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Pair Potentials (pair + potential)
Selected AbstractsThe two-Yukawa model and its applications: the cases of charged proteins and copolymer micellar solutionsJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2007Sow-Hsin Chen Charged and uncharged colloidal systems are known from experiment to display an extremely rich phase behavior, which is ultimately determined by the effective pair potential between particles in solution. As a confirmation, the recent striking observation of an equilibrium cluster phase in charged globular protein solutions [Stradner, Sedgwick, Cardinaux, Poon, Egelhaaf & Schurtenberger (2004). Nature, 432, 492,495] has been interpreted as the effect of competing short-range attractive and long-range repulsive interactions. The `two-Yukawa (2Y) fluid' model assumes an interparticle potential consisting of a hard core plus an attractive and a repulsive Yukawa tail. We show that this rather simple model can indeed explain satisfactorily the structural properties of diverse colloidal materials, measured in small-angle neutron scattering (SANS) experiments, including the cases of equilibrium cluster formation and soft-core repulsion. We apply this model to the analysis of SANS data from horse-heart cytochrome c protein solutions (whose effective potential can be modeled as a hard-sphere part plus a short-range attraction and a weaker screened electrostatic repulsion) and micellar solutions of a triblock copolymer (whose effective potential can be modeled as a hard-sphere part plus a repulsive shoulder and a short-range attraction). The accuracy of the 2Y model predictions is successfully tested against Monte Carlo simulations in both cases. [source] Processing and Properties of a Porous Oxide Matrix Composite Reinforced with Continuous Oxide FibersJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 10 2003Magnus G. Holmquist A process to manufacture porous oxide matrix/polycrystalline oxide fiber composites was developed and evaluated. The method uses infiltration of fiber cloths with an aqueous slurry of mullite/alumina powders to make prepregs. By careful manipulation of the interparticle pair potential in the slurry, a consolidated slurry with a high particle density is produced with a sufficiently low viscosity to allow efficient infiltration of the fiber tows. Vibration-assisted infiltration of stacked, cloth prepregs in combination with a simple vacuum bag technique produced composites with homogeneous microstructures. The method has the additional advantage of allowing complex shapes to be made. Subsequent infiltration of the powder mixture with an alumina precursor was made to strengthen the matrix. The porous matrix, without fibers, possessed good thermal stability and showed linear shrinkage of 0.9% on heat treatment at 1200°C. Mechanical properties were evaluated in flexural testing in a manner that precluded interlaminar shear failure before failure via the tensile stresses. It was shown that the composite produced by this method was comparable to porous oxide matrix composites manufactured by other processes using the same fibers (N610 and N720). The ratio of notch strength to unnotch strength for a crack to width ratio of 0.5 was 0.7,0.9, indicating moderate notch sensitivity. Interlaminar shear strength, which is dominated by matrix strength, changed from 7 to 12 MPa for matrix porosity ranging from 38% to 43%, respectively. The porous microstructure did not change after aging at 1200°C for 100 h. Heat treatment at 1300°C for 100 h reduced the strength for the N610 and N720 composites by 35% and 20%, respectively, and increased their brittle nature. [source] Quantitative prediction of protein,protein binding affinity with a potential of mean force considering volume correctionPROTEIN SCIENCE, Issue 12 2009Yu Su Abstract Quantitative prediction of protein,protein binding affinity is essential for understanding protein,protein interactions. In this article, an atomic level potential of mean force (PMF) considering volume correction is presented for the prediction of protein,protein binding affinity. The potential is obtained by statistically analyzing X-ray structures of protein,protein complexes in the Protein Data Bank. This approach circumvents the complicated steps of the volume correction process and is very easy to implement in practice. It can obtain more reasonable pair potential compared with traditional PMF and shows a classic picture of nonbonded atom pair interaction as Lennard-Jones potential. To evaluate the prediction ability for protein,protein binding affinity, six test sets are examined. Sets 1,5 were used as test set in five published studies, respectively, and set 6 was the union set of sets 1,5, with a total of 86 protein,protein complexes. The correlation coefficient (R) and standard deviation (SD) of fitting predicted affinity to experimental data were calculated to compare the performance of ours with that in literature. Our predictions on sets 1,5 were as good as the best prediction reported in the published studies, and for union set 6, R = 0.76, SD = 2.24 kcal/mol. Furthermore, we found that the volume correction can significantly improve the prediction ability. This approach can also promote the research on docking and protein structure prediction. [source] The pair-functional method for direct solution of molecular structures.