Related papers: Structural Properties of Small Semiconductor-Bindi…
In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of…
We analyze the problem of the helix-coil transition in explicit solvents analytically by using spin-based models incorporating two different mechanisms of solvent action: explicit solvent action through the formation of solvent-polymer…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
We compare two recently proposed methods for the characterization of phase transitions in small systems. The usefulness of these techniques is evaluated for the case of structural transition in alanine-based peptides.
The conformations of semiflexible (bio)polymers are studied in flow through geometrically structured microchannels. Using mesoscale hydrodynamics simulations, we show that the polymer undergoes a rod-to-helix transition as it moves from the…
We report on self-assembly, clustering, and conformational phases of peptides on inorganic semiconductor surfaces. The peptide-covered surface fraction can differ by a factor of 25, depending mainly on surface and peptide polarity. Low…
We investigate the cooperative effects of a single finite chain of monomers near an attractive substrate by first constructing a conformational pseudo-phase diagram based on the thermal fluctuations of energetic and structural quantities.…
Although the electrical transport properties of mesoscopic metallic samples have been investigated extensively over the past two decades, the thermal properties have received far less attention. This may be due in part to the difficulty of…
Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation…
We test the effectiveness of the multicanonical algorithm for the tertiary structure prediction of peptides and proteins. As a simple example we study Met-enkephalin. The lowest-energy conformation obtained agrees with that determined by…
We propose the use of microcanonical analyses for numerical studies of peptide aggregation transitions. Performing multicanonical Monte Carlo simulations of a simple hydrophobic-polar continuum model for interacting heteropolymers of finite…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
We employ a mesoscopic model for studying aggregation processes of protein-like hydrophobic-polar heteropolymers. By means of multicanonical Monte Carlo computer simulations, we find strong indications that peptide aggregation is a phase…
Peptides are recognized for their varied self-assembly behaviors, forming a wide array of structures and geometries, such as spheres, fibers, and hydrogels, each presenting a unique set of material properties. The functionalities of these…
We present a new method, the analytical rebridging scheme, for Monte Carlo simulation of proline-containing, cyclic peptides. The cis/trans isomerization is accommodated by allowing for two states of the amide bond. We apply our method to…
We have used scanning probe microscopy to investigate self-assembled monolayers of chemically synthesized peptides. We find that the peptides form a dense uniform monolayer, above which is found a sparse additional layer. Using scanning…
In detailed microcanonical analyses of densities of states obtained by extensive multicanonical Monte Carlo computer simulations, we investigate the caloric properties of conformational transitions adsorbing polymers experience near…
We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an $\alpha$-helix conformation. The polypeptide is assumed to be adsorbed…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Helix-coil transition in polypeptides is an example of a spin model with a preferred spin direction, in the sense that a theoretical formulation of this problem requires to assign a preferred value of spin to the helical conformation in…