| 1. |
- Guevara-Garca, Alfredo, et al.
(författare)
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Pointing the way to the products Comparison of the stress tensor and the second-derivative tensor of the electron density
- 2011
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 134:23, s. 234106-
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Tidskriftsartikel (refereegranskat)abstract
- The eigenvectors of the electronic stress tensor can be used to identify where new bond paths form in a chemical reaction. In cases where the eigenvectors of the stress tensor are not available, the gradient-expansion- approximation suggests using the eigenvalues of the second derivative tensor of the electron density instead; this approximation can be made quantitatively accurate by scaling and shifting the second-derivative tensor, but it has a weaker physical basis and less predictive power for chemical reactivity than the stress tensor. These tools provide an extension of the quantum theory of atoms and molecules from the characterization of molecular electronic structure to the prediction of chemical reactivity. © 2011 American Institute of Physics.
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| 2. |
- Jenkins, Samantha, 1967-, et al.
(författare)
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An investigation of the merging and collapsing of software
- 2007
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Ingår i: Advances in Complex Systems. - : World Scientific Publishing Co. - 0219-5259. ; 10:3, s. 379-393
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Tidskriftsartikel (refereegranskat)abstract
- We explore the use of complex networks for understanding of the interaction of computer software applications written in the Java object-oriented language with the "library classes" that they use (those provided by the Java Runtime Environment) as, essentially, a merged network of classes. The dependence of the software on the library is quantified using a recently introduced model that identifies phases close to a second-order phase transition existing in scale-free networks. An example is given of a piece of software whose class network collapses without the presence of the library classes, providing validation of a novel structural coupling measure; Rcoupling. The structural properties of the merged software-Java class networks were found to correlate with the proportion of Java classes contained within the subset delimited by Rcoupling. A mechanism for the preservation of the software class network is also provided for the cases studied where the removal of the library classes does not cause collapse.
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| 3. |
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| 4. |
- Jenkins, Samantha, 1967-, et al.
(författare)
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Molecular dynamics simulation of nanocolloidal amorphous silica particles : Part I.
- 2007
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 127:22, s. 224711-
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Tidskriftsartikel (refereegranskat)abstract
- Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles in aqueous solution, with diameter of 4.4 nm and with four different background electrolyte concentrations, to extract the mean force acting between the two silica nanoparticles. Dependences of the interparticle forces on the separation and the background electrolyte concentration were demonstrated. The nature of the interaction of the counterions with charged silica surface sites (deprotonated silanols) was investigated. A "patchy" double layer of adsorbed sodium counterions was observed. Dependences of the interparticle potential of mean force on the separation and the background electrolyte concentration were demonstrated. Direct evidence of the solvation forces is presented in terms of changes of the water ordering at the surfaces of the isolated and double nanoparticles. The nature of the interaction of the counterions with charged silica surface sites (deprotonated silanols) was investigated in terms of quantifying the effects of the number of water molecules separately inside each pair of nanoparticles by defining an impermeability measure. A direct correlation was found between the impermeability (related to the silica surface "hairiness") and the disruption of water ordering. Differences in the impermeability between the two nanoparticles are attributed to differences in the calculated electric dipole moment.
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| 5. |
- Jenkins, Samantha, 1967-, et al.
(författare)
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Molecular dynamics simulation of nanocolloidal amorphous silica particles: Part III
- 2009
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Ingår i: The Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 130
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Tidskriftsartikel (refereegranskat)abstract
- Explicit-solvent molecular dynamics simulations were applied to four pairs of amorphous silica nanoparticles, two pairs having a diameter of 2.0 nm and two pairs with diameter 3.2 nm. The silica nanoparticles were immersed in a background electrolyte consisting of Ca2+ and Cl− ions and water and mean forces acting between the pair of silica nanoparticles were extracted at four different background electrolyte concentrations. The pH was indirectly accounted for via the ratio of silicon to sodium used in the simulations. Dependence of the interparticle potential of mean force on the center-of-mass separation and the silicon to sodium ratio (5:1 and 20:1) is demonstrated. A Si:Na+ ratio of 5:1 gave more repulsive interparticle potentials and lower numbers of internanoparticle or “bridging” hydrogen bonds. Conversely a Si:Na+ ratio of 20:1 yielded more attractive potentials and higher numbers of bridging hydrogen bonds. The nature of the interaction of the counterions with charged silica surface sites (deprotonated silanols) was also investigated. The effect of the sodium double layer on water ordering was observed. The number of water molecules trapped inside the nanoparticles was investigated, and at the highest background ionic concentrations were found to consistently behave in accordance with there being an osmotic pressure. This study highlights the effect of divalent (Ca2+) background ions on the interparticle potentials compared with previous work using monovalent (Na+) background ions. Mechanisms of coagulation and the stability of silica nanocolloids found from this work appear to be in agreement with findings from experiments described in the literature.
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| 6. |
- Jenkins, Samantha, 1967-, et al.
(författare)
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Molecular dynamics simulations of nanocolloidal amorphous silica particles: Part II
- 2008
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Ingår i: The Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 128:16
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Tidskriftsartikel (refereegranskat)abstract
- Explicit molecular dynamics simulations were applied to a pair of amorphous silica nanoparticles with diameter of 3.2 nm immersed in a background electrolyte. Mean forces acting between the pair of silica nanoparticles were extracted at four different background electrolyte concentrations. The dependence of the interparticle potential of mean force on the separation and the silicon to sodium ratio, as well as on the background electrolyte concentration, are demonstrated. The pH was indirectly accounted for via the ratio of silicon to sodium used in the simulations. The nature of the interaction of the counterions with charged silica surface sites (deprotonated silanols) was also investigated. The effect of the sodium double layer on the water ordering was investigated for three Si:Na+ ratios. The number of water molecules trapped inside the nanoparticles was investigated as the Si:Na+ ratio was varied. Differences in this number between the two nanoparticles in the simulations are attributed to differences in the calculated electric dipole moment. The implications of the form of the potentials for aggregation are also discussed.
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| 7. |
- Jenkins, Samantha, 1967-, et al.
(författare)
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The role of hydrogen bonding in nanocolloidal amorphous silica particles in electrolyte solutions
- 2009
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Ingår i: Journal of colloid and interface science. - : Elsevier BV. - 1095-7103 .- 0021-9797.
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Tidskriftsartikel (refereegranskat)abstract
- Explicit solvent (water) molecular dynamics simulations were undertaken containing three pairs of amorphous silica nanoparticles, having diameters of 2.0nm, 2.4nm and 2.8nm, respectively. Mean forces acting between the silica nanoparticles were calculated in a background electrolyte, i.e., NaCl at four different concentrations. Dependence of the inter-particle potential of mean force on the center of mass separation, silicon to sodium ratio (Si:Na(+)), background electrolyte concentration, number of hydrogen bonds directly linking pairs of silica nanoparticles and the density of charged surface sites, are calculated. The pH was indirectly accounted for via the ratio of silicon to sodium used in the simulations. The close relationship between the variation of the number of hydrogen bonds between the pairs of silica nanoparticles and the inter-particle potential of mean force indicates that the degree of inter-particle hydrogen bonding quantifies, for a given size of nanoparticle, the degree of nanoparticle 'stickiness'. Simulations also show that the number of hydrogen bonds between the charged surface (O(-)) sites and the surrounding water molecules increases with increase in charged sites, in agreement with the interaction behavior of silica nanoparticles usually seen in experiments.
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