Related papers: Lattice model for self-folding at the microscale
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…
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…
Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures…
A model describing the three-dimensional folding of the triangular lattice on the face-centered cubic lattice is generalized allowing the presence of defects corresponding to cuts in the two-dimensional network. The model can be expressed…
We study the folding of the regular triangular lattice in three dimensional embedding space, a model for the crumpling of polymerised membranes. We consider a discrete model, where folds are either planar or form the angles of a regular…
We study the folding of the regular two-dimensional triangular lattice embedded in the regular three-dimensional Face Centered Cubic lattice, in the presence of quenched random spontaneous curvature. We consider two types of quenched…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…
We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries.…
A vertex model introduced by M. Bowick, P. Di Francesco, O. Golinelli, and E. Guitter (cond-mat/9502063) describing the folding of the triangular lattice onto the face centered cubic lattice has been studied in the hexagon approximation of…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
Molecular building blocks interacting at the nanoscale organize spontaneously into stable mono- layers that display intriguing long-range ordering motifs on the surface of atomic substrates. The patterning process, if appropriately…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are…
In this paper, we introduce a three-dimensional mathematical model of collagen contraction with microbuckling based on the two-dimensional model previously developed by the authors. The model both qualitatively and quantitatively replicates…
The phase structure of self-avoiding polymerized membranes is studied by extensive Hybrid Monte Carlo simulations. Several folding transitions from the flat to a collapsed state are found. Using a suitable order parameter and finite size…
A polymer folding model on the square lattice is constructed with attractive contact interactions of strength 1/c^2, 0<c<1. The corresponding model on a dynamical random lattice, with freely fluctuating co-ordination number at each vertex,…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
A lattice model with soft repulsion followed by attraction is developed for a monolayer of hybrid core-shell particles self-assembling at an interface. The model is solved exactly in one dimension. One, two or three periodic structures and…
We study the problem of "phantom" folding of the two-dimensional square lattice, in which the edges and diagonals of each face can be folded. The non-vanishing thermodynamic folding entropy per face $s \simeq .2299(1)$ is estimated both…