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.

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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 fundamental equation of electrostatics, i.e. the integral equation for the polarization of a macroscopic dielectric in an arbitrary external field, is written in a form that allows explicit inclusion of the toroidal boundary conditions as well as the cutoff of dipolar interactions often used in the computer simulation of polar systems. The toroidal boundary conditions are accounted for in a natural way if the integral equation is formulated (and solved) in Fourier space. Rigorous expressions for the polarization induced by a homogeneous field as well as for the equilibrium dipole moment fluctuations, both as a function of the dielectric constant, are then easily derived for general systems in two and three dimensions. The equations obtained for spherical cutoff geometry with reaction field are identical to those valid for an infinite periodic system (Ewald sum plus reaction field). When applied to the case of a highly polar Stockmayer system (μ*2=3·0, θ*=0·822, T*=1·15) the formulas lead to a consiste...

Dipole moment fluctuation formulas in computer simulations of polar systems

We present Mn $3s$ x-ray photoelectron spectra of manganese oxides with the Mn formal valency from $2+$ to $4+.$ We found that the ${\mathrm{Sr}}^{2+}$ doping or cation deficiency in manganites do not change the Mn $3s$ splitting in manganites with the Mn formal valency from $3.0+$ to $3.3+.$ We suggest that doping holes are localized in O $2p$ states.

Mn 3s exchange splitting in mixed-valence manganites.

Despite the sizable literature on computer simulations of water and aqueous solutions, very little is known about one of the most interesting properties of water, namely its dielectric constant. In this paper it is demonstrated that the methodological as well as technological problems that have hitherto impeded the calculation of dielectric properties of realistic model systems have now been overcome. Using a small dedicated array processor, a series of extensive simulations with the MCY (Matsuoka–Clementi–Yoshimine) potential for water have been performed in reaction field geometry, and it is shown that consistent (i.e., free from boundary effects) and accurate results may be obtained for the full frequency‐dependent dielectric constant, from the static up to the submillimeter range. At the same time it is found that the rather popular MCY model is not able to satisfactorily reproduce the dielectric properties of real water: Both the static dielectric constant and the principal dielectric relaxation time are much lower than the experimental values, and the temperature dependence of the Kirkwood g factor has the wrong sign. It is concluded that in the future the calculation of the dielectric constant, being a measure of orientational correlations between molecules, will play an important part in assessing the reliability of model potentials for water.

The dielectric constant of water. Computer simulations with the MCY potential

Mixed-valence vanadium oxides studied by XPS

In this second paper in a series of systematic investigations seeking to relate the dielectric properties of water to the features of the intermolecular potential, extensive molecular dynamics simulations with the empirical TIP4P effective pair potential are compared with the experimental data for water as well as with the results reported previously for the MCY a b i n i t i omodel. The frequency dependence of the dielectric constant obtained for the two models is contrasted with the predictions of a Mori three‐variable theory and analyzed in detail using a phenomenological description of dielectric relaxation. It is shown that both models are capable of reproducing all reorientational processes observed in the experimental spectrum. However, qualitative agreement with the experimental results for the Debye relaxation time and the static Kirkwood g‐factor g K is only obtained with the TIP4P model, although the values are still too low and ∂g K /∂T has the wrong sign. The differences between the models are interpreted as being due to the different position chosen for the center of negative charge, and it is argued that moving the latter further towards the oxygen would, for simple rigid point charge models, yield considerably improved agreement with experiment.

Martin Neumann

Papers

Dipole moment fluctuation formulas in computer simulations of polar systems

Mn 3s exchange splitting in mixed-valence manganites.

The dielectric constant of water. Computer simulations with the MCY potential

Mixed-valence vanadium oxides studied by XPS

Dielectric relaxation in water. Computer simulations with the TIP4P potential