相关论文: Hydrogen Bonds in Polymer Folding

Hydrogen bonds play a pivotal role in chemistry, biology, and condensed-matter physics, where quantum tunnelling can strongly influence structure and dynamics. Isotope substitution (H $\rightarrow$ D) provides a sensitive probe of such…

We study a homopolymer model of a protein chain, where each monomer carries a dipole moment. To mimic the geometry of the peptidic bond, these dipoles are constrained to be locally perpendicular to the chain. The tensorial character of the…

The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…

Adding dynamic bonds in polymer networks enables reprocessing and recycling; however the full impact of reversible bonds on dynamic network mechanics remains unclear. We build model dynamic networks and observe substantial deviations from…

Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…

In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…

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…

The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…

The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…

We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: 1) binding energy of folding…

Hydrogen bonds are of paramount importance in the chemistry of clays, mediating the interaction between the clay surface and water, and for some materials between separate layers. It is well-established that the accuracy of a computational…

We address the problem of inverse polymer swelling. This phenomenon, in which a collapsed polymer chain swells upon decreasing temperature, can be observed experimentally in so-called thermoreversible homopolymers in aqueous solution, and…

We study hydrogen-bond dynamics in liquid water at low temperatures using molecular dynamics simulations. We find that bond lifetime (``fast dynamics'') has Arrhenius temperature dependence. We also calculate the bond correlation function…

What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of…

Hydrogen is key in reducing greenhouse gas emissions in materials production. At the same time, it significantly affects mechanical properties, often causing unwanted embrittlement. However, rather than solely addressing these…

Polymers contain functional groups that participate in hydrogen bond (H-bond) with water molecules, establishing a robust H-bond network that influences bulk properties. This study utilized molecular dynamics (MD) simulations to examine the…

A GW calculation based on a truncated Coulomb interaction with an added small q limit was applied to 2D van der Waals heterolayered structures, and the Kane dispersion model was used to determine the accurate band gap edge. All ab initio…

Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address…

The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…

We have studied the thermodynamics of isolated homopolymer chains of varying stiffness using a lattice model. A complex phase behaviour is found; phases include chain-folded `crystalline' structures, the disordered globule and the coil. It…