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Radial Distribution Functions (radial + distribution_function)

Distribution by Scientific Domains

Chemistry	73%

Selected Abstracts

An in vitro model system for cytoskeletal confinement

CYTOSKELETON, Issue 10 2009
Sarah Köster
Abstract The motility, shape, and functionality of the cell depend sensitively on cytoskeletal mechanics which in turn is governed by the properties of filamentous proteins - mainly actin, microtubules, and intermediate filaments. These biopolymers are confined in the dense cytoplasm and therefore experience strong geometric constraints on their equilibrium thermal fluctuations. To obtain a better understanding of the influence of confinement on cytoskeletal filaments we study the thermal fluctuations of individual actin filaments in a microfluidic in vitro system by fluorescence microscopy and determine the persistence length of the filaments by analyzing the radial distribution function. A unique feature of this method is that we obtain the persistence length without detailed knowledge of the complete contour of the filament which makes the technique applicable to a broad range of biological polymers, including those with a persistence length smaller than the optical resolution. Cell Motil. Cytoskeleton 2009. © 2009 Wiley-Liss, Inc. [source]

Insight into Proton Conduction of Immobilised Imidazole Systems Via Simulations and Impedance Spectroscopy,

FUEL CELLS, Issue 3-4 2008
W. L. Cavalcanti
Abstract The proton conduction in immobilised imidazole systems has been investigated in order to support the design of new membrane materials for polymer electrolyte membrane fuel cells (PEMFC). In the experimental part of this work, proton conductivities are measured via impedance spectroscopy. The simulation and modelling are performed combining molecular dynamics simulations and energy barrier calculations; the analysis is done via the proton jump energy barrier, collision ratio and radial distribution function. The dependence of the proton mobility on the temperature, spacer length and the density of conducting groups per area is presented. Donors and acceptors groups approach to each other within a distance from 2.8 to 3,Å where the energy barrier for a proton transfer is very low, which favours the proton jump under the studied conditions. The proton conductivity increases with increase in the spacer length. The simulation results are in good agreement with the proton conductivities presented. [source]

A study on thermal conductivity of a quasi-ordered liquid layer on a solid substrate

HEAT TRANSFER - ASIAN RESEARCH (FORMERLY HEAT TRANSFER-JAPANESE RESEARCH), Issue 7 2007
Xiao-Yan Shi
Abstract In the present paper, a study on thermal conductivity of a quasi-ordered liquid layer on a solid surface was performed by molecular dynamic simulation. Results showed that the motion of the molecules and their radial distribution function in the quasi-ordered liquid layer were similar to those of solid molecules. By using the Green,Kubo formula, the thermal conductivity of the layer was calculated. It was found that it increased with the increase of the parameters of ordering. The size effect and the influence of the boundary condition were also discussed. © 2007 Wiley Periodicals, Inc. Heat Trans Asian Res, 36(7): 429,434, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20171 [source]

Aspects of the modelling of the radial distribution function for small nanoparticles

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2007
Vladimir I. Korsunskiy
An approach to modelling radial distribution functions (RDFs) of nanoparticle samples over a wide range of interatomic distances is presented. Two different types of contribution to the model RDF are calculated. The first explicitly reflects the structure of the nanoparticle parts with more or less crystalline atomic structure. It can be calculated precisely and contains comparatively sharp peaks, which are produced by the set of discrete interatomic distances. The second includes RDF contributions from distances between weakly correlated atoms positioned within different nanoparticles or within different parts of a nanoparticle model. The calculation is performed using the approximation of a uniform distribution of atoms and utilizes the ideas of the characteristic functions of the particle shape known in small-angle scattering theory. This second RDF contribution is represented by slowly varying functions of interatomic distance r. The relative magnitude of this essential part of the model RDF increases with increasing r compared with the part that represents the ordered structure. The method is applied to test several spherical and core/shell models of semiconductor nanoparticles stabilized with organic ligands. The experimental RDFs of ZnSe and CdSe/ZnS nanoparticle samples were obtained by high-energy X-ray diffraction at beamline BW5, HASYLAB, DESY. The ZnSe nanoparticles have a spherical core with approximately 26,Å diameter and zincblende structure. The RDF of the CdSe/ZnS nanoparticle sample shows resolved peaks of the first- and the second-neighbour distances characteristic for CdSe (2.62 and 4.27,Å) and for ZnS (2.33 and 3.86,Å) and for the first time clearly confirms the presence of CdSe and ZnS nanophases in such objects. The diameters of the CdSe and ZnS spherical cores are estimated as 27 and 15,Å. CdSe and ZnS are present in the sample for the most part as independent nanoparticles. A smaller amount of ZnS forms an irregularly shaped shell around the CdSe cores, which consists of small independently oriented ZnS particles. [source]

