Published in International Journal of Thermophysics
Thermal Resistance for gold (Au)–water and silver (Ag)–water interfaces are calculated using a reversed non-equilibrium molecular dynamics simulation. Temperature and heat flow dependence of Interfacial thermal resistance (ITR) based on a solid–liquid–solid nano channel system are explained. The results are compared with existing literature to inve...
Published in Journal of Molecular Modeling
This paper deals with the effect of introducing an additional interaction site onto molecular-mechanical models of nitrogen-containing heterocyclic compounds. The introduction of only one additional site next to nitrogen atoms is shown to result in significant improvement of the quality of the models along with negligible slowdown of calculation sp...
The present study focuses on the roles of structure, stress and temperature on the mobility of facets bounding twin domains and on the overall impact on the growth kinetics of { 10 1 2 } twins in Mg. We first use molecular dynamics simulations (MD) to study the relationship between interface structures, stress, temperature and mobility. As facets c...
Published in BMC Research Notes
ObjectiveThe purpose of this work is to optimize the processing of molecular dynamics (MD) trajectory data obtained for large biomolecular systems. Two popular software tools were chosen as the reference: the tng and the xdrfile libraries. Current implementation of tng algorithms and library is either fast or storage efficient and xdrfile is storag...
Published in Nature Communications
The nature of the bulk hydrated electron has been a challenge for both experiment and theory. Here the authors use a machine-learning model trained on MP2 data to achieve an accurate determination of the structure, diffusion mechanisms, and vibrational spectroscopy of the solvated electron.
Published in Journal of Molecular Modeling
The biomolecular recognition of D-mannose-binding lectin from Artocarpus heterophyllus (ArtinM) by Horseradish Peroxidase (HRP) mediated by glycosylation allows their application in a multitude of biological systems. The present work describes the use of molecular dynamics (MD) to assess the Gibbs free energy associated with the formation of a Arti...
The folder contains Microsoft Excel files (.xlsx) of Raman spectra, Thermogravimetric Analysis data, and TEM Energy Dispersive X-ray spectroscopy (EDX) data for the samples analysed in the work, the results from the macroscale thermomechanical model and the Python code for the microscale model.
Published in Medicine in drug discovery
SARS-CoV-2 is a global challenge due to its ability to spread much faster than the SARS-CoV, which was attributed to the mutations in the receptor binding domain (RBD). These mutations enhanced the electrostatic interactions. Recently, a new strain is reported in the UK that includes a mutation (N501Y) in the RBD, that is possibly increasing the in...
Published in Tribology Letters
AbstractIn this work, molecular dynamics simulations are performed to investigate the nanoscale wear behavior of SiC particle-reinforced aluminum matrix composites (SiC/Al NCs) through nanoscratching using a spherical diamond indenter. A series of simulations are conducted to explore the effects of scratching depth, scratching speed, temperature, i...
Published in 3 Biotech
The filamentous fungi Trichoderma spp. are widely used for plant growth promotion and disease control. They form stable symbiosis-like relationship with roots. Unlike plant pathogens and mycorrhizae, the molecular events leading to the development of this association is not well understood. Pathogens deploy effector proteins to suppress or evade pl...
