Related papers: Folding and form: Insights from lattice simulation…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
The phase diagram of a vertex model introduced by P. Di Francesco (Nucl. Phys. B 525, 507 1998) representing the configurations of a square lattice which can fold with different bending energies along the main axes and the diagonals has…
Collections of cells exhibit coherent migration during morphogenesis, cancer metastasis, and wound healing. In many cases, bigger clusters split, smaller sub-clusters collide and reassemble, and gaps continually emerge. The connections…
The effect of next-nearest-neighbor hopping $t_{2}$ on the ground-state phase diagram of the one-dimensional Kondo lattice is studied with density-matrix renormalization-group techniques and by comparing with the phase diagram of the…
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…
Spreading from a seed is studied by Monte Carlo simulation on a square lattice with two types of sites affecting the rates of birth and death. These systems exhibit a critical transition between survival and extinction. For time- dependent…
We have investigated, by the Monte Carlo simulation, spin systems which represent moments of arrayed magnetic nanoparticles interacting with each other only by the dipole-dipole interaction. In the present paper we aim the understanding of…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
We use complete enumeration and Monte Carlo techniques to study two-dimensional self-avoiding polymer chains with quenched ``charges'' $\pm 1$. The interaction of charges at neighboring lattice sites is described by $q_i q_j$. We find that…
We investigate theoretically how the stress propagation characteristics of granular materials evolve as they are subjected to increasing pressures, comparing the results of a two-dimensional scalar lattice model to those of a molecular…
At the cutting edge of materials science, matter is designed to self-organize into structures that perform a wide range of functions. The past two decades have witnessed major innovations in the versatility of building blocks, ranging from…
Extending previous rigorous results, we prove existence of an ordering transition at finite temperature for a class of nematogenic lattice models, where spins are associated with a one- or two-dimensional lattice, and interact via…
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…
We study the extended Hubbard model on the triangular lattice as a function of filling and interaction strength. The complex interplay of kinetic frustration and strong interactions on the triangular lattice leads to exotic phases where…
Phase diagram of microcanonical ensembles of self-attracting particles is studied for two types of short-range potential regularizations: self-gravitating fermions and classical particles interacting via attractive soft…
Origami structures are characterized by a network of folds and vertices joining unbendable plates. For applications to mechanical design and self-folding structures, it is essential to understand the interplay between the set of folds in…
Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with…
The quantum-classical crossover from the Fermi liquid towards the Wigner solid is numerically revisited, considering small square lattice models where electrons interact via a Coulomb $U/r$ potential. The studies of models without disorder…
The global phase behavior of the lattice restricted primitive model with nearest neighbor exclusion has been studied by grand canonical Monte Carlo simulations. The phase diagram is dominated by a fluid (or charge-disordered solid) to…
The model of localized fermions on the triangular lattice is analyzed in means of the Monte Carlo simulations in the grand canonical ensemble. The Hamiltonian of the system has a form of the extended Hubbard model (at the atomic limit) with…