CURRENT ISSUE
MANUSCRIPT SUBMISSION
FUTURE ISSUES
ALL ISSUES
DATABASES
Blog Archives
Dissipative Particle Dynamics via Molecular Dynamics
We demonstrate that the main features of DPD may be obtained using molecular dynamics employing a determin- istic thermostat. This apparent isomorphism holds as long as the MD pair potentials are sufficiently smooth a ...
Deviations From Classical Hydrodynamic Theory in Highly Confined Planar Poiseuille Flow of a Polymer Solution
The behaviour of polymer solutions in highly confined geometries remains a subject of interest in rheology and fluid dynamics. In this paper, we investigate how well the classical hydrodynamic description based on the ...
Transient Heat Flow in a One-component Lennard-Jones/spline Fluid. A Non-equilibrium Molecular Dynamics Study
A one-component Lennard-Jones/spline fluid at equilibrium was perturbed by a sudden change of the temperature at one of the system’s boundaries. The system’s response was determined by non-equilibrium molecular dynamics (NEMD). The results show that heat was transported by two mechanisms: (1) ...
Simulation of Ionic Copolymers by Molecular Dynamics
Using GROMACS (a molecular dynamics package) we simulate ionic copolymers and compare the numerical results with those obtained by the lattice Monte Carlo simulations. While the results are qualitatively similar for both methods, the simulation times are significantly longer for the molecular dyn ...
Yokohama to Ruby Valley: Around the World in 80 Years. II.
We two had year-long research leaves in Japan, working together fulltime with several Japanese plus Tony De Groot back in Livermore and Harald Posch in Vienna. We summarize a few of the high spots from that very productive year (1989-1990), followed by an additional fifteen years’ work in Liver ...
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 ...
GALLERY
CURRENT ISSUE
 |
Institute of Bioorganic Chemistry Polish Academy of Sciences 61-704 Poznań, Z. Noskowskiego 12/14 |
 |