Related papers: Structure optimization in an off-lattice protein m…
We determined scaling laws for the numerical effort to find the optimal configurations of a simple model potential energy surface (PES) with a perfect funnel structure that reflects key characteristics of the protein interactions.…
Accurate protein structure prediction from amino-acid sequences is critical to better understanding the protein function. Recent advances in this area largely benefit from more precise inter-residue distance and orientation predictions,…
Lattice field theory methods, usually associated with non-perturbative studies of quantum chromodynamics, are becoming increasingly common in the calculation of ground-state and thermal properties of strongly interacting non-relativistic…
Chain molecules play a key role in the polymer field and in living cells. Our focus is on a new homopolymer model of a linear chain molecule subject to an attractive self-interaction promoting compactness. We analyze the model using simple…
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…
We study the attractive Hubbard model with mass imbalance to clarify low temperature properties of the fermionic mixtures in the optical lattice. By combining dynamical mean-field theory with the continuous-time quantum Monte Carlo…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
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.…
We demonstrate that a kind of highly excited state of strongly attractive Hubbard model, named of Fermi super-Tonks-Girardeau state, can be realized in the spin-1/2 Fermi optical lattice system by a sudden switch of interaction from the…
Scaling of folding times in Go models of proteins and of decoy structures with the Lennard-Jones potentials in the native contacts reveal %robust power law trends when studied under optimal folding conditions. The power law exponent depends…
Lattice models with supersymmetry are known to exhibit a variety of remarkable properties that do not exist in the relativistic models. In this paper, we introduce an interacting generalization of the Kitaev chain of Majorana fermions with…
The potential energy landscape in the Kob-Andersen Lennard-Jones binary mixture model has been studied carefully from liquid down to the supercooled regime, from T =2 down to T =0.46. One thousand of independent configurations along the…
Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a…
We propose a novel method for refining force-field parameters of protein systems. In this method, the agreement of the secondary-structure stability and instability between the protein conformations obtained by experiments and those…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
The conformational properties of flexible polymers in d dimensions in environments with extended defects are analyzed both analytically and numerically. We consider the case, when structural defects are correlated in \varepsilon_d…
In the first part of the thesis we consider the constraints of causality and unitarity for particles interacting via strictly finite-range interactions. We generalize Wigner's causality bound to the case of non-vanishing partial-wave…
Here, we propose a platform based on ultra-cold fermionic molecules trapped in optical lattices to simulate nonadiabatic effects, as they appear in certain molecular dynamical problems. The idea consists of a judicious choice of two…
The Minimally Entangled Typical Thermal States (METTS) are an ensemble of pure states, equivalent to the Gibbs thermal state, that can be efficiently represented by tensor networks. In this article, we use the Projected Entangled Pair…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…