Related papers: Stacking and Hydrogen Bonding. DNA Cooperativity a…
Numerical simulation of the dynamics of planar two- and three-layer molecular structures formed by $\beta$-sheets of polyglycine peptide chains and systems of parallel Kevlar (para-aramid) molecules placed on a graphene sheet has been…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
A self-consistent-field theory (SCFT) in the grand canonical ensemble formulation is used to study transitions in a helix-coil multiblock copolymer globule. The helices are modeled as stiff rods. In addition to the established coil-globule…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
Liquid mixtures of many interacting components often exhibit numerous coexisting types of droplets. An exciting example is the cytosol of biological cells, where diverse droplets, called condensates, are essential for cellular function.…
The quasi-equilibrium evolution of the helical fraction occurring in a biopolymer network (gelatin gel) under an applied stress has been investigated by observing modulation in its optical activity. Its variation with the imposed chain…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…
Classical hard spheres crystallize at equilibrium at high enough density. Crystals made up of stackings of 2-dimensional hexagonal close-packed layers (e.g. fcc, hcp, etc.) differ in entropy by only about $10^{-3}k_B$ per sphere (all…
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 explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
We present a study on the melting dynamics of neighbouring ice bodies by means of idealised simulations, focusing on collective effects, with the goal of obtaining fundamental insight into how collective interactions influence the melting…
The stability of a $\beta$-sheeted conformation and its transition into a random coil are studied with a 2D lattice biopolymer model. At low temperature and low external force, the polymer folds back and forth on itself and forms a…
We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between inter and…
Hydrophobic polyelectrolytes (HPE) can solubilize bilayer membranes, form micelles or can reversibly aggregate as a function of pH. The transitions are often remarkably sharp. We show that these cooperative transitions occur by a…
Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…
Inspired by recent advances in atomic homo and heterostructures, we consider the vertical stacking of plasmonic lattices as a new degree of freedom to create a coupled system showing a modified optical response concerning the monolayer. The…
We present a numerical study of the Hubbard model on simply stacked honeycomb and square lattices, motivated by a recent experimental realization of such models with ultracold atoms in optical lattices. We perform simulations with different…
The detailed nature of spatially heterogeneous dynamics of glycerol-silica nanocomposites is unraveled by combining dielectric spectroscopy with atomistic simulation and statistical mechanical theory. Analysis of the spatial mobility…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…