相关论文: Molecular Dynamics Simulation of Amyloid Beta Dime…

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…

We consider collisional properties of weakly bound heteronuclear molecules (dimers) formed in a two-species mixture of atoms with a large mass difference. We focus on dimers containing light fermionic atoms as they manifest collisional…

By using tight binding molecular dynamics simulations, we discuss the possibilities to form (Na$_{19}$)$_2$ and (Na$_{20}$)$_2$ cluster dimers in sodium cluster collisions. In the case of Na$_{19}$ + Na$_{19}$, we show that the formation of…

A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction…

Mono- and poly-disperse melts of oligomers (average length 10 monomers) of trans-1,4-polyisoprene are simulated in full atomistic detail. The force-field is developed by means of a mixture of ab initio quantum-chemistry and an automatic…

Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…

We extend our previous stochastic cellular automata based model for areal aggregation of prion proteins on neuronal surfaces. The new anisotropic model allow us to simulate both strong beta-sheet and weaker attachment bonds between…

We study the dynamics of a dimer moving on a periodic one-dimensional substrate as a function of the initial kinetic energy at zero temperature. The aim is to describe, in a simplified picture, the microscopic dynamics of diatomic molecules…

Metal ions, including copper and zinc, have been implicated in the pathogenesis of Alzheimers disease through a variety of mechanisms including increased amyloid \b{eta} affinity and redox effects. Recent reports have demonstrated that the…

Planar brushes formed by end-grafted semiflexible polyampholyte chains, each chain containing equal number of positively and negatively charged monomers is studied using molecular dynamics simulations. Keeping the length of the chains…

B cells encounter antigen over a wide affinity range. The strength of B cell signaling in response to antigen increases with affinity, a process known as "affinity discrimination". In this work, we use a computational simulation of B cell…

We study structural properties of a ring polymeric melt confined in a film in comparison to a linear counterpart using molecular dynamics simulations. Local structure orderings of ring and linear polymers in the vicinity of the surface are…

Molecular dimers are widely utilized as a tool to investigate the structure-property relationships behind the complex photophysical processes of condensed-phase systems, where structural tuning remains a challenge. This approach often…

We investigate the energetics of reactions involving pairs of alkali metal dimers. Atom exchange reactions to form homonuclear dimers are energetically allowed for some but not all of the heteronuclear dimers. We carry out high-level…

We review recent molecular dynamics simulations of thermally activated undulations and defects in the lamellar $L_\alpha$ phase of a binary amphiphile-solvent mixture, using an idealized molecular coarse-grained model: Solvent particles are…

Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous…

Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…

An important process for antimatter experiments is the cooling of particles in a Penning-Malmberg trap to experimentally useful temperatures. A non-neutral plasma of one species (e.g. antiprotons) can be collisionally cooled on another…

The classical nucleation theory finds the rate of nucleation proportional to the monomer concentration raised to the power, which is the `critical nucleaus size', ${n_c}$. The implicit assumption, that amyloids nucleate in the same way, has…

We explore pattern formation in an active fluid system involving two chemical species that regulate active stress: a fast-diffusing species ($A$) and a slow-diffusing species ($I$). The growth of species $A$ is modelled using a nonlinear…