Related papers: Folding and form: Insights from lattice simulation…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
We propose and solve a simple model describing secondary structure formation in random hetero-polymers. It describes monomers with a combination of one-dimensional short-range interactions (representing steric forces and hydrogen bonds) and…
By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
It is known that the limiting behavior of the contact process strongly depends upon the geometry of the graph on which particles evolve: while the contact process on the regular lattice exhibits only two phases, the process on homogeneous…
We study the folding of the regular two-dimensional triangular lattice embedded in the regular three-dimensional Face-Centred Cubic lattice, a discrete model for the crumpling of membranes. Possible folds are complete planar folds, folds…
Models of folding of a triangular lattice embedded in a discrete space are studied as simple models of the crumpling transition of fixed-connectivity membranes. Both the case of planar folding and three-dimensional folding on a…
Molecular dynamics simulations of folding in an off-lattice protein model reveal a nucleation scenario, in which a few well-defined contacts are formed with high probability in the transition state ensemble of conformations. Their…
We present Monte Carlo computer simulations for melts of semiflexible randomly knotted and randomly concatenated ring polymers on the fcc lattice and in slit confinement. Through systematic variation of the slit width at fixed melt density,…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
Triangular lattice models for pattern formation by hard-core soft-shell particles at interfaces are introduced and studied in order to determine the effect of the shell thickness and structure. In model I, we consider particles with…
A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative…
We propose an off-lattice model for a self-avoiding homopolymer chain with two different competing attractive interactions, mimicking the hydrophobic effect and the hydrogen bond formation respectively. By means of Monte Carlo simulations,…
We study the model of a partially directed flexible or semi-flexible homopolymer on a square lattice, subject to an externally applied force, in a direction either parallel to, or perpendicular to the preferred direction. The polymer is…
Understanding the drift motion and dynamical locking of crystalline clusters on patterned substrates is important for the diffusion and manipulation of nano- and micro-scale objects on surfaces. In a previous work, we studied the…
We study the ground state (GS) and the phase transition in a hexagonal-close-packed lattice with both XY and Ising models by using extensive Monte Carlo simulation. We suppose the in-plane interaction $J_1$ and inter-plane interaction…
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…
Chevron rollovers of some proteins imply that their logarithmic folding rates are nonlinear in native stability. This is predicted by lattice and continuum G\=o models to arise from diminished accessibilities of the ground state from…
The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable…
We studied the possibility to approximate a Lennard Jones interaction by a pairwise contact potential. First we used a Lennard-Jones potential to design off-lattice, protein-like heteropolymer sequences, whose lowest energy (native)…