# Maria Fyta

**JP Dr. Maria Fyta**

Group leader

Office: | 1.032 |
---|---|

Phone: | +49 711 685-63935 |

Fax: | +49 711 685-63658 |

Email: | mfyta _at_ icp.uni-stuttgart.de |

Address: | JP Dr. Maria Fyta Institute for Computational Physics Universität Stuttgart Allmandring 3 70569 Stuttgart Germany |

**Personal webpage: http://www.icp.uni-stuttgart.de/~mfyta**

## Contents

## Open positions

There are currently two open HiWi positions related to the Simulation Methods in Physics course.

Typesetting a course script: The first opening concerns a HiWi position for typesetting the course script in LaTeX and in English. There is already a hand-written version of the script.

Preparing problem sets: The task of the second HiWi job is the preparation and testing of new exercises for the course. For this computational skills are needed.

## Research interests

Our work is based on a variety of computational tools, ranging from classical (Monte-Carlo schemes within empirical potential approaches, Molecular Dynamics), semi-empirical (parametrized tight-binding schemes), quantum mechanical (implementations of the density functional theory), and multiscale methodologies (coupled Langevin molecular-dynamics and lattice-Boltzmann method for modeling molecular motion in a fluid solvent). A brief description of our research projects are given below. More details can be found in http://www.icp.uni-stuttgart.de/~mfyta/projects.html

### Integration of biomolecules and materials

Using a variety of computational schemes ranging from density-functional-theory-based calculations to coarse-grained approaches we model biomaterials. These biomaterials consist of a material part, a surface or a nanocrystal on which a biomolecule has been attached. We investigate the stability and optoelectronic properties of these biologically modified materials in view of the variety of novel applications these can form, in bio-sensing, DNA-labeling, etc.

### DNA translocation through narrow pores

We investigate the process of a polymer translocating through a nanopore using a multiscale computational scheme. This approach involves a mesoscopic fluid solver seamlessly coupled to an atomistic scheme for the biomolecule motion. We begin our study with a rather anonymous polymer translocating in water, but are now able to monitor the translocation process for a realistic DNA molecule which is threaded through the pore in the presence of an ionic solution. We are interested in the statistics and dynamics of the process, as well as the DNA conformations and the ionic distribution within and around the pore. The translocation of DNA through a nanopore promises a variety of novel applications, with ultra-fast DNA-sequencing being among them.

### Optoelectronic and mechanical properties of carbon nanostructures

A high interest on carbon-based nanomaterials has led us to a variety of relevant studies, some of which are outlined here:

#### Diamondoids

We turn our interest to nanocage diamond structures, named diamondoids and investigate their properties by means of *ab initio* and Molecular Dynamics approaches. We mainly focus on the free standing crystallites, but also assemble these on surfaces and try to tune the properties through effects such as doping, electric field, etc.

#### Nitrogen-vacancy defect centers in diamond

Density-functional theory based calculations have allowed us to take a closer look into the negatively charged NV center in diamond. We give an estimate of the energy sequence of the excited state and calculate the hyperfine tensors in the ground