Maria Fyta

Ab initio supercell calculations on nitrogen-vacancy center in diamond: Electronic structure and hyperfine tensors

The nitrogen-vacancy center in diamond is a promising candidate for realizing the spin qubits concept in quantum information. Even though this defect has been known for a long time, its electronic structure and other properties have not yet been explored in detail. We study the properties of the nitrogen-vacancy center in diamond through density functional theory within the local spin density approximation by using supercell calculations. While this theory is strictly applicable for ground state properties, we are able to give an estimate for the energy sequence of the excited states of this defect. We also calculate the hyperfine tensors in the ground state. The results clearly show that (i) the spin density and the appropriate hyperfine constants are spread along a plane and unevenly distributed around the core of the defect and (ii) the measurable hyperfine constants can be found within about

Multiscale Coupling of Molecular Dynamics and Hydrodynamics: Application to DNA Translocation through a Nanopore

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MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations

from the vacancy site. These results have important implications on the decoherence of the electron spin which is crucial in realizing the spin qubits in diamond.

Hydrodynamic correlations in the translocation of a biopolymer through a nanopore : Theory and multiscale simulations

We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin molecular dynamics (MD) techniques with a mesoscopic lattice Boltzmann (LB) method for the solvent dynamics. A unique feature of the present approach is that hydrodynamic interactions between the solute macromolecule and the aqueous solvent are handled explicitly, and yet in a computationally tractable way due to the dual particle‐field nature of the LB solver. The suitability of the present LB‐MD multiscale approach is demonstrated for the problem of polymer fast translocation through a nanopore. We also provide an interpretation of our results in the context of DNA translocation through a nanopore, a problem that has attracted much theoretical and experimental attention recently.

Ionic force field optimization based on single-ion and ion-pair solvation properties: Going beyond standard mixing rules

We present a parallel version of MUPHY, a multi-physics/scale code based upon the combination of microscopic Molecular Dynamics (MD) with a hydro-kinetic Lattice Boltzmann (LB) method. The features of the parallel version of MUPHY are hereby demonstrated for the case of translocation of biopolymers through nanometer-sized, multi-pore configurations, taking into explicit account the hydrodynamic interactions of the translocating molecules with the surrounding fluid. The parallel implementation exhibits excellent scalability on the IBM BlueGene platform and includes techniques which may improve the flexibility and efficiency of other complex multi-physics parallel applications, such as hemodynamics, targeted-drug delivery and others.

Force fields for divalent cations based on single-ion and ion-pair properties

We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the surrounding solvent. The simulations confirm that the coupling of the correlated molecular motion to hydrodynamics results in significant acceleration of the translocation process. Based on these results, we construct a phenomenological model which incorporates the statistical and dynamical features of the translocation process and predicts a power-law dependence of the translocation time on the polymer length with an exponent alpha approximately 1.2. The actual value of the exponent from the simulations is alpha=1.28+/-0.01, which is in excellent agreement with experimental measurements of DNA translocation through a nanopore, and is not sensitive to the choice of parameters in the simulation. The mechanism behind the emergence of such a robust exponent is related to the interplay between the longitudinal and transversal dynamics of both translocated and untranslocated segments. The connection to the macroscopic picture involves separating the contributions from the blob shrinking and shifting processes, which are both essential to the translocation dynamics.

Ionic force field optimization based on single-ion and ion-pair solvation properties

Using molecular dynamics (MD) simulations in conjunction with the SPC/E water model, we optimize ionic force-field parameters for seven different halide and alkali ions, considering a total of eight ion-pairs. Our strategy is based on simultaneous optimizing single-ion and ion-pair properties, i.e., we first fix ion-water parameters based on single-ion solvation free energies, and in a second step determine the cation-anion interaction parameters (traditionally given by mixing or combination rules) based on the Kirkwood-Buff theory without modification of the ion-water interaction parameters. In doing so, we have introduced scaling factors for the cation-anion Lennard-Jones (LJ) interaction that quantify deviations from the standard mixing rules. For the rather size-symmetric salt solutions involving bromide and chloride ions, the standard mixing rules work fine. On the other hand, for the iodide and fluoride solutions, corresponding to the largest and smallest anion considered in this work, a rescaling of the mixing rules was necessary. For iodide, the experimental activities suggest more tightly bound ion pairing than given by the standard mixing rules, which is achieved in simulations by reducing the scaling factor of the cation-anion LJ energy. For fluoride, the situation is different and the simulations show too large attraction between fluoride and cations when compared with experimental data. For NaF, the situation can be rectified by increasing the cation-anion LJ energy. For KF, it proves necessary to increase the effective cation-anion Lennard-Jones diameter. The optimization strategy outlined in this work can be easily adapted to different kinds of ions.

