Related papers: Folding and form: Insights from lattice simulation…
We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective…
We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA…
Spatiotemporal patterns in multicellular systems are important to understanding tissue dynamics, for instance, during embryonic development and disease. Here, we use a multiphase field model to study numerically the behavior of a…
The critical behavior of the contact process in disordered and periodic binary 2d-lattices is investigated numerically by means of Monte Carlo simulations as well as via an analytical approximation and standard mean field theory.…
The Go model is extended to the case when the non-native contact energies may be either attractive or repulsive. The folding temperature is found to increase with the energy of non-native contacts. The repulsive non-native contact energies…
We study the phase transition phenomena for long-range oriented percolation and contact process. We studied a contact process in which the range of each vertex are independent, updated dynamically and given by some distribution $N$. We also…
Recently it has been shown that a two-dimensional model of self-attracting polymers based on attracting segments displays two phase transitions, a theta-like collapse between swollen polymers and a globular state and another between the…
We present Monte Carlo simulations of a three-state lattice gas, half-filled with two types of particles which attract one another, irrespective of their identities. A bias drives the two particle species in opposite directions,…
We derive a Hamiltonian for a two-leg ladder which includes an arbitrary number of charge and spin interactions. To illustrate this Hamiltonian we consider two examples and use a renormalization group technique to evaluate the ground state…
We study a contact process with creation at first- and second-neighbor sites and inhibition at first neighbors, in the form of an annihilation rate that increases with the number of occupied first neighbors. Mean-field theory predicts three…
Origami crease patterns are folding paths that transform flat sheets into spatial objects. Origami patterns with a single degree of freedom (DOF) have creases that fold simultaneously. More often, several substeps are required to…
We study numerical simulations of large (N~10^4) two-dimensional quasi-static granular assemblies subjected to a slowly increasing deviator stress. We report some peculiarities in the behavior of these packings that have not yet been…
Monte Carlo simulations and finite-size scaling analysis have been carried out to study the critical behavior in a submonolayer lattice-gas of interacting monomers adsorbed on one-dimensional channels arranged in a triangular…
A model for a monolayer of two types of particles spontaneously forming ordered patterns is studied by a mesoscopic theory and by MC simulations. We assume hard-cores of the same size for both components, short-range attraction long-range…
We survey the interactions between foliations and contact structures in dimension three, with an emphasis on sutured manifolds and invariants of sutured contact manifolds. This paper contains two original results: the fact that a closed…
Various interacting lattice path models of polymer collapse in two dimensions demonstrate different critical behaviours. This difference has been without a clear explanation. The collapse transition has been variously seen to be in the…
The effect of different move sets on the folding kinetics of the Monte Carlo simulations is analysed based on the conformation-network and the temperature-dependent folding kinetics. A new scheme of implementing Metropolis algorithm is…
We study numerically how multiple deformable capsules squeeze into a constriction. This situation is largely encountered in microfluidic chips designed to manipulate living cells, which are soft entities. We use fully three-dimensional…
We combine large-scale atomistic modelling with continuum elastic theory to study the shapes of graphene sheets embedding nanoscale kirigami. Lattice segments are selectively removed from a flat graphene sheet and the structure is allowed…
We study the static properties of a semiflexible polymer exposed to a quenched random environment by means of computer simulations. The polymer is modeled as two-dimensional Heisenberg chain. For the random environment we consider hard…