Related papers: Pearl-Necklace-Like Local Ordering Drives Polypept…
By means of a variational approach we study the conditions under which a polyelectrolyte in a bad solvent will undergo a transition from a rod-like structure to a ``necklace'' structure in which the chain collapses into a series of globules…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
Chain-like macromolecules in solution, whether biological or synthetic, transform from an extended conformation to a compact one when temperature or other system parameters change. This collapse transition is relevant in various phenomena,…
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…
Conformational transitions of flexible molecules, especially those driven by hydrophobic effects, tend to be hindered by desolvation barriers. For such transitions, it is thus important to characterize and understand the interplay between…
Molecular dynamics simulation methods are used to study the folding of polymer chains into packed cubic states. The polymer model, based on a chain of linked sites moving in the continuum, includes both excluded volume and torsional…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
We propose a simple phenomenological model for describing the conformational dynamics of biopolymers via the nonlinearity-induced buckling and collapse (i.e. coiling up) instabilities. Taking into account the coupling between the internal…
Attractive colloidal particles can form a disordered elastic solid or gel when quenched into a two-phase region, if the volume fraction is sufficiently large. When the interactions are comparable to thermal energies the stress-bearing…
When a flexible polymer is sucked into a localized small hole, the chain can initially respond only locally and the sequential nonequilibrium processes follow in line with the propagation of the tensile force along the chain backbone. We…
The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is…
We investigate the collapse and expansion dynamics of a linear polyelectrolyte (PE) with hydrodynamic interactions. Using dissipative particle dynamics with a bead-spring PE model, long-range electrostatics and explicit ions we examine how…
We investigate the internal structure of a polymer during collapse from an expanded coil to a compact globule. Collapse is more probable in local regions of high curvature, so a smoothing of the fractal polymer structure occurs that…
Using numerical simulations we examine colloids with a long-range Coulomb interaction confined in a two-dimensional trough potential undergoing dynamical compression. As the depth of the confining well is increased, the colloids move via…
Under an external field a double-stranded peptide chain can separate in a fragile or ductile transition. It is usually believed that these two regimes are driven either by chemical and thermal fields, or through non-local mechanical…
Protein folding is a phenomenon that has been studied for about 50 years and still remains as an unsolved problem. The main feature of this process is that it occurs as an all or none process, so a protein, can jump directly between folded…
Dynamics of a polymer chain in solution gets significantly affected by the temperature and the frictional forces arising due to solvent viscosity. Here, using an explicit solvent framework for polymer simulation with the liberty to tune the…
Hydrogels have had a profound impact in the fields of tissue engineering, drug delivery, and materials science as a whole. Due to the network architecture of these materials, imbibement with water often results in uniform swelling and…
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…
Colloidal gels consist of percolating networks of interconnected arms. Their mechanical properties depend on the individual arms, and on their collective behaviour. We use numerical simulations to pull on a single arm, built from a model…