Insights into the fracture mechanisms and strength of amorphous and nanocomposite carbon.

We develop force field parameters for the divalent cations Mg(2+), Ca(2+), Sr(2+), and Ba(2+) for molecular dynamics simulations with the simple point charge-extended (SPC/E) water model. We follow an approach introduced recently for the optimization of monovalent ions, based on the simultaneous optimization of single-ion and ion-pair properties. We consider the solvation free energy of the divalent cations as the relevant single-ion property. As a probe for ion-pair properties we compute the activity derivatives of the salt solutions. The optimization of the ionic force fields is done in two consecutive steps. First, the cation solvation free energy is determined as a function of the Lennard-Jones (LJ) parameters. The peak in the ion-water radial distribution function (RDF) is used as a check of the structural properties of the ions. Second, the activity derivatives of the electrolytes MgY(2), CaY(2), BaY(2), SrY(2) are determined through Kirkwood-Buff solution theory, where Y = Cl(-), Br(-), I(-). The activity derivatives are determined for the restricted set of LJ parameters which reproduce the exact solvation free energy of the divalent cations. The optimal ion parameters are those that match the experimental activity data and therefore simultaneously reproduce single-ion and ion-pair thermodynamic properties. For Ca(2+), Ba(2+), and Sr(2+) such LJ parameters exist. On the other hand, for Mg(2+) the experimental activity derivatives can only be reproduced if we generalize the combination rule for the anion-cation LJ interaction and rescale the effective cation-anion LJ radius, which is a modification that leaves the cation solvation free energy invariant. The divalent cation force fields are transferable within acceptable accuracy, meaning the same cation force field is valid for all halide ions Cl(-), Br(-), I(-) tested in this study.

Ab initio determination of coarse-grained interactions in double-stranded DNA

Molecular dynamics simulations of ionic solutions depend sensitively on the force fields employed for the ions. To resolve the fine differences between ions of the same valence and roughly similar size and in particular to correctly describe ion-specific effects, it is clear that accurate force fields are necessary. In the past, optimization strategies for ionic force fields either considered single-ion properties (such as the solvation free energy at infinite dilution or the ion-water structure) or ion-pair properties (in the form of ion-ion distribution functions). In this paper we investigate strategies to optimize ionic force fields based on single-ion and ion-pair properties simultaneously. To that end, we simulate five different salt solutions, namely, CsCl, KCl, NaI, KF, and CsI, at finite ion concentration. The force fields of these ions are systematically varied under the constraint that the single-ion solvation free energy matches the experimental value, which reduces the two-dimensional {sigma,epsilon} parameter space of the Lennard-Jones interaction to a one dimensional line for each ion. From the finite-concentration simulations, the pair potential is extracted and the osmotic coefficient is calculated, which is compared to experimental data. We find a strong dependence of the osmotic coefficient on the force field, which is remarkable as the single-ion solvation free energy and the ion-water structure remain invariant under the parameter variation. Optimization of the force field is achieved for the cations Cs(+) and K(+), while for the anions I(-) and F(-) the experimental osmotic coefficient cannot be reached. This suggests that in the long run, additional parameters might have to be introduced into the modeling, for example by modified mixing rules.

Multiscale Simulation of Nanobiological Flows

Tight-binding molecular dynamics simulations shed light into the fracture mechanisms and the ideal strength of tetrahedral amorphous carbon and of nanocomposite carbon containing diamond crystallites, two of the hardest materials. It is found that fracture in the nanocomposites, under tensile or shear load, occurs intergrain and so their ideal strength is similar to the pure amorphous phase. The onset of fracture takes place at weakly bonded sites in the amorphous matrix. On the other hand, the nanodiamond inclusions significantly enhance the elastic moduli, which approach those of diamond.