Related papers: Hydrophobic interactions and hydrogen bonds in \be…
The water dynamics, as characterized by the local hydrophobicity (LH), is investigated for tetrameric hemoglobin and dimeric melittin. For the T0 to R0 transition in Hb it is found that LH provides additional molecular-level insight into…
Lipid bilayer membranes have a native (albeit small) permeability for water molecules. Under an external load, provided that the bilayer structure stays intact and does not suffer from poration or rupture, a lipid membrane deforms and its…
In addition to the biologically active monomer of the protein Insulin circulating in human blood, the molecule also exists in dimeric and hexameric forms that are used as storage. The Insulin monomer contains two distinct surfaces, namely…
We study a continuum model of the lipid bilayer based on minimizing the free energy of a mixture of water and lipid molecules. This paper extends previous work by Blom & Peletier (2004) in the following ways. (a) It formulates a more…
There is a long-standing question about the molecular configuration of interfacial water molecules in the proximity of solid surfaces, particularly carbon atoms which play a crucial role in electrochemistry and biology. In this study, the…
In this work we study the spreading dynamics of tiny liquid droplets on solid surfaces in the case where the ends of the molecules feel different interactions with respect to the surface. We consider a simple model of dimers and short…
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short…
We consider a model of bilayer lipid membrane with bola-lipids. The bola-lipid is modeled by linking tails of the hydrophobic chains in the opposite monolayers within bilayer as a first approximation. A number of thermodynamical…
The hydrophobic/polar HP model on the square lattice has been widely used to investigate basics of protein folding. In the cases where all designing sequences (sequences with unique ground states) were enumerated without restrictions on the…
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…
We present an exhaustive study of more than 250 ab initio potential energy surfaces (PESs) of the model dipeptide HCO-L-Ala-NH2. The model chemistries (MCs) used are constructed as homo- and heterolevels involving possibly different RHF and…
Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate. For simplicity, we consider a…
Chemical reactions and biological processes are often governed by the structure and transport dynamics of the interface between two liquid phases. Despite their importance, our microscopic understanding of liquid-liquid interfaces has been…
Protein solubility and conformational stability are a result of a balance of interactions both within a protein and between protein and solvent. The electrostatic solvation free energy of oligoglycines, models for the peptide backbone,…
We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…
The thermodynamic, kinetic and magnetic properties of the hydrogen monomer on doped graphene layers were studied by ab initio simulations. Electron doping was found to heighten the diffusion potential barrier, while hole doping lowers it.…
By taking into account base-base stacking interactions we improve the Generalized Model of Polypeptide Chain (GMPC). Based on a one-dimensional Potts-like model with many-particle interactions, the GMPC describes the helix-coil transition…
The formation of protein precursors, due to the condensation of atomic carbon under the low-temperature conditions of the molecular phases of the interstellar medium, opens alternative pathways for the origin of life. We perform peptide…
We consider a model fluid with long-ranged, dispersion interparticle potentials confined between competing parallel walls. One wall is solvophilic and would be completely wet at bulk liquid-gas coexistence while the other is solvophobic and…
Hydrogen bonds are a common feature in protein folding and aggregation. Due to their chemical peculiarities in terms of strength and directionality, a particular attention must be paid to the definition of the hydrogen bond potential…