Related papers: Controlling Secondary Structures of Bio-Polymers w…
The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase…
In view of the important role helix-sheet transitions play in protein aggregation, we introduce a simple model to study secondary structural transitions of helix-coil-sheet systems using a Potts model starting with an effective Hamiltonian.…
The nature of the globule-coil transition of surface-confined polymers has been an issue of debate. Here this 2D collapse transition is studied through a partially directed lattice model. In the general case of polymers with positive…
By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and…
The equilibrium states of one-dimensional proton conductors in the systems with hydrogen bonds are investigated. Our extended hard-core boson lattice model includes short-range interactions between hydrogen ions, their transfer along the…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
Microphase separated structure consisting of the periodic alternation of the layers of stretched homopolymer chains surrounded by perpendicularly oriented oligomeric tails is studied for both, strongly bonded (ionic) systems and weakly…
The first-order phase transitions in the lattice model of Janus-like particles confined in slit-like pores are studied. We assume a cubic lattice with molecules that can freely change their orientation on a lattice site. Moreover, the…
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…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
We address the problem of inverse polymer swelling. This phenomenon, in which a collapsed polymer chain swells upon decreasing temperature, can be observed experimentally in so-called thermoreversible homopolymers in aqueous solution, and…
We study a model describing some aspects of the dynamics of biopolymers. The models involve either one or two finite chains with a number N of sites that represent the "units" of a biophysical system. The mechanical degrees of freedom of…
We introduce a class of $n$-dimensional (possibly inhomogeneous) spin-like lattice systems presenting modulated phases with possibly different textures. Such systems can be parameterized according to the number of ground states, and can be…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
Recent advances in Generalized Ensemble simulations and microcanonical analysis allowed the investigation of structural transitions in polymer models over a broad range of local bending and torsion strengths. It is reasonable to argue that…
We consider a lattice polymer model (random walk), in which the walk is allowed to visit lattice bonds at most twice. Such a model might have some relevance to describe statistical properties of RNA molecules. In order to mimic base…
Biological cells exhibit a hierarchical spatial organization, where various compartments harbor condensates that form by phase separation. Cells can control the emergence of these condensates by affecting compartment size, the amount of the…
A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
We consider the Ising model on the two-dimensional square lattice where on each horizontal line, called "layer", the interaction is given by a ferromagnetic Kac potential with coupling strength $J_\gamma(x,y)=\gamma J(\gamma(x-y))$, where…