@article{schroeder07a, title = {Simulation studies of ionic liquids: orientational correlations and static dielectric properties.}, author = {C. Schr{\"o}der and T. Rudas and O. Steinhauser}, journal = {J. Chem. Phys.}, month = {Dec}, number = 24, pages = 244506, volume = 125, year = 2006, url = {http://dx.doi.org/10.1063/1.2404674}, timestamp = {2007.05.09}, pmid = {17199354}, pdf = {._schroeder07a.pdf}, owner = {otten}, doi = {10.1063/1.2404674}, abstract = {The ionic liquids BMIM+I-, BMIM+BF4-, and BMIM+PF6- were simulated by means of the molecular dynamics method over a time period of more than 100 ns. Besides the common structural analysis, e.g., radial distribution functions and three dimensional occupancy plots, a more sophisticated orientational analysis was performed. The angular correlation functions g(00)110(r) and g(00)101(r) are the first distance dependent coefficients of the pairwise orientational distribution function g(rij,Omega1,Omega2,Omega12). These functions help to interpret the three dimensional plot and reveal interesting insights into the local structure of the analyzed ionic liquids. Furthermore, the collective network of ionic liquids can be characterized by the Kirkwood factor Gkappa(r) [J. Chem. Phys. 7, 911 (1939)]. The short-range behavior (r<10 A) of this factor may be suitable to predict the water miscibility of the ionic liquid. The long-range limit of Gkinfinity is below 1 which demonstrates the strongly coupled nature of the ionic liquid networks. In addition, this factor relates the orientational structure and the dielectric properties of the ionic liquids. The static dielectric constant epsilon(omega=0) for the simulated system is 8.9-9.5. Since in ionic liquids the very same molecule contributes to the total dipole moment as well as carries a net charge, a small, but significant contribution of the cross term between the total dipole moment and the electric current to epsilon(omega=0) is observed.}, biburl = {http://www.bibsonomy.org/bibtex/2625dfdc5645067ee3766255ec94e9087/kaigrass}, keywords = {Ionic Chemical; Molecular; Capacitance; Computer Structure-Activity Simulation; Electric Models, Statistics; Conformation; Relationship Electrostatics; Liquids; Molecular} } @article{pugnaloni06a, title = {Cluster pair correlation function of simple fluids: energetic connectivity criteria.}, author = {Luis A Pugnaloni and Guillermo J Zarragoicoechea and Fernando Vericat}, journal = {J. Chem. Phys.}, month = {November}, number = 19, pages = 194512, volume = 125, year = 2006, timestamp = {2007.02.14}, pmid = {17129128}, owner = {olenz}, doi = {10.1063/1.2378920}, abstract = {We consider the clustering of Lennard-Jones particles by using an energetic connectivity criterion proposed long ago by Hill [J. Chem. Phys. 32, 617 (1955)] for the bond between pairs of particles. The criterion establishes that two particles are bonded (directly connected) if their relative kinetic energy is less than minus their relative potential energy. Thus, in general, it depends on the direction as well as on the magnitude of the velocities and positions of the particles. An integral equation for the pair connectedness function, proposed by two of the authors [Phys. Rev. E 61, R6067 (2000)], is solved for this criterion and the results are compared with those obtained from molecular dynamics simulations and from a connectedness Percus-Yevick-type integral equation for a velocity-averaged version of Hill's energetic criterion.}, biburl = {http://www.bibsonomy.org/bibtex/2548ff25801882be89c0078e8045118a0/kaigrass}, keywords = {Kinetics; Models, Thermodynamics Chemical; Solutions; Size; Transition; Phase Particle} } @article{nkodo01a, title = {Diffusion coefficient of DNA molecules during free solution electrophoresis.}, author = {A. E. Nkodo and J. M. Garnier and B. Tinland and H. Ren and C. Desruisseaux and L. C. McCormick and G. Drouin and G. W. Slater}, journal = {Electrophoresis}, month = {Aug}, number = 12, pages = {2424--2432}, volume = 22, year = 2001, url = {http://dx.doi.org/3.0.CO;2-1}, timestamp = {2007.06.11}, pii = {3.0.CO;2-1}, pmid = {11519946}, pdf = {Electrophoresis/Electrophoresis-general/nkodo01a.pdf}, owner = {grass}, doi = {3.0.CO;2-1}, abstract = {The free-draining properties of DNA normally make it impossible to separate nucleic acids by free-flow electrophoresis. However, little is known, either theoretically or experimentally, about the diffusion coefficient of DNA molecules during free-flow electrophoresis. In fact, many authors simply assume that the Nernst-Einstein relation between the mobility and the diffusion coefficient still holds under such conditions. In this paper, we present an experimental study of the diffusion coefficient of both ssDNA and dsDNA molecules during free-flow electrophoresis. Our results unequivocally show that a simplistic use of Nernst-Einstein's relation fails, and that the electric field actually has no effect on the thermal diffusion process. Finally, we compare the dependence of the diffusion coefficient upon DNA molecular size to results obtained previously by other groups and to Zimm's theory.}, biburl = {http://www.bibsonomy.org/bibtex/2bffe5cba560a93c7602077b09da6d0b0/kaigrass}, keywords = {Photochemistry; Benzoxazoles; Chemical; DNA; Heat; Oligodeoxyribonucleotides; Diffusion; Fluorometry; Models, Algorithms; Weight; Electrophoresis, Lasers; Fluorescent Quinolinium Dyes; Single-Stranded; Viral; Compounds Molecular Capillary; DNA,} }