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Computer simulations give precious insight into the microscopic behavior of supercooled liquids and glasses, but their typical time scales are orders of magnitude shorter than the experimentally relevant ones. We recently closed this gap…
Homogeneous nucleation process of polyethylene (PE) is studied with full-atom molecular dynamic simulation. To account the complex shape with low symmetry and the peculiar intra-chain conformational order of polymer, we introduce a shape…
We present a scaling theory describing the collapse of a homopolymer chain in poor solvent. At time t after the beginning of the collapse, the original Gaussian chain of length N is streamlined to form N/g segments of length R(t), each…
For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as…
We investigate a lattice model of polymers where the nearest-neighbour monomer-monomer interaction strengths differ according to whether the local configurations have so-called ``hydrogen-like'' formations or not. If the interaction…
We report on the buckling and subsequent collapse of orthotropic elastic spherical shells under volume and pressure control. Going far beyond what is known for isotropic shells, a rich morphological phase space with three distinct regimes…
I report on the experimental confirmation that critical percolation statistics underlie the ordering kinetics of twisted nematic phases in the Allen-Cahn universality class. Soon after the ordering starts from a homogeneous disordered phase…
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength…
The rapid collapse of a polymer, due to external forces or changes in solvent, yields a long-lived `crumpled globule.' The conjectured fractal structure shaped by hierarchical collapse dynamics has proved difficult to establish, even with…
The conformations of interacting linear polymers on a dynamical planar random lattice are studied using a random two-matrix model. An exact expression for the partition function of self-avoiding chains subject to attractive contact…
Polyelectrolytes in poor solvents show a necklace structure where collapsed polymer pearls are linked to stretched strings. In the present paper the elasticity of such chains is studied in detail. Different deformation regimes are…
Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…
Polar activity is shown here to induce a progressive local deformation of linear polymer chains, making a clear distinction between head and tail, while the overall chain conformation gets more compact. This breakdown of self-similarity,…
In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since…
Complex crystal structures are composed of multiple local environments, and how this type of order emerges spontaneously during crystal growth has yet to be fully understood. We study crystal growth across various structures and along…
Spherical confinement can act either stabilizing or destabilizing on the collapsed state of a semi-flexible polymer. General free-energy arguments suggest that the order of the unconstrained collapse transition is the distinguishing factor:…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
The thermodynamic behavior of collapse transition in a fully flexible coarse-grained model of energy polydisperse polymer (EPP), a statistical model of random heteropolymer, is investigated in an implicit solvent by means of molecular…