Related papers: A Multicanonical Molecular Dynamics Study on a Sim…
Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…
A simple model of globular proteins which incorporates anisotropic attractions is proposed. It is closely related to models used to model simple hydrogen-bonding molecules such as water. Theories for both the fluid and solid phases are…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
A systematic study of pressure ionization is carried out in the chemical picture by the example of fluid helium. By comparing the variants of the chemical model, it is demonstrated that the behavior of pressure ionization depends on the…
Biomimetic scale-covered substrates provide geometric tailorability via scale orientation, spacing and also interfacial properties of contact in various deformation modes. No work has investigated the effect of friction in twisting…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
We investigate the role of the Coulomb interaction on the liquid-gas phase transition of nuclear matter with three different values of proton fraction ($Y_p$=0.5,0.3 and 0.1), relevant for heavy-ion physics as well as various astrophysical…
A microscopic model is proposed for the interactions between sickle hemoglobin molecules based on information from the protein data bank. A Monte Carlo simulation of a simplified two patch model is carried out, with the goal of…
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic…
Molecular dynamic simulations were employed to study a water-like model confined between hydrophobic and hydrophilic plates. The phase behavior of this system is obtained for different distances between the plates and particle-plate…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
The long debated protein dynamical transition was recently found also in non-biological macromolecules, such as poly-N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description…
We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both…
Many proteins have the potential to aggregate into amyloid fibrils, which are associated with a wide range of human disorders including Alzheimer's and Parkinson's disease. In contrast to that of folded proteins, the thermodynamic stability…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as…
Polyampholytes (PAs) are heteropolymers with long range Coulomb interactions. Unlike polymers with short range forces, PA energy levels have non-vanishing correlations and are thus very different from the Random Energy Model (REM).…
A hydrophilic liquid, such as water, forms hydrogen bonds with a hydrophilic substrate. The strength and locality of the hydrogen bonding interactions prohibit slip of the liquid over the substrate. The question then arises how the contact…
We present results of molecular simulations of a model protein whose hydrophobic collapse proceeds as a cascade of downhill transitions between distinct intermediate states. Different intermediates are stabilized by means of appropriate…