited in fundamental research as…
We develop and validate a simulation framework for colloidal gelation. We first reproduce the benchmark results of Santos, Campanella, and Carignano for spherical, gel-forming particles, then extend the methodology to more complex systems…
This theoretical study concerns a pH oscillator based on the urea-urease reaction confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane…
The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…