Investigation of nanocrystalline CdS,glutathione particles by radial distribution function

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 6 2003
V. I. Korsounski
Using high-energy synchrotron radiation, powder diffraction experiments were carried out on CdS nanocrystals stabilized with glutathione. The radial distribution function was calculated from the data and analysed. The nanoparticle core, of diameter estimated as 15,20,Å, consists of Cd and S atoms in the proportion 1:1. Inside the core, both Cd and S atoms coordinate each other approximately tetrahedrally. The surface S atoms are connected to just two or three Cd atoms of the core and belong to the glutathione molecules of the particle shell. These S atoms are also a part of the core structure and contribute about one half of the total number of S atoms per particle. First-neighbour Cd,S distances are 2.523,Å with a narrow distance distribution. No difference is observed between the lengths of Cd,S bonds involving the sulfur of the glutathione molecules and the sulfur atoms which are solely bound to Cd. The bond angle Cd,S,Cd at the surface bridging S atoms of glutathione is ca 99.5°, i.e. significantly smaller than an average one of 109.5° characteristic of the Cd and S atom packing inside the core. Beyond the range of the near interatomic distances, the influence of the surface and the defects cause a significant distinction of the particle core structure from those of zincblende and wurtzite, characteristic of bulk CdS. [source]

Artemisinin Derivatives with Antimalarial Activity against Plasmodium falciparum Designed with the Aid of Quantum Chemical and Partial Least Squares Methods

MOLECULAR INFORMATICS, Issue 8 2003

Abstract Artemisinin derivatives with antimalarial activity against Plasmodium falciparum resistant to mefloquine are designed with the aid of Quantum Chemical and Partial Least Squares Methods. The PLS model with three principal components explaining 89.55% of total variance, Q2=0.83 and R2=0.92 was obtained for 14/5 molecules in the training/external validation set. The most important descriptors for the design of the model were one level above the lowest unoccupied molecular orbital energy (LUMO+1), atomic charges in atoms C9 and C11 (Q9) and (Q11) respectively, the maximum number of hydrogen atoms that might make contact with heme (NH) and RDF030,m (a radial distribution function centered at 3.0,Å interatomic distance and weighted by atomic masses). From a set of ten proposed artemisinin derivatives, a new compound (26), was predicted with antimalarial activity higher than the compounds reported in literature. Molecular graphics and modeling supported the PLS results and revealed heme-ligand and protein-ligand stereoelectronic relationships as important for antimalarial activity. The most active 26 and 29 in the prediction set possess substituents at C9 able to extend to hemoglobin exterior, what determines the high activity of these compounds. [source]

Theoretical Study on Co3+ in Aqueous Solution in Terms of ABEEM/MM Model

CHINESE JOURNAL OF CHEMISTRY, Issue 6 2007
Qing-Mei Guan
Abstract A detailed theoretical investigation on Co3+ hydration in aqueous solution has been carried out by means of molecular dynamics (MD) simulations based on the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM). The effective Co3+ ion-water potential has been constructed by fitting to ab initio structures and binding energies for ionic clusters. And then the ion-water interaction potential was applied in combination with the ABEEM-7P water model to molecular dynamics simulations of single Co3+(aq.) solution, managing to reproduce many experimental structural and dynamical properties of the solution. Here, not only the common properties (radial distribution function, angular distribution function and solvation energy) obtained for Co3+ in ABEEM-7P water solution were in good agreement with those from the experimental methods and other molecular dynamics simulations but also very interesting properties of charge distributions, geometries of water molecules, hydrogen bond, diffusion coefficients, vibrational spectra are investigated by ABEEM/MM model. [source]

Bound state spectra of the 3D rational potential

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2008
Amlan K. Roy
Abstract We present bound state spectra of the 3D rational potential, V(r) = r2 + ,r2/(1 + gr2), g > 0, by means of the generalized pseudospectral method. All the 30 states corresponding to n = 0,9 are considered for the first time for a broad range of coupling parameters. These results surpass the accuracy of all other existing calculations published so far except the finite-difference method, which yields similar accuracy as ours. Variation of energies and radial distribution functions is followed with respect to the interaction parameters. Special emphasis has been laid on higher excitations and negative values of the interaction, where relatively less work has been reported. The energy sequence is found to be different for positive and negative interaction; numerically following a mirror-image relationship usually, if not always. Additionally, 20 energy splittings arising from certain levels belonging to n = 0,9 are systematically studied as functions of the potential parameters. Several new states (including the higher ones) are presented. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source]

