The charge-induced unfolding and refolding of unsolvated cytochrome c have been studied by molecular dynamics (MD) simulations. Simulations were performed for protonated charge states between +3 and +19. The charge-induced unfolding of cytochrome c in the gas phase has previously been examined by ion mobility measurements. The main features of the experimental results are reproduced by the MD s...

Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed wit...

We have performed NMR spin-lattice relaxation experiments and molecular dynamics (MD) computer simulations on atactic polystyrene (a-PS). The segmental correlation times of three different molecular weight a-PS (Mn ) 1600, 2100, 10 900 g/mol) were extracted from NMR by measuring the 2H spin-lattice relaxation times (T1) over a broad temperature range (390-510 K). MD simulations of an a-PS melt ...

In this study, we have investigated radius dependence of hydrogen storage within armchair (n,n) single walled carbon nanotubes (SWCNT) in a square arrays. To this aim, we have employed equilibrium molecular dynamics (MD) simulation. Our simulations results reveal that radius of carbon nanotubes are an important and influent factor in hydrogen distribution inside carbon nanotubes and consequentl...

The mechanism of action of cellulose-degrading enzymes is illuminated through a multidisciplinary collaboration that uses molecular dynamics (MD) simulations and expands the capabilities of MD codes to allow simulations of enzymes and substrates on petascale computational facilities. There is a class of glycoside hydrolase enzymes called cellulases that are thought to decrystallize and processi...

We present here a quantitative study of dislocation cross-slip, an essential thermally activated process in deformation metals, discrete dynamics (DDD) simulations. implemented stress-dependent line-tension model DDD simulations, with minimal information from molecular (MD) This allows reproducing simulations the probabilistic cross-slip rate calculated MD for Cu large range stresses and temper...

Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the d...