molecular dynamics

摘要： Bacterial leaf blight(BLB)caused by Xanthomonas oryzae pv.oryzae(Xoo)is one of the most damaging diseases to rice across the world.Various chemicals have been employed so far for the management of bacterial leaf blight.On the other hand,these compounds are damaging to the ecosystem and have an impact on non-target species such as humans and animals.As a result,there is a need to create a new natural inhibitor for BLB management.Deformylase(PDF)enzyme is present in all eubacteria and its necessity in bacterial protein synthesis reveals it as an attractive target for drug development.In this study,the active components of Nigella sativa have been selected based on their previously reported antimicrobial activity and screened on the active site of bacterial PDF by the in silico art of techniques.Among these compounds,dithymoquinone and p-cymene strongly bind with the PDF enzyme with binding energy values of 7.77 kcal/mol and 7.26 kcal/mol,respectively,which is comparatively higher than the control compound(−6.73 kcal/mol).Hence,the“dithymoquinone-PDF”and“p-cymene-PDF”complexes were selected for further study,and their stability was assessed by molecular dynamic(MD)simulation.In MD simulation,both selected compounds exhibited steady-state interaction with PDF for 20 ns.It has been hypothesized that p-cymene and dithymoquinone inhibit peptide deformylase and could be used as antibacterials or pesticides against Xoo against the BLB disease.

摘要： A brief theory and simulation overview for the purpose of design is presented with examples applies to modeling the physical properties,behavior,and phenomena of nanomaterial.This review paper constructs perspectives that consider coupling traditional domains of simulation by novel pathways to produce accurate representations of nanomaterial properties,behavior and phenomena.It is all about size scaling and how different approaches are able to simulate,integrate or simply pass the baton to the next level of complexity.In macroscopic world,the atomic or molecular information alone may not be directly useful.Nor is the bulk information useful in the microscopic world without intimate knowledge of molecular makeup.Therefore,when designing Nanomaterials,knowledge of properties spanning the complete range of size is the prerequisite of a recommended self-consistent approach.In fact,regarding applications in both industry and academia,the simulation first approach often can lead to great savings in time.This review paper focuses mostly on optical and electronic properties but a section is added that provides a segue into mechanical properties for future consideration.