Related papers: Protein folding simulations with Interacting Growt…
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…
We demonstrate that the recently proposed pruned-enriched Rosenbluth method (P. Grassberger, Phys. Rev. E 56 (1997) 3682) leads to extremely efficient algorithms for the folding of simple model proteins. We test them on several models for…
We present the Monte Carlo with Absorbing Markov Chains (MCAMC) method for extremely long kinetic Monte Carlo simulations. The MCAMC algorithm does not modify the system dynamics. It is extremely useful for models with discrete state spaces…
By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
We use the lattice model of directed walks to investigate the conformational as well as the adsorption properties of a semiflexible homopolymer chain immersed in a good solvent in two and three dimensions. To account for the stiffness in…
In this paper, we investigate a model for a $1+1$ dimensional self-interacting and partially directed self-avoiding walk, usually referred to by the acronym IPDSAW. The interaction intensity and the free energy of the system are denoted by…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Various subsets of self-avoiding walks naturally appear when investigating existing methods designed to predict the 3D conformation of a protein of interest. Two such subsets, namely the folded and the unfoldable self-avoiding walks, are…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
We perform a numerical study of a new microcanonical polymer model on the three dimensional cubic lattice, consisting of ideal chains whose range and number of nearest-neighbor contacts are fixed to given values. Our simulations suggest an…
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…
The exact grand-canonical solution of a generalized interacting self-avoid walk (ISAW) model, placed on a Husimi lattice built with squares, is presented. In this model, beyond the traditional interaction $\omega_1=e^{\epsilon_1/k_B T}$…
Long chains of the HP lattice protein model are studied by the Multi-Self-Overlap Ensemble(MSOE) Monte Carlo method, which was developed recently by the authors. MSOE successfully finds the lowest energy states reported before for sequences…
We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model when proteins fold under…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
We have investigated a polymer growth process on the triangular lattice where the configurations produced are self-avoiding trails. We show that the scaling behaviour of this process is similar to the analogous process on the square…
Two proteins, one belonging to the mainly alpha class and the other belonging to the alpha/beta class, are selected to test a kinetic mechanism for protein folding. Targeted molecular dynamics is applied to generate folding pathways for…
This article is dedicated to the study of the 2-dimensional interacting prudent self-avoiding walk (referred to by the acronym IPSAW) and in particular to its collapse transition. The interaction intensity is denoted by $\beta>0$ and the…