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We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
Neural Collapse refers to the curious phenomenon in the end of training of a neural network, where feature vectors and classification weights converge to a very simple geometrical arrangement (a simplex). While it has been observed…
Charge and spin-Peierls instabilities in quarter-filled (n=1/2) compounds consisting of coupled ladders and/or zig-zag chains are investigated. Hubbard and t-J models including local Holstein and/or Peierls couplings to the lattice are…
A small model polypeptide represented in atomic detail is folded using Monte Carlo dynamics. The polypeptide is designed to have a native conformation similar to the central part of the helix-turn-helix protein ROP. Starting from a…
We constrast the dynamics in model unentangled polymer melts of chains of three different stiffnesses: flexible, intermediate, and rodlike. Flexible and rodlike chains, which readily solidify into close-packed crystals (respectively with…
Entangled states are ubiquitous amongst fibrous materials, whether naturally occurring (keratin, collagen, DNA) or synthetic (nanotube assemblies, elastane). A key mechanical characteristic of these systems is their ability to reorganise in…
Competing interactions stabilize exotic mesoscopic structures, yet the microscopic mechanisms by which they influence non-equilibrium processes leading to disordered states remain largely unexplored, despite their critical role in…
We employ mesoscopic simulations to study active polymers in a solvent via multi-particle collision dynamics. We investigate linear chains in which either the head or tail monomer exerts an active force, directed away from or towards its…
The presence of ordered structures such as helices in collapsed states of polymer chains is still an open question challenging physics and biology. In this work, we present a potential model for polymer chains with monomers that are not…
A spontaneous buckling transition in thin layers of monodomain nematic liquid crystalline gel was observed by polarized light microscopy. The coupling between the orientational ordering of liquid crystalline solvent and the translational…
Spatial distributions are presented that quantitatively capture how polymer properties (e.g., segment alignment, density, and potential energy) vary with distance from nascent polymer crystals (nuclei) in prototypical polyethylene melts. It…
The form factor of partially sulfonated polystyrene PSSNa (degree of sulfonation f =1, 0.72, 0.64 and 0.36), at polymer concentration 0.17M and 0.34M, without or with added salt (0 M, 0.34M, & 0.68M), is measured by Small Angle Neutron…
Steady state dynamics of clustering, long range order, and inelastic collapse are experimentally observed in vertically shaken granular monolayers. At large vibration amplitudes, particle correlations show only short range order like…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
Identifying the necessary conditions for the onset of rigidity in a gel remains a challenge. It has been suggested that local particle coordination could be used to establish such conditions, but rigid gels occur for various coordination…
The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein…
We perform axisymmetric numerical simulations to investigate the coalescence dynamics of a liquid drop in a deep liquid pool. This study aims to generalize the mechanisms of partial coalescence across a range of drop shapes, elucidate the…
Poly(N-isopropylacrylamide) (PNIPAM) is a temperature-responsive polymer that undergoes large volumetric deformations through a transition from a swollen to a collapsed state at the volume phase transition temperature (VPTT). Locally, these…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…
The temporal measurement order and therefore the originator of the instantaneous collapse of the wavefunction of a spatiality entangled particle pair can change depending on the reference frame of an observer. This can lead to a paradox in…