ISAACS, interactive structure analysis of amorphous and crystalline systems

JOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 1 2010
Sébastien Le Roux
ISAACS (interactive structure analysis of amorphous and crystalline systems) is a cross-platform program developed to analyze the structural characteristics of three-dimensional structure models built by computer simulations. The models may have any degree of periodicity (i.e. crystallinity) and local symmetry. The following structural information is computed from the models: total and partial radial distribution functions and structure factors for X-ray or neutron scattering, coordination numbers, bond-angle and near atomic neighbor distributions, bond-valence sums, ring statistics, and spherical harmonics invariants. The information may be visualized conveniently and stored for further use. [source]

Aspects of the modelling of the radial distribution function for small nanoparticles

Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2009
Shih-Wei Chao
Abstract Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon,carbon separation was sampled in a step 0.1 Å for a range of 3,9 Å, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen,hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source]

Coarse-grained force field for the nucleosome from self-consistent multiscaling

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2008
Karine Voltz
Abstract A coarse-grained simulation model for the nucleosome is developed, using a methodology modified from previous work on the ribosome. Protein residues and DNA nucleotides are represented as beads, interacting through harmonic (for neighboring) or Morse (for nonbonded) potentials. Force-field parameters were estimated by Boltzmann inversion of the corresponding radial distribution functions obtained from a 5-ns all-atom molecular dynamics (MD) simulation, and were refined to produce agreement with the all-atom MD simulation. This self-consistent multiscale approach yields a coarse-grained model that is capable of reproducing equilibrium structural properties calculated from a 50-ns all-atom MD simulation. This coarse-grained model speeds up nucleosome simulations by a factor of 103 and is expected to be useful in examining biologically relevant dynamical nucleosome phenomena on the microsecond timescale and beyond. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source]

Inverse Monte Carlo procedure for conformation determination of macromolecules

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2003
Mark Bathe
Abstract A novel numerical method for determining the conformational structure of macromolecules is applied to idealized biomacromolecules in solution. The method computes effective inter-residue interaction potentials solely from the corresponding radial distribution functions, such as would be obtained from experimental data. The interaction potentials generate conformational ensembles that reproduce thermodynamic properties of the macromolecule (mean energy and heat capacity) in addition to the target radial distribution functions. As an evaluation of its utility in structure determination, we apply the method to a homopolymer and a heteropolymer model of a three-helix bundle protein [Zhou, Y.; Karplus, M. Proc Natl Acad Sci USA 1997, 94, 14429; Zhou, Y. et al. J Chem Phys 1997, 107, 10691] at various thermodynamic state points, including the ordered globule, disordered globule, and random coil states. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 876,890, 2003 [source]

Comparative analysis of CFD models of dense gas,solid systems

AICHE JOURNAL, Issue 5 2001
B. G. M. van Wachem
Many gas,solid CFD models have been put forth by academic researchers, government laboratories, and commercial vendors. These models often differ in terms of both the form of the governing equations and the closure relations, resulting in much confusion in the literature. These various forms in the literature and in commercial codes are reviewed and the resulting hydrodynamics through CFD simulations of fluidized beds compared. Experimental data on fluidized beds of Hilligardt and Werther (1986), Kehoe and Davidson (1971), Darton et al.(1977), and Kuipers (1990) are used to quantitatively assess the various treatments. Predictions based on the commonly used governing equations of Ishii (1975) do not differ from those of Anderson and Jackson (1967) in terms of macroscopic flow behavior, but differ on a local scale. Flow predictions are not sensitive to the use of different solid stress models or radial distribution functions, as different approaches are very similar in dense flow regimes. The application of a different drag model, however, significantly impacts the flow of the solids phase. A simplified algebraic granular energy-balance equation is proposed for determining the granular temperature, instead of solving the full granular energy balance. This simplification does not lead to significantly different results, but it does reduce the computational effort of the simulations by about 20%. [source]

EXAFS and molecular dynamics studies of ionic solutions

JOURNAL OF SYNCHROTRON RADIATION, Issue 2 2001
Paola D'Angelo
This paper focuses on recent advances in the X-ray absorption spectroscopy (XAS) analysis of ionic solutions. The asymmetry of radial distribution functions associated with the solvent molecules surrounding the ions has to be taken into account to perform a reliable structural analysis. Molecular dynamics (MD) simulations provide reliable 's which can be used as starting models in the XAS data analysis. The combined MD-XAS investigation reduces meaningfully the indetermination of the structural parameters, especially for coordination numbers and Debye,Waller factors. Double-electron excitation channels can be present in the XAS spectra of ionic solutions and they have to be accounted for in the background extraction. The ability of the XAS technique to probe three-body correlation functions in ionic solutions with the aid of MD has been shown. The analysis of the low- k region of the spectra allows the detection of a weak but significant hydrogen structural signal. The XAS technique is especially well suited to determine the detailed shape of the nearest-neighbor peak in the atom,atom pair correlation functions of disordered systems. The information that they contain about the short-range atom,atom pairwise interactions can be very helpful for specifying and properly modifying model potentials used in MD simulations. [source]

