Related papers: On the Helix-coil Transition in Alanine-based Poly…
The extension elasticity of rod-coil mutliblock copolymers is analyzed for two experimentally accessible situations. In the quenched case, when the architecture is fixed by the synthesis, the force law is distinguished by a sharp change in…
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…
A self-consistent field theory was developed in the grand-canonical ensemble formulation to study transitions in a helix-coil multiblock globule. Helical and coil parts are treated as stiff rods and self-avoiding walks of variable lengths…
In this paper, we investigate the conformational dynamics of alanine dipeptide under an external electric field by nonequilibrium molecular dynamics simulation. We consider the case of a constant and of an oscillatory field. In this context…
Configurations of a single semiflexible polymer is studied when it is pushed into a nanochannel in the case where the polymer persistence length $l_p$ is much longer than the channel diameter $D$, i.e. $l_p/D \gg 1$. Using numerical…
Acid-base equilibria directly influence the functionality and behavior of particles in a system. Due to the ionizing effects of acid-base functional groups, particles will undergo charge exchange. The degree of ionization and their…
In order to study the relation between backbone and side chain ordering in proteins, we have performed multicanonical simulations of deka-peptide chains with various side groups. Glu10, Gln10, Asp10, Asn10, and Lys10 were selected to cover…
Based on the Zimm-Bragg model we study cooperative helix-coil transition driven by a finite-speed change of temperature. There is an asymmetry between the coil-to-helix and helix-to-coil transition: the latter is displayed already for…
The liquid-gas transition of an electroneutral mixture of oppositely charged colloids, studied by Monte Carlo simulations, is found in the low temperature -- low density region. The critical temperature shows a non-monotonous behavior as a…
We study a minimal extension of the worm-like chain to describe polypeptides having alpha-helical secondary structure. In this model presence/absence of secondary structure enters as a scalar variable that controls the local chain bending…
Self-assembled monolayers of polyalanine $\alpha$-helices exhibit distinct structural phases with implications for chiral-induced spin selectivity. We combine scanning tunneling microscopy and theoretical modeling to reveal how chiral…
Triacylglycerols (TAGs) are among the most important ingredients in food, cosmetic and pharmaceutical products. Many physical properties of such products, incl. morphology, texture and rheology, are determined by the phase behaviour of the…
We report here a new entropic mechanism of protein thermostability due to residual dynamics of rotamer isomerization in native state. All-atom simulations show that Lysines have much greater number of accessible rotamers than Arginines in…
We propose a potential for wormlike polymer chains which can be used to model the low-temperature conformational structures. We successfully reproduced helix ground states up to 6.5 helical loops, using the multicanonical Monte Carlo…
Lithium halides with the general formula Li$_x$M$_y$X$_6$, where M indicates transition metal ions and X halide anions are very actively studied as solid-state electrolytes, because of relatively low cost, high stability and Li…
We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local…
We introduce a microscopic model of a lipid with a charged headgroup and flexible hydrophobic tails, a neutral solvent, and counter ions. Short-ranged interactions between hydrophilic and hydrophobic moieties are included as are the Coulomb…
The liquid-gas phase transition is studied in a multi-component nuclear system using a local Skyrme interaction with Coulomb and surface effects. Some features are qualitatively the same as the results of Muller and Serot which uses…
It is becoming increasingly clear that initial state effects inherent to collisions of nuclei play an important role in the interpretation of data from heavy ion collisions at RHIC and the LHC. Such effects are more apparent in kinematic…
In contrast to the well-known destabilization of globular proteins by high pressure, re- cent work has shown that pressure stabilizes the formation of isolated {\alpha}-helices. However all simulations to date have obtained a qualitatively…