Related papers: Hydrogen Bonds in Polymer Folding
We report molecular dynamics simulations of a hydrophobic polymer-chain in aqueous solution between $260 {K}$ and $420 {K}$ at pressures of $1 {bar}$, $3000 {bar}$, and $4500 {bar}$. The simulations reveal a hydrophobically collapsed state…
We use appropriately defined short ranged reference models of liquid water to clarify the different roles local hydrogen bonding, van der Waals attractions, and long ranged electrostatic interactions play in the solvation and association of…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
In equilibrium and supercooled liquids, polymorphism is manifested by thermodynamic regions defined in the phase diagram, which are predominantly of different short- and medium-range order (local structure). It is found that on the phase…
The glass transition in hydrogen-bonded glass formers differs from the glass transition in other glass formers. The Eshelby rearrangements of the highly viscous flow are superimposed by strongly asymmetric hydrogen bond rupture processes,…
Fluid polyamorphism, the existence of multiple amorphous fluid states in a single-component system, has been observed or predicted in a variety of substances. A remarkable example of this phenomenon is the fluid-fluid phase transition in…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
The strength of hydrogen bonding in water is stronger than that of van der waals interaction, therefore water may play an important role in the process of hydrophobic effects. When a hydrophobic solute is dissolved into water, an interface…
Conformational phases of a semiflexible off-lattice homopolymer model near an attractive substrate are investigated by means of multicanonical computer simulations. In our polymer-substrate model, nonbonded pairs of monomers as well as…
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…
Studying the thermodynamics of the systems produced in ultra-relativistic heavy-ion collisions is crucial in understanding the QCD phase diagram. Recently, a new avenue has opened regarding the implications of large initial angular momentum…
We consider a model of two (fully) compact polymer chains, coupled through an attractive interaction. These compact chains are represented by Hamiltonian paths (HP), and the coupling favors the existence of common bonds between the chains.…
During compression of a water dimer calculated with high-precision first-principles methods, the trends of H-bond and O-H bond lengths show quantum effect of the electronic structure. We found that the H-bond length keeps decreasing, while…
Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
Hydrogels have a distinct combination of mechanical and water-transport behaviors. As hydrogels stiffen, they become less permeable. Here, we combine semi-dilute polymer theory with the Kozeny-Carman equation to develop a simple scaling law…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
Polymer behavior in mixed solvents often exhibits intriguing phenomena, such as cosolvency, where a polymer that collapses in two individually poor solvents becomes soluble in their mixture. In this study, we employ a combination of…
Associative polymer networks have shown a major promise in fabrication of self-healing and responsive materials. The can also serve as simple models to study more complex biological systems where transient interactions play an important…