相关论文: Molecular Dynamics Simulation of Amyloid Beta Dime…
Molecular communication (MC) within the synaptic cleft is vital for neurotransmitter diffusion, a process critical to cognitive functions. In Alzheimer's Disease (AD), beta-amyloid oligomers (A$\beta$os) disrupt this communication, leading…
Understanding the atomic-scale structure and dynamics of amorphous oxide surfaces is essential for interpreting their chemical reactivity, mechanical stability, and interfacial behavior, yet direct experimental characterization remains…
In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive…
A simple model for the formation of the polymer-enzyme conjugates has been proposed and described using corresponding extension of the Wertheim's first-order thermodynamic perturbation theory (TPT1) for the system of associating chain…
For the first time, the combination of experimental preparation and results of fully atomistic simulations of an oligoelectrolyte multilayer (OEM) made of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt)…
Molecular dynamics simulations of selected members of the cyano-biphenyl series of dimers (CBnCB) have been set up using atomistic detail interactions among intermolecular pairs of united atoms and allowing fully for the flexibility of the…
Accumulation of amyloid beta proteins is a defining feature of Alzheimer's disease, and is usually accompanied by cerebrovascular pathology. Evidence suggests that amyloid beta and cerebrovascular pathology are mutually reinforcing; in…
Protein amyloidosis is a cytopathological process characterized by the formation of highly beta-sheet-rich fibrils. How this process occurs and how to prevent/treat the associated diseases are not completely understood. Here, we carry out a…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…
Intrinsically disordered proteins (IDPs) do not possess well-defined three-dimensional structures in solution under physiological conditions. We develop all-atom, united-atom, and coarse-grained Langevin dynamics simulations for the IDP…
Molecular dynamics simulation is used to study vacancy cluster formation in $\beta$- and $\alpha$-$Si_3N_4$ with varying vacancy contents (0 - 25.6 at%). Vacancies are randomly created in supercells, which were subsequently heat-treated for…
Using very long molecular dynamics simulation runs, temperature protocols spanning up to five orders of magnitude in time-scales are performed to investigate thermally activated structural relaxation in a model amorphous solid. The…
In this work, we explore the dynamics of active entangled chains using molecular dynamics simulations of a modified Kremer-Grest model. The active chains are diluted in a mesh of very long passive linear chains, to avoid constraint release…
We present and study a minimal structure-based model for the self-assembly of peptides into ordered beta-sheet-rich fibrils. The peptides are represented by unit-length sticks on a cubic lattice and interact by hydrogen bonding and…
In spite of the great success that all-atom molecular dynamics simulations have seen in revealing the nature of the lipid bilayer, the interplay between a membrane's curvature and dynamics remains elusive. This is largely due to the…
Soft matter materials and polymers are widely used in the controlled delivery of drugs. Simulation and modeling provide insight at the atomic scale enabling a level of control unavailable to experiments. We present a workflow protocol for…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher…
We present results from Molecular Dynamics simulations of the thermal glass transition in a dense polymer melt. In previous work we compared the simulation data with the idealized version of mode coupling theory (MCT) and found that the…