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

In drug discovery, predicting the absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of small-molecule drugs is critical for ensuring safety and efficacy. However, the process of accurately predicting these…

Peptides and proteins exhibit a common tendency to assemble into highly ordered fibrillar aggregates, whose formation proceeds in a nucleation-dependent manner that is often preceded by the formation of disordered oligomeric assemblies.…

We study, using dissipative particle dynamics simulations, the effect of active lipid flip-flop on model fluid bilayer membranes. We consider both cases of symmetric as well as asymmetric flip-flops. Symmetric flip-flop leads to a steady…

In this paper we study a model describing a copolymer in a micro-emulsion. The copolymer consists of a random concatenation of hydrophobic and hydrophilic monomers, the micro-emulsion consists of large blocks of oil and water arranged in a…

The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…

Molecular dynamics simulations have been employed to study the formation of a physical (thermoreversible) gel by amphiphilic A-B-A triblock copolymers in aqueous solution. In order to mimic the structure of hydrogel-forming polypeptides…

The cell membrane is inherently asymmetric and heterogeneous in its composition, a feature that is crucial for its function. Using atomistic molecular dynamics simulations, the physical properties of a 3-component asymmetric mixed lipid…

We study, via DEM simulations, the apparent mass $m$ and loss factor $\eta$ of particle dampers (PD) attached to a vertically driven, single degree of freedom mechanical system. Although many studies focus on $\eta$, less work has been…

Dynamics of molecular motor dimers, consisting of rigidly bound particles that move along two parallel lattices and interact with underlying molecular tracks, is investigated theoretically by analyzing discrete-state stochastic…

Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…

We propose a hybrid Molecular Dynamics/Multi-particle Collision Dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte-Carlo scheme to deal with single monomer addition…

This study presents a coarse-grained molecular dynamics simulation model to investigate the process of oxidative aging in polymers. The chemical aging effect is attributed to the auto-oxidation mechanism, which is initiated by radicals,…

Aptamers are chemically produced oligonucleotides, able to bind a variety of targets such as drugs, proteins and pathogens with high sensitivity and selectivity. Therefore, aptamers are largely employed for producing label-free biosensors,…

The relaxation dynamics and thermodynamic properties of supercooled and glassy gambogic acid are investigated using both theory and experiment. We measure the temperature dependence of the relaxation times in three polymorphs (alpha-,…

Protein phase transitions govern numerous diseases, including neurodegenerative disorders such as Parkinson's and Alzheimer's. In Parkinson's disease, distinct species of the protein alpha-synuclein undergo phase transitions from highly…

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,…

Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse grained model, we systematically studied the folding and adsorption behavior of a…

Polyamide 6,6 (PA66) is a key engineering polymer, whose unique mechanical properties arise from strong interchain hydrogen bonding. However, its hygroscopic nature makes it highly sensitive to water uptake, which markedly alters its…

We derive stationary measures for certain zero-temperature random polymer models, which we believe are new in the case of the zero-temperature limit of the beta random polymer (that has been called the river delta model). To do this, we…

We investigate the formation of beta-sheet structures in proteins without taking into account specific sequence-dependent hydrophobic interactions. To accomplish this, we introduce a model which explicitly incorporates both solvation…