In this work, we performed molecular dynamics simulations to study the of a shock wave-induced single nanobubble collapsing near one flexible and two rigid boundaries. The boundary consisted polyethylene, boundaries were made aluminum iron. waves impinging on inside system generated using momentum mirror approach. For relative wall distances, studied shock-induced its collapse atomic velocity c...

In this paper, a method of simulating the docking of small flexible ligands to flexible receptors in water is reported. The method is based on molecular dynamics simulations and is an extension of an algorithm previously reported by Di Nola et al. (Di Nola et al., Proteins 1994;19:174-182). The method allows a fast exploration of the receptor surface, using a high temperature of the center of m...

Two flexible multivalent molecular units are employed to self-assemble highly regular supramolecular porous networks at the solid/liquid interface. Scanning tunnelling microscopy imaging corroborated with molecular dynamics simulations make it possible to elucidate the conformational freedom behind the binding motif, which identify the architecture as a highly regular soft network.

Self-assembly is a common phenomenon in the macro-molecular environment inside the cell and is critical for many cellular functions. Viral capsid assembly has been studied as a key model for self-assembly systems by researchers from different fields. There nonetheless remains a substaintial gap between experimental observations and current models, as the direct measurement of the assembly dynam...

Many real time processes have complex, uncertain and nonlinear dynamics. Boilers are nonlinear, time varying, multi-input multi-output (MIMO) systems, whose states generally vary with operating conditions. The major problem in controlling that system is that its drum water pressure and steam flow dynamics include an integrator that results a critically stable behavior. Conventional controller p...

Driven by recent two-dimensional infrared experiments by Woutersen and Hamm, trialanine has emerged as a paradigm to study conformational dynamics of a small peptide in aqueous solution. Employing the exceptional amount of experimental and ab initio data, in this work, trialanine serves as a model problem to perform a comprehensive comparison of six popular force fields, including the recent ve...

The melting of a 64 ion microcrystal of KCI was studied by means of a molecular dynamics computer simulation. We used a central pair interaction with an inverse power law repulsion. The thermodynamics, kinetic and structural properties such as melting temperature, latent heat, mean square displacement, diffusion constant, radial distribution function and bond angle distribution are calculated. ...