Structure Determination in Colloidal Crystal Photonic Bandgap Structures

JOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 6 2002
John Ballato
Structure/optical property relationships in photonic bandgap structures are evaluated by a novel combination of sample sectioning, microscopy, and image analysis. Disordered colloidal crystals of solution-derived, monosized SiO2 particles were sectioned by focused ion beam (FIB) milling and then imaged using field emission scanning electron microscopy (FE-SEM). Pair correlation and radial distribution functions of the particulate arrangement were generated directly from a binary color scale rendering of the FE-SEM images, therein defining the level of order or disorder in the structure. These experimentally obtained spatial correlation functions were used to compute the scattering spectral properties in an analogous, although inverse (i.e., solving the inverse scattering problem), method to that used in X-ray diffraction for structure determination. Using a first-order approximation to the scattering from a disordered structure, the bandwidth and midgap values for the colloidal crystal photonic bandgap materials were within 15% of those measured. This new methodology promises to provide a simple and direct approach for quantifying the structure/optical property relationships in ordered and disordered photonic crystals directly from standard microstructural imaging techniques. [source]

Temperature-induced phase transition in simulated amorphous Al2O3

PHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 2 2006
Vo Van Hoang
Abstract Our previous simulation studies indicated the existence of pressure-induced phase transition in liquid and amorphous Al2O3. In the current paper, we present the structural transformation of simulated amorphous Al2O3 from an octahedral to a tetrahedral network structure by heating from the high-density amorphous (hda) model at constant pressure P = 0 GPa. The structure of the models was analyzed through the partial radial distribution functions (PRDFs), coordination number distributions, bond-angle distributions and interatomic distances. Furthermore, significant differences in structural characteristics of low-density amorphous (lda) models obtained by heating from the hda one and by cooling from the low-density melt have been found and are presented. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

Structural, thermodynamic and other associated properties of partially ordered Ag-In alloy

PHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 3 2003
R. Venkatesh
Abstract Extensive computations have been performed using the Lebowitz solution of hard sphere mixtures as a reference system, and perturbed the hard sphere direct correlation function, COij(r), with square well attractive tail. We used mean spherical model to compute the total and partial direct correlation functions in the attractive and repulsive regions of the interacting potential of Ag,In alloy at different compositions. The potential parameters were those obtained for pure metals. With these potential parameters (the partial and total) structure factors were evaluated, and then Fourier transformed to get the partial and total radial distribution functions. Further the well-known Bhatia,Thornton correlation functions namely the number-number, concentration-concentration, and number-concentration correlation functions have been computed. We also obtained total and partial coordination numbers from partial and total pair correlation functions respectively. With the help of these pair correlation functions we give the distances between atoms namely Ag,Ag, In,In and Ag,In at different compositions of In in Ag,In alloy. It is found that these distances practically remain constant and are independent of composition, which has been attributed to the formation of segregated clusters of atomic dimensions. Using Kirkwood,Buff's equation, compressibillities have been calculated as a function of composition. The temperature derivative of diffusion coefficient for pure constituents has been formulated and the computed results were compared with the available experimental values. With this model the diffusion coefficients and the friction coefficients of the constituents have been obtained through the use of Helfand's trajectory principle with a reasonable success in the alloy as well. It is found that these metals of the alloy tend to segregate. The ratio of diffusion coefficients of the metals in the alloy is almost a constant and is equal to 0.9. This shows that the alloy forms a regular solution in spite of their tendency to segregate. (© 2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source]

The Jahn,Teller Effect of the TiIII Ion in Aqueous Solution: Extended Ab Initio QM/MM Molecular Dynamics Simulations,

CHEMPHYSCHEM, Issue 10 2004
Chinapong Kritayakornupong Dr.
Abstract Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, including only the first and the first and second hydration shells in the QM region, were performed for TiIIIin aqueous solution. The hydration structure of TiIIIis discussed in terms of radial distribution functions, coordination-number distributions and several angle distributions. Dynamical properties, such as librational and vibrational motions and TiIIIO vibrations, were evaluated. A fast dynamical Jahn,Teller effect of TiIII(aq) was observed in the QM/MM simulations, in particular when the second hydration shell was included into the QM region. The results justify the computational effort required for the inclusion of the second hydration shell into the QM region and show the importance of this effort for obtaining accurate hydration-shell geometries, dynamical properties, and details of the Jahn,Teller effect. [source]