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This study reports a general scenario for the out-of-equilibrium features of collapsing polymeric architectures. We use molecular dynamics simulations to characterize the coarsening kinetics, in bad solvent, for several macromolecular…
The solvent quality determines the collapsed or the expanded state of a polymer. For example, a polymer dissolved in a poor solvent collapses, whereas in a good solvent it opens up. While this standard understanding is generally valid,…
Using molecular dynamics simulations we study the behavior of a dilute solution of strongly charged polyelectrolytes in poor solvents, where we take counterions explicitly into account. We focus on the chain conformational properties under…
In this work we investigated the question of how the molecular nature of the dielectric media and the polymer-solvent dielectric mismatch affect the collapse of a polyelectrolyte chain in solution by means of dissipative particle dynamics…
In the field of freezing colloidal suspensions, it is important to understand the particle-scale behavior of particle packing. Here, we reveal the dynamics of particle packing by identifying the behavior of each single particle in situ. The…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
Accurately predicting the three-dimensional structures of protein-ligand complexes remains a fundamental challenge in computational drug discovery that limits the pace and success of therapeutic design. Deep learning methods have recently…
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…
We discuss the relation between the emergence of new phases with broken symmetry within the framework of simple models of biopolymers. We start with a classic model for a chain molecule of spherical beads tethered together, with the steric…
In this work, the nonequilibrium pathways of the collapse of the helix-forming biopolymer polyalanine are investigated. To this end, the full time evolution of the helix-coil transition is simulated using molecular dynamics simulations. At…
We study theoretically using scaling arguments the behavior of polyelectrolyte gels in poor solvents. Following the classical picture of Katchalsky, our approach is based on single chain elasticity but it accounts for the recently proposed…
We investigate the collapse of three inelastic particles in dimension $d \geq 2$. We obtain general results of convergence and asymptotics concerning the variables of the dynamical system describing a collapsing system of particles. We…
The dynamics of flexible polymer molecules are often assumed to be governed by hydrodynamics of the solvent. However there is considerable evidence that internal dissipation of a polymer contributes as well. Here we investigate the dynamics…
We analyse the dynamics of different routes to collapse of a constrained polyelectrolyte gel in contact with an ionic bath. The evolution of the gel is described by a model that incorporates non-linear elasticity, Stefan-Maxwell diffusion…
A conceptual difficulty in the Hooke's-law description of ideal Gaussian polymer-chain elasticity is sometimes apparent in analyses of experimental data or in physical models designed to simulate the behavior of biopolymers. The problem,…
The peculiar linear temperature-dependent swelling of core-shell microgels has been conjectured to be linked to the core-shell architecture combining materials of different transition temperatures. Here the structure of pNIPMAM-core and…
A new quantitative theory for polyelectrolytes in salt free dilute solutions is developed. Depending on the electrostatic interaction strength, polyelectrolytes in solutions can undergo strong stretching (with polyelectrolyte dimension…
Dried droplets of polymer solutions of different molecular weights and concentrations leave various types of 'coffee-ring' patterns. These patterns are consequence of contact line motion. We have observed for very low molecular weight the…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
We report arrays of monodisperse water-in-oil microdroplets printed onto a substrate in a form of a compact linear chain -- a 1D-crystal -- pinned at one end. The chain spontaneously collapses under capillary forces via a sequence of…