Related papers: A Minimal Off-Lattice Model for Alpha-helical Prot…
Fundamental questions about the role of the quaternary structures are addressed using a statistical mechanics off-lattice model of a dimer protein. The model, in spite of its simplicity, captures key features of the monomer-monomer…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…
We investigate the one-dimensional Hubbard model with a confining potential, which may describe cold fermionic atoms trapped in an optical lattice. Combining the variational Monte Carlo simulations with the new stochastic reconfiguration…
In the standard approach to lattice proteins the models based on nearest neighbor interaction are used. In this kind of models it is difficult to explain the existence of secondary structures --- special preferred conformations of protein…
See chem-ph/9505003.
The HP model of protein folding, where the chain exists in a free medium, is investigated using a parallel Monte Carlo scheme based upon Wang-Landau sampling. Expanding on the work of Wust and Landau by introducing a lesser known replica…
In this work we introduce a worldline based fermion Monte Carlo algorithm for studying few body quantum mechanics of self-interacting fermions in the Hamiltonian lattice formulation. Our motivation to construct the method comes from our…
Monte Carlo simulations are a powerful tool to investigate the thermodynamic properties of atomic systems. In practice however, sampling of the complete configuration space is often hindered by high energy barriers between different regions…
A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable.…
The optimal design of DNA origami systems that assemble rapidly and robustly is hampered by the lack of a model for self-assembly that is sufficiently detailed yet computationally tractable. Here, we propose a model for DNA origami that…
In the past years, the folding kinetics of many small single-domain proteins has been characterized by mutational Phi-value analysis. In this article, a simple, essentially parameter-free model is introduced which derives folding routes…
The thermodynamics of the small SH3 protein domain is studied by means of a simplified model where each bead-like amino acid interacts with the others through a contact potential controlled by a 20x20 random matrix. Good folding sequences,…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
We propose a method for predicting helical membrane protein structures by computer simulations. Our method consists of two parts. In the first part, amino-acid sequences of the transmembrane helix regions are obtained from one of existing…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher…
We present an algorithm for the exhaustive enumeration of all monomer sequences and conformations of short lattice proteins as described by the hydrophobic-polar (HP) model. The algorithm is used for an exact identification of all designing…
Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally…