The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

A smooth particle mesh Ewald method

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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Quantum mechanical continuum solvation models.

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.

/pdf/gromacs-fast-flexible-and-free-15aazpel5u.pdf

GROMACS: Fast, flexible, and free

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Titanium Dioxide Nanomaterials: Synthesis, Properties, Modifications, and Applications

The translational (center of mass) kinetic energy of solid and liquid para-hydrogen have been recently measured by means of Deep Inelastic Neutron Scattering. We have evaluated the same quantity, in similar thermodynamic conditions, by means of Path Integral Monte Carlo computer simulation, modelling the system as composed of a set of spherical molecules interacting through a pairwise additive Lennard-Jones potential. In spite of the crude approximations on the interaction potential, the agreement is excellent. The pressure was also computed by means of the same simulations. This quantity, compared with the equation of state for solid para-hydrogen given by Driessen and Silvera, gives an agreement of a lesser quality and a negative value for the liquid state. We attribute this discrepancy to the limitations of the Lennard-Jones potential.

Kinetic energy of solid and liquid para-hydrogen: a path integral Monte Carlo simulation

Electronic structure of the mixed-valent system V2-xMoxO5

We present synchrotron based soft x-ray emission (XES) measurements (Nb $L{\ensuremath{\beta}}_{2,15},$ Nb $L{\ensuremath{\gamma}}_{1},$ Nb ${M}_{3},$ Nb ${M}_{4,5},$ O K\ensuremath{\alpha}) and theoretical calculations of x-ray emission spectra of ${\mathrm{KNbO}}_{3}$. The obtained results are compared with x-ray photoemission spectroscopy valence-band measurements and band-structure calculations. The Nb ${M}_{4,5}$ emission spectra show strong dispersion and by tuning the exciting synchrotron radiation through the Nb 3d threshold ${(E}_{\mathrm{exc}}=206.5--240.6\mathrm{eV}),$ we identify contributions to the valence emission from the decay of both holes, ${3d}_{5/2}$ and ${3d}_{3/2}.$ It is also shown that it is generally possible to measure ${M}_{3}(4d5\stackrel{\ensuremath{\rightarrow}}{s}{3p}_{3/2})$ x-ray emission spectra of 4d metals in order to study the distribution of 4d valence-band states.

Electronic structure of KNbO 3 : Nb M 4,5 x-ray-fluorescence measurements

By applying an exponential mode analysis to ring polymer molecular dynamics simulations of dense fluid parahydrogen, we find that the dynamical processes establishing the time behavior of the Kubo velocity autocorrelation function display the same nature as those already observed in high-density classical fluids. This result permits us to demonstrate that the exponential mode decomposition is a unique tool to identify which dynamical processes lead to one of the most notable properties of quantum fluids: the large value of the mean kinetic energy per particle and the importance of the zero-temperature quantum effects in determining it.

Dynamical Origin of the Total and Zero-Point Kinetic Energy in a Quantum Fluid.

We report the results of a ring polymer molecular dynamics study of the Kubo velocity autocorrelation function of a quantum fluid as para-hydrogen aimed at the comparison with its classical counterpart. Quite different density conditions were considered for both the classical and quantum cases, in order to compare the two systems before and after the dynamical crossover typically undergone by the velocity autocorrelation function (VAF) of fluids at densities around the triple point, where the shape of the function changes from a monotonic to an oscillatory behavior with a negative minimum. A detailed study of the phase diagram of classical para-hydrogen was necessary for a reasonable choice of the classical states to be taken into consideration, in the spirit of the classical principle of corresponding states. The shape of the quantum and classical VAF was thoroughly analyzed, exhibiting at all studied densities clear differences that might be taken as evidence of quantum effects. We show that these differences are substantially reduced by applying a state-dependent time scaling with respect to a reference time identified with the inverse of the collision rate. An even better coincidence in shape is found by comparing the two systems at slightly non-corresponding reduced densities, suggesting that the quantum system behaves almost like the classical one, but at systematically less dense reduced states of the latter. We also find an unexpected and quite interesting density trend of the collision rate of both classical and quantum para-hydrogen, which accounts for the effectiveness of the scaling throughout the explored density range. The mean kinetic energy and the diffusion coefficients are also discussed in some detail.

Martin Neumann

Papers

Kinetic energy of solid and liquid para-hydrogen: a path integral Monte Carlo simulation

Electronic structure of the mixed-valent system V2-xMoxO5

Electronic structure of KNbO 3 : Nb M 4,5 x-ray-fluorescence measurements

Dynamical Origin of the Total and Zero-Point Kinetic Energy in a Quantum Fluid.

Density and time scaling effects on the velocity autocorrelation function of quantum and classical dense fluid para-hydrogen.