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Blog Archives
Parametrization of 2-thiouracil and 4-thiouracil in CHARMM all-atom empirical force field
A new set of force field parameters complementing the CHARMM27 all atom empirical force field for nucleic acids was developed for 2-thiouracil and 4-thiouracil, two naturally modified RNA bases. The new parameters allow for molecular modeling and molecular dynamics simulations of RNA containing 2 ...
Computational Physics with Particles – Nonequilibrium Molecular Dynamics and Smooth Particle Applied Mechanics
Microscopic and macroscopic particle-simulation methods can both be applied to interesting nonequilibrium problems. Here I develop and discuss the ordinary differential equations underlying these two approaches and illustrate them with applications of interest to statistical mechanics and computa ...
Flexibility of Dicer Studied by Implicit Solvent Molecular Dynamics Simulations
Dicer is an enzyme responsible for processing double-stranded RNAs and plays a key role in an RNAi mechanism. Structural insight into the Dicer is provided by the crystal structure of eukaryotic Dicer from Giardia intestinalis. It has been proposed that the structure has three structurally rigid ...
Method of Planes Normal Pressure for Slit Geometries in Molecular Dynamics Simulations
The resolution and convergence properties of the Method of Planes (MOP) local pressure tensor method is analyzed for a slit geometry in which a system of interacting particles is placed between movable walls composed of atoms. Boundary-driven Molecular Dynamics (BMD) simulations were performed fo ...
Mechanical Properties of Single-walled Carbon Nanotubes Simulated with AIREBO Force-Field
In this work we determined the mechanical properties (Young’s modulus, Poisson’s ratio, and shear modulus) of 400 single-walled carbon nanotubes of radii from 2.1; ((0, 5) nanotube) to 17.3 Å ((0, 45) nanotube). All nanotubes were simulated with AIREBO forcefield. It turns out that z ...