This work presents a ReaxFF reactive force-field for use in molecular dynamics simulations of the ZnO– water system. The force-field parameters were fitted to a data-set of energies, geometries and charges derived from quantum-mechanical B3LYP calculations. The presented ReaxFF model provides a good fit to the QM reference data for the ZnO–water system that was present in the data-set. The forc...

Sodium, calcium and magnesium ions are essential for the biological activity of many polyelectrolytes. This activity depends on a condensation of the metal ions. There are several clues, which suggest that interactions between the polyelectrolyte and metal ions depend on a hydration of the ion. This accounts for the great interest in the hydration of metal ions, particularly in the systems cont...

This paper introduces MD, a complete high-performance parallel molecular dynamics simulation system. MD eeciently manages the control and data ow required for the basic molecular dynamics calculations as well as for global statistics and scientiic visualization. We brieey examine the structure of MD, present an analysis of its performance for several physical systems, and examine ways in which ...

A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD). In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the Cα atoms of a Coarse-Grained (CG) protein model. The solution...

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In this paper, modulation diversity (MD) for Rayleigh fading intersymbol interference (ISI) channels is proposed. In particular, the achievable performance with MD is analyzed and a design criterion for MD codes is deduced from an upper bound on the pairwise error probability. This design rule is similar to the well–known design rule for MD codes for flat fading and does not depend on the power...

We present a simple method for calculating a continuum temperature field directly from a molecular dynamics (MD) simulation. Using the idea of a projection matrix previously developed for use in the bridging scale, we derive a continuum temperature equation which only requires information that is readily available from MD simulations, namely the MD velocity, atomic masses and Boltzmann constant...

Simulation of DNA electrophoresis facilitates the design of DNA separation devices. Various methods have been explored for simulating DNA electrophoresis and other processes using implicit and explicit solvent models. Explicit solvent models are highly desired but their applications may be limited by high computing cost in simulating large number of solvent particles. In this work, a coarse-gra...

A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure. Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dyn...

We derive exact expressions for the forces and torques between biaxial molecules interacting via the RE-squared potential, a recent variant of the Gay-Berne potential. Moreover, efficient routines have been provided for rigid body MD simulations, resulting in 1.6 times speedup compared to the two-point finite difference approach. It has also been shown that the time cost of a MD simulation will...