相关论文: On the propensity of Asn-Gly-containing heptapepti…
A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with about 20 residues each. The test set contains both alpha-helical (Trp cage, Fs) and beta-sheet (GB1p,…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Understanding of the molecular interaction between asphaltenes and other molecules, which may act as its solvents, provides insights into the nature of its stability in petroleum fluids and its phase transitions. Molecular dynamics…
Using the Dominant Reaction Pathways method, we perform an ab-initio quantum-mechanical simulation of a conformational transition of a peptide chain. The method we propose makes it possible to investigate the out-of-equilibrium dynamics of…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
In simulations of aqueous systems it is common to freeze the bond vibration and angle bending modes in water to allow for a longer time-step $\delta t$ for integrating the equations of motion. Thus $\delta t = 2$ fs is often used in…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
We present fully atomistic Molecular Dynamics simulation results on a main-chain polymer, 1,4-Polybutadiene, in the merging region of the $\alpha$- and $beta$-relaxations. A real space analysis reveals the occurrence of localized motions…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions…
Recent experiments with amyloid-beta (Abeta) peptide suggest that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of Abeta oligomers depends on their structure, which is…
Recent experiments have identified peptides with adhesion affinity for GaAs and Si surfaces. Here we use all-atom Monte Carlo (MC) simulations with implicit solvent to investigate the behavior in aqueous solution of four such peptides, all…
Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodelling cell membranes. However, the molecular driving forces behind these processes are not well…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
Predicting the asymmetric structure and dynamics of solvated hydroxide and hydronium in water has been a challenging task from ab initio molecular dynamics (AIMD). The difficulty mainly comes from a lack of accurate and efficient…
Previous research based on electronic structure calculations and molecular dynamics (MD) simulations have demonstrated that graphdiyne (GDY) is a very suitable two-dimensional membrane for the separation of small molecules in a gas mixture…
Two types of approaches to modeling molecular systems have demonstrated high practical efficiency. Density functional theory (DFT), the most widely used quantum chemical method, is a physical approach predicting energies and electron…
Molecular dynamics simulations have been used in different scientific fields to investigate a broad range of physical systems. However, the accuracy of calculation is based on the model considered to describe the atomic interactions. In…
We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-metha\-nol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient…