Dielectric spectra analysis: reliable parameter estimation using interval analysis

Dielectric spectroscopy is an extremely versatile method for characterizing the molecular dynamics over a large range of time scales. Unfortunately, the extraction of model parameters by data fitting is still a crucial problem which is now solved by our program S.A.D.E. S.A.D.E. is based on the algorithm S.I.V.I.A. which was proposed and implemented by Jaulin in order to solve constraint satisfaction problems. The problem of dielectric data analysis is reduced to a problem of choosing the appropriate physical model. In this article, Debye relaxations were used and validated to fit the relaxations of a DGEBA prepolymer and the polarization of the spectrometer electrodes. The conductivity was evaluated too

Effective charge versus bare charge for colloids in the infinite dilution limit

We propose an analytical approximation for the dependence of the effective charge on the bare charge for spherical and cylindrical macro-ions as a function of the size of the colloid and salt content, for the situation of a unique colloid immersed in a sea of electrolyte (where the definition of an effective charge is non ambiguous). Our approach is based on the Poisson-Boltzmann (PB) mean-field theory. Mathematically speaking, our estimate is asymptotically exact in the limit $\kappa a\gg 1$, where $a$ is the radius of the colloid and $\kappa$ the inverse screening length. In practice, a careful comparison with effective charges parameters obtained by numerically solving the full non-linear PB theory proves that it is good down to $\kappa a\sim 1$. This is precisely the limit appropriate to treat colloidal suspensions. A particular emphasis is put on the range of parameters suitable to describe both single and double strand DNA molecules under physiological conditions.Comment: Proceedings of the International Conference on Strongly Coupled Coulomb Systems, Santa Fe (2002

Polyelectrolytes in the presence of multivalent ions: gelation versus segregation

We analyze solutions of strongly charged chains bridged by linkers such as multivalent ions. The gelation induced by the strong short range electrostatic attractions is dramatically suppressed by the long range electrostatic correlations due to the charge along the uncrosslinked monomers and ions. A modified Debye-Huckel approach of crosslinked clusters of charged chains is used to determined the mean field gelation transition self-consistently. Highly dilute polyelectrolyte solutions tend to segregate macroscopically. Semidilute solutions can form gels if the Bjerrum length $l_B$ and the distance between neighboring charged monomers along the chain $b$ are both greater than the ion size $a$

Adsorption of mono- and multivalent cat- and anions on DNA molecules

Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point charge pattern following the double-helical phosphate strands. The geometrical shape of the DNA molecules is modelled on different levels ranging from a simple cylindrical shape to structured models which include the major and minor grooves between the phosphate strands. The densities of the ions adsorbed on the phosphate strands, in the major and in the minor grooves are calculated. First, we find that the adsorption pattern on the DNA surface depends strongly on its geometrical shape: counterions adsorb preferentially along the phosphate strands for a cylindrical model shape, but in the minor groove for a geometrically structured model. Second, we find that an addition of monovalent salt ions results in an increase of the charge density in the minor groove while the total charge density of ions adsorbed in the major groove stays unchanged. The adsorbed ion densities are highly structured along the minor groove while they are almost smeared along the major groove. Furthermore, for a fixed amount of added salt, the major groove cationic charge is independent on the counterion valency. For increasing salt concentration the major groove is neutralized while the total charge adsorbed in the minor groove is constant. DNA overcharging is detected for multivalent salt. Simulations for a larger ion radii, which mimic the effect of the ion hydration, indicate an increased adsorbtion of cations in the major groove.Comment: 34 pages with 14 figure

Structural study of an amorphous NiZr2 alloy by anomalous wide angle X-ray scattering and Reverse Monte Carlo simulations

The local atomic structure of an amorphous NiZr2 alloy was investigated using the anomalous wide-angle x-ray scattering (AWAXS), differential anomalous scattering (DAS) and reverse Monte Carlo (RMC) simulations techniques. The AWAXS measurements were performed at eight different incident photon energies, including some close to the Ni and Zr K edges. From the measurements eight total structure factor S(K,E) were derived. Using the AWAXS data four differential structure factors DSFi(K,Em,En) were derived, two about the Ni and Zr edges. The partial structure factors SNi-Ni(K), SNi-Zr(K) and SZr-Zr(K) were estimated by using two different methods. First, the S(K,E) and DSFi(K,Em,En) factors were combined and used in a matrix inversion process. Second, three S(K,E) factors were used as input data in the RMC technique. The coordination numbers and interatomic distances for the first neighbors extracted from the partial structure factors obtained by these two methods show a good agreement. By using the three-dimensional structure derived from the RMC simulations, the bond-angle distributions were calculated and they suggest the presence of distorted triangular-faced polyhedral units in the amorphous NiZr2 structure. We have used the Warren chemical short-range order parameter to evaluate the chemical short-range order for the amorphous NiZr2 alloy and for the NiZr2 compound. The calculated values show that the chemical short-range order found in these two materials is similar to that found in a solid solution.Comment: Submitted to Phys. Rev. B, 8 figure

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

Alkali (Li+, Na+, K+, Rb+, and Cs+) and halide (F−, Cl−, Br−, and I−) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models. Although it has been clearly demonstrated that truly accurate treatments of ions will require inclusion of nonadditivity and polarizability (particularly with the anions) and ultimately even a quantum mechanical treatment, our goal was to simply push the limits of the additive treatments to see if a balanced model could be created. The applied methodology is general and can be extended to other ions and to polarizable force-field models. Our starting point centered on observations from long simulations of biomolecules in salt solution with the AMBER force fields where salt crystals formed well below their solubility limit. The likely cause of the artifact in the AMBER parameters relates to the naive mixing of the Smith and Dang chloride parameters with AMBER-adapted Åqvist cation parameters. To provide a more appropriate balance, we reoptimized the parameters of the Lennard-Jones potential for the ions and specific choices of water models. To validate and optimize the parameters, we calculated hydration free energies of the solvated ions and also lattice energies (LE) and lattice constants (LC) of alkali halide salt crystals. This is the first effort that systematically scans across the Lennard-Jones space (well depth and radius) while balancing ion properties like LE and LC across all pair combinations of the alkali ions and halide ions. The optimization across the entire monovalent series avoids systematic deviations. The ion parameters developed, optimized, and characterized were targeted for use with some of the most commonly used rigid and nonpolarizable water models, specifically TIP3P, TIP4PEW, and SPC/E. In addition to well reproducing the solution and crystal properties, the new ion parameters well reproduce binding energies of the ions to water and the radii of the first hydration shells