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2001The new pair-functional direct method has been implemented and tested. Like the Patterson function, the pairing force has valuable imaging properties at high resolution. Two simple iterative algorithms were designed to refine on the total pair potential and the normalized intensity correlation coefficient of an atomic model. The first algorithm is a peak-picking method which selects the best-paired high peaks from a density map and then uses the strong reflections to generate a new Fourier filtered map. The second algorithm, the pair-and-square method, uses a tangent formula step instead of the Fourier and is a little more efficient. Computational experiments on a point-atom grid model, with perfect data, reached exact ab initio solutions for up to 600 atoms. Point-atom models were also solved by searching for reduced structures that contained as few as one quarter of the atoms. Seeded searches, guided by a small known fragment, solved up to 30000 atoms on the grid. Realistic tests on actual molecules showed that Sheldrick's [Acta Cryst. (1990), A46, 467,473] test structures of 50,200 atoms can be solved under a variety of conditions. [source] Application of statistical potentials to protein structure refinement from low resolution ab initio modelsBIOPOLYMERS, Issue 4 2003Hui Lu Abstract Recently ab initio protein structure prediction methods have advanced sufficiently so that they often assemble the correct low resolution structure of the protein. To enhance the speed of conformational search, many ab initio prediction programs adopt a reduced protein representation. However, for drug design purposes, better quality structures are probably needed. To achieve this refinement, it is natural to use a more detailed heavy atom representation. Here, as opposed to costly implicit or explicit solvent molecular dynamics simulations, knowledge-based heavy atom pair potentials were employed. By way of illustration, we tried to improve the quality of the predicted structures obtained from the ab initio prediction program TOUCHSTONE by three methods: local constraint refinement, reduced predicted tertiary contact refinement, and statistical pair potential guided molecular dynamics. Sixty-seven predicted structures from 30 small proteins (less than 150 residues in length) representing different structural classes (,, ,, ,,/,) were examined. In 33 cases, the root mean square deviation (RMSD) from native structures improved by more than 0.3 Å; in 19 cases, the improvement was more than 0.5 Å, and sometimes as large as 1 Å. In only seven (four) cases did the refinement procedure increase the RMSD by more than 0.3 (0.5) Å. For the remaining structures, the refinement procedures changed the structures by less than 0.3 Å. While modest, the performance of the current refinement methods is better than the published refinement results obtained using standard molecular dynamics. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 575,584, 2003 [source] Hypernetted Chain Calculations for Two-Component PlasmasCONTRIBUTIONS TO PLASMA PHYSICS, Issue 4-5 2007V. Schwarz Abstract We have performed HNC calculations for dense beryllium plasma as studied experimentally using x-ray Thomson scattering, recently. We treated non-equilibrium situations with different electron and ion temperatures which are relevant in pump-probe experiments on ultra-short time scales. To consider quantum effects adequately, we used effective pair potentials to describe the interactions. Results are compared with classical as well as quantum corrected Debye model calculations. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Comparative analysis of ArnCl2 (2 , n , 30) clusters taking into account molecular relaxation effectsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 13 2006G. G. Ferreira Abstract Cluster structures are discussed in a nonrigid analysis, using a modified minima search method based on stochastic processes and classical dynamics simulations. The relaxation process is taken into account considering the internal motion of the Cl2 molecule. Cluster structures are compared with previous works in which the Cl2 molecule is assumed to be rigid. The interactions are modeled using pair potentials: the Aziz and Lennard,Jones potentials for the ArAr interaction, a Morse potential for the ClCl interaction, and a fully spherical/anisotropic Morse,Spline,van der Waals (MSV) potential for the ArCl interaction. As expected, all calculated energies are lower than those obtained in a rigid approximation; one reason may be attributed to the nonrigid contributions of the internal motion of the Cl2 molecule. Finally, the growing processes in molecular clusters are discussed, and it is pointed out that the growing mechanism can be affected due to the nonrigid initial conditions of smaller clusters such as ArnCl2 (n , 4 or 5), which are seeds for higher-order clusters. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Ab initio QM/MM dynamics of H3O+ in waterJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2006Pathumwadee Intharathep Abstract A molecular dynamics (MD) simulation based on a combined ab initio quantum mechanics/molecular mechanics (QM/MM) method has been performed to investigate the solvation structure and dynamics of H3O+ in water. The QM region is a sphere around the central H3O+ ion, and contains about 6,8 water molecules. It is treated at the Hartree-Fock (HF) level, while the rest of the system is described by means of classical pair potentials. The Eigen complex (H9O) is found to be the most prevalent species in the aqueous solution, partly due to the selection scheme of the center of the QM region. The QM/MM results show that the Eigen complex frequently converts back and forth into the Zundel (H5O) structure. Besides the three nearest-neighbor water molecules directly hydrogen-bonded to H3O+, other neighbor waters, such as a fourth water molecule which interacts preferentially with the oxygen atom of the hydronium ion, are found occasionally near the ion. Analyses of the water exchange processes and the mean residence times of water molecules in the ion's hydration shell indicate that such next-nearest neighbor water molecules participate in the rearrangement of the hydrogen bond network during fluctuative formation of the Zundel ion and, thus, contribute to the Grotthuss transport of the proton. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006 [source] Molecular modeling of H2 purification on Na-LSX zeolite and experimental validationAICHE JOURNAL, Issue 1 2005B. Weinberger Analysis of hydrogen purification process by adsorption in the dehydrated Na-LSX zeolite is described. New measurements of hydrogen and nitrogen adsorption selectivity of this zeolite have been performed up to a pressure of 20 MPa and at temperatures of 273, 293 and 313 K, by using a gravimetric-volumetric method. Structural characterizations were realized by helium density displacement, nuclear magnetic resonance, X-ray diffraction and scanning electronic microscopy. Furthermore, Monte Carlo simulations of gas adsorption were performed in a zeolite model of Na-LSX, using pair potentials to represent the interaction between gas molecules and zeolite atoms. Comparison of simulation results and experimental data enabled testing of the validity of such a modeling of the gas-zeolite interaction. © 2004 American Institute of Chemical Engineers AIChE J, 51:142,148, 2005 [source] Optical properties and transformation mechanism of oxygen centres and their aggregates in CaF2 crystalsPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 1 2005A.S. Mysovsky Abstract Oxygen-vacancy dipoles and dimers in CaF2 crystals have been studied ab initio at DFT level and with the shell model using pair potentials. The calculated dipole reorientation barrier is 0.64 eV and the activation energy for diffusion of the dipoles is 1.61 eV. Optical absorption of O2, -VA dipole have been calculated with TD DFT and identified with experimental absorption bands, which appeared to have complex structure. The photodissociation mechanism of the dipole is discussed. Several configurations of the dimer (O2, -VA)2 were calculated. The association energy for the most favourable one is 0.48 eV. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] The pair-functional method for direct solution of molecular structures.ACTA CRYSTALLOGRAPHICA SECTION A, Issue 2 2001The pair-functional principle shows how to construct a unique statistical ensemble of strongly interacting atoms that corresponds to any feasible measured set of X-ray intensities. The ensemble and all its distribution functions are strictly periodic in the crystal lattice, so that each unit cell has exactly the same arrangement of atoms at all times. The mean particle density in the cell is uniform because the ensemble has undefined phases and the origin is not fixed. The atoms in this maximum-entropy ensemble interact through pairwise additive periodic statistical forces within the unit cell. The ensemble average pair-correlation function is matched to the observed originless Patterson function of the crystal. The derived pairing force then becomes approximately proportional to the Ornstein,Zernicke direct correlation function of the ensemble. The atoms have a many-body Boltzmann distribution and the logarithm of the likelihood of any particular conformation is related to its total pairing potential. The pairing potential of a group of atoms acts like a local field in the cell. This property is used in the pair-functional method. Molecular structures can be solved by a direct search in real space for clusters of atoms with high pair potentials. During a successful search, the atoms move from their original random positions to form larger and larger clusters of correctly formed fragments. Finally, every atom belongs to a single cluster, which is the correct solution. [source] Application of statistical potentials to protein structure refinement from low resolution ab initio modelsBIOPOLYMERS, Issue 4 2003Hui Lu Abstract Recently ab initio protein structure prediction methods have advanced sufficiently so that they often assemble the correct low resolution structure of the protein. To enhance the speed of conformational search, many ab initio prediction programs adopt a reduced protein representation. However, for drug design purposes, better quality structures are probably needed. To achieve this refinement, it is natural to use a more detailed heavy atom representation. Here, as opposed to costly implicit or explicit solvent molecular dynamics simulations, knowledge-based heavy atom pair potentials were employed. By way of illustration, we tried to improve the quality of the predicted structures obtained from the ab initio prediction program TOUCHSTONE by three methods: local constraint refinement, reduced predicted tertiary contact refinement, and statistical pair potential guided molecular dynamics. Sixty-seven predicted structures from 30 small proteins (less than 150 residues in length) representing different structural classes (,, ,, ,,/,) were examined. In 33 cases, the root mean square deviation (RMSD) from native structures improved by more than 0.3 Å; in 19 cases, the improvement was more than 0.5 Å, and sometimes as large as 1 Å. In only seven (four) cases did the refinement procedure increase the RMSD by more than 0.3 (0.5) Å. For the remaining structures, the refinement procedures changed the structures by less than 0.3 Å. While modest, the performance of the current refinement methods is better than the published refinement results obtained using standard molecular dynamics. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 575,584, 2003 [source] | |||||||||||||