Related papers: Quinary lattice model of secondary structures of p…
A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential…
A lattice Boltzmann model for amphiphilic fluid dynamics is presented. It is a ternary model, in that it conserves mass separately for each chemical species present (water, oil, amphiphile), and it maintains an orientational degree of…
The longitudinal response of single semiflexible polymers to sudden changes in externally applied forces is known to be controlled by the propagation and relaxation of backbone tension. Under many experimental circumstances, realized, e.g.,…
Membrane proteins often form dimers and higher-order oligomers whose stability and spatial organization depend sensitively on their lipid environment. To investigate the physical principles underlying this coupling, we employ a lattice…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
Few-body physics plays a central role in many branches of physics, such as nuclear physics and atomic physics. Advances in controlling ultra-cold quantum gases provide an ideal testbed for few-body physics theory. In this work, we study…
We study the designability of all compact 3x3x3 and 6x6 lattice-protein structures using the Miyazawa-Jernigan (MJ) matrix. The designability of a structure is the number of sequences that design the structure, i.e. sequences that have that…
Self-avoiding walks are studied on the 3-simplex fractal lattice as a model of linear polymer conformations in a dilute, non-homogeneous solution. A model is supplemented with bending energies and attractive-interaction energies between…
We use Wang-Landau and replica exchange techniques to study the effect of an increasing stiffness on the formation of secondary structures in protein-like systems. Two possible models are considered. In both models, a polymer chain is…
Lattice models are useful for understanding behaviors of interacting complex many-body systems. The lattice dimer model has been proposed to study the adsorption of diatomic molecules on a substrate. Here we analyze the partition function…
We point out that a newly introduced recursive algorithm for lattice polymers has a much wider range of applicability. In particular, we apply it to the simulation of off-lattice polymers with Lennard-Jones potentials between non-bonded…
We consider pairwise interaction energies and we investigate their minimizers among lattices with prescribed minimal vectors (length and coordination number), i.e. the one corresponding to the crystal's bonds. In particular, we show the…
Lipid monolayers and bilayers have been used as experimental models for the investigation of membrane thermal transitions. The main transition takes place near ambient temperatures for several lipids and reflects the order-disorder…
We introduce a framework for adsorption of a single polymer in which the topology of the polymer is quenched before adsorption, in contrast to more standard adsorption models having annealed topology. Our "topology" refers either to the…
A novel lattice approach is presented for studying systems comprising a large number of interacting nonrelativistic fermions. The construction is ideally suited for numerical study of fermions near unitarity--a strongly coupled regime…
A Coulomb lattice-gas model with a host lattice screening mechanism is adapted to describe the ordering phenomena in alkali-metal fullerides of body-centered-cubic structure. It is assumed that the electric charge of an alkali ion residing…
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
We present a continuum model for symmetry-breaking phase transformations in intercalation compounds, based on Ericksen's multi-well energy formulation. The model predicts the nucleation and growth of crystallographic microstructures in…
Using a fast tree-searching algorithm and a Pentium cluster, we enumerated all the sequences and compact conformations (structures) for a protein folding model on a cubic lattice of size $4\times3\times3$. We used two types of amino acids…
The primary structure of proteins, that is their sequence, represents one of the most abundant set of experimental data concerning biomolecules. The study of correlations in families of co--evolving proteins by means of an inverse…