相关论文: Kinetics of drug release from clay using enhanced …
The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large…
Binding kinetic parameters can be correlated with drug efficacy, which led to the development of various computational methods for predicting binding kinetic rates and gaining insight into protein-drug binding paths and mechanisms in recent…
Many problems in materials science and biology involve particles interacting with strong, short-ranged bonds, that can break and form on experimental timescales. Treating such bonds as constraints can significantly speed up sampling their…
We analyze the displacements of the particles of a glass-forming molecular liquid perpendicular to a confining solid surface, using extensive molecular dynamics simulations with atomistic models. In the vicinity of an attractive surface,…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…
Swimming cells often have to self-propel through fluids displaying non-Newtonian rheology. While past theoretical work seems to indicate that stresses arising from complex fluids should systematically hinder low-Reynolds number locomotion,…
Many processes in chemistry and physics take place on timescales that cannot be explored using standard molecular dynamics simulations. This renders the use of enhanced sampling mandatory. Here we introduce an enhanced sampling method that…
The advances in materials and biological sciences have necessitated the use of molecular simulations to study polymers. The Markov chain Monte Carlo simulations enable the sampling of relevant microstates of polymeric systems by traversing…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
ParSplice D. Perez, E. D. Cubuk, A. Waterland, E. Kaxiras, and A. F. Voter, Long-Time Dynamics through Parallel Trajectory Splicing, Journal of Chemical Theory and Computation, 2016 is a molecular dynamics method for parallel-in-time…
The use of laboratory robotics for autonomous experiments offers an attractive route to alleviate scientists from tedious tasks while accelerating material discovery for topical issues such as climate change and pharmaceuticals. While some…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
Exact relaxation times and eigenfunctions for a simple mechanical model of polymer dynamics are obtained using supersymmetry methods of quantum mechanics. The model includes the finite extensibility of the molecule and does not make use of…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…
Measurements of the capillary-driven thinning and breakup of fluid filaments are widely used to extract extensional rheological properties of complex materials. For viscoelastic (e.g., polymeric) fluids, the determination of the longest…
Drug-loaded hydrogels provide a means to deliver pharmaceutical agents to specific sites within the body at a controlled rate. The aim of this paper is to understand how controlled drug release can be achieved by tuning the initial…
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD preparation protocols, water molecules are typically added…
In this study, polyurethane-films loaded diclofenac were used to analyze the drug release kinetics and mechanisms. For this purpose, the experimental procedures were developed under static and dynamic conditions with different initial drug…