Related papers: From Collapse to Freezing in Random Heteropolymers
We study the collapse transition of a polymer on a square lattice with both nearest-neighbor and next nearest-neighbor interactions, by calculating the exact partition function zeros up to chain length 36. The transition behavior is much…
Collapse of the polymer chain upon the sharp decrease of solvent quality is studied. During collapse, any pair of polymer units appearing in a sufficiently close vicinity in space has the possibility with a certain probability to form an…
After a discussion of the definition and number of pseudoknots, we reconsider the self-attracting homopolymer paying particular attention to the scaling of the number of pseudoknots at different temperature regimes in two and three…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
A conceptual difficulty in the Hooke's-law description of ideal Gaussian polymer-chain elasticity is sometimes apparent in analyses of experimental data or in physical models designed to simulate the behavior of biopolymers. The problem,…
We study the phase transitions of a random copolymer chain with quenched disorder. We apply a replica variational approach based on a Gaussian trial Hamiltonian in terms of the correlation functions of monomer Fourier coordinates. This…
Random sequential adsorption with diffusional relaxation, of two by two square objects on the two-dimensional square lattice is studied by Monte Carlo computer simulation. Asymptotically for large lattice sizes, diffusional relaxation…
The collapse and swelling behavior of a generic homopolymer is studied using implicit-solvent, explicit-cosolvent Langevin dynamics computer simulations for varying interaction strengths. The systematic investigation reveals that polymer…
In random heteropolymer globules with short-range interactions between the monomers, freezing takes place at the microscopic length scale only, and can be described by a 1-step replica symmetry breaking. The fact that the long-range Coulomb…
Molecular process of polymer collapse was reproduced by isothermal molecular dynamics simulation. The initial polymer chains were obtained by mean of random walks in continuum space. Two potential models were considered to represent short…
To study the localization of random heteropolymers at an interface separating two selective solvents within the model of Garel, Huse, Leibler and Orland, Europhys. Lett. {\bf 8} 9 (1989), we propose an approach based on a disorder-dependent…
Two-length-scale pair potentials arise ubiquitously in condensed matter theory as effective interparticle interactions in molecular, metallic and soft matter systems. The existence of two different bond lengths generated by the shape of…
The sensitivity of the native states of protein-like heteropolymers to mutations modelled as perturbations in the interaction potential between amino acids is studied. The stability threshold against mutations is shown to be zero for random…
The pressure-temperature phase diagram of a one-component system, with particles interacting through a spherically symmetric pair potential in two dimensions is studied. The interaction consists of a hard core plus an additional repulsion…
We consider the rupture dynamics of a homopolymer chain pulled at one end at a constant loading rate r. Compared to single bond breaking, the existence of the chain introduces two new aspects into rupture dynamics: the non-Markovian aspect…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…
We study a percolation model on the square lattice, where clusters "freeze" (stop growing) as soon as their volume (i.e. the number of sites they contain) gets larger than N, the parameter of the model. A model where clusters freeze when…
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,…