Blog Archives

Time-Symmetry Breaking in Hamiltonian Mechanics. Part II. A Memoir for Berni Julian Alder [1925–2020]

Hoover Wm.G., Hoover C.G.

This memoir honors the late Berni Julian Alder, who inspired both of us with his pioneering development of molecular dynamics. Berni’s work with Tom Wainwright, described in the 1959 Scientific American [1], brought Bill to interview at Livermore in 1962. Hired by Berni, Bill enjoyed over 40 ye ...

Improvements to the two-phase sandwich method for calculating the melting points of pure metals

Rybacki Kamil, Winczewski Szymon, Pleechystyy Valeriy, Rybicki Jarosław

The thermophysical properties of metal alloys are often investigated via molecular dynamics (MD) simulations. An exact and reliable estimation of the thermophysical parameters from the MD data requires a properly and carefully elaborated methodology. In this paper, an improved two-phase sandwich ...

Dissipative Particle Dynamics via Molecular Dynamics

Travis Karl

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

Menzel Adrian, Daivis Peter, Todd Billy

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

Hafskjold Bjørn

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

Dzięcielski Michał, Knychała Piotr, Banaszak Michał

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.

Hoover Wm.G. , Hoover C.G.

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

Sarzyńska Joanna, Kuliński Tadeusz

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

Hoover Wm.G.

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

Sarzyńska Joanna, Mickiewicz Agnieszka, Miłostan Maciej, Łukasiak Piotr, Błażewicz Jacek, Figlerowicz Marek, Kuliński Tadeusz

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 ...