Using both computational and experimental methods, the capacity of four different surfactant molecules to inhibit agglomeration sII hydrate particles was assessed. The simulations were carried out using steered non-steered Molecular Dynamics (MD), simulating coalescence process a slab water droplet, covered with molecules. work based on rocking cell measurements, determining minimum effective d...

Jarzynski’s equality is applied to free energy calculations from steered molecular dynamics simulations of biomolecules. The helix-coil transition of deca-alanine in vacuum is used as an example. With about ten trajectories sampled, the second order cumulant expansion, among the various averaging schemes examined, yields the most accurate estimates. We compare umbrella sampling and the present ...

In order to suggest detailed mechanistic hypotheses for the formation and dehydration of a key carbinolamine intermediate in the T4 pyrimidine dimer glycosylase (T4PDG) reaction, we have investigated these reactions using steered molecular dynamics with a coupled quantum mechanics-molecular mechanics potential (QM/MM). We carried out simulations of DNA abasic site carbinolamine formation with a...

The current thesis presents work on the structure and dynamics of oligosaccharides and polysaccharides as well as the free energetics of carbohydrate-protein interactions. By applying various computational tools such as molecular dynamics simulations, our in-house fast sugar structure prediction software, replica exchange molecular dynamics, homology modeling, umbrella sampling, steered molecul...

in this paper, we use molecular dynamics and finite element simulations to determine the mechanical properties of single-crystal metal of silver (ag) with nano-holes. the lattice transition method from 3-dimensions into 2-dimentions in molecular dynamics simulation as well as plane stress model in finite element method, is used to lessen the simulation time consuming. elasticity module reductio...

In this paper we present new virtual spring manipulator-based tools for steering particles in molecular dynamics simulations in virtual environments. We briefly overview the MolDRIVE system, our visualization and computational steering environment for molecular dynamics real-time simulations, which is the platform for our particle steering implementation. Our study concentrates on visual feedba...

Aquaglyceroporin GlpF selectively conducts water and linear polyalcohols, such as glycerol, across the inner membrane of Escherichia coli. We report steered molecular dynamics simulations of glycerol conduction through GlpF, in which external forces accelerate the transchannel conduction in a manner that preserves the intrinsic conduction mechanism. The simulations reveal channel-glycerol hydro...

Lactate dehydrogenase A (LDHA) is an important enzyme in fermentative glycolysis, generating most energy for cancer cells that rely on anaerobic respiration even under normal oxygen concentrations. This renders LDHA a promising molecular target for the treatment of various cancers. Several efforts have been made recently to develop LDHA inhibitors with nanomolar inhibition and cellular activity...

Oseltamivir (Tamiflu) is currently the frontline antiviral drug employed to fight the flu virus in infected individuals by inhibiting neuraminidase, a flu protein responsible for the release of newly synthesized virions. However, oseltamivir resistance has become a critical problem due to rapid mutation of the flu virus. Unfortunately, how mutations actually confer drug resistance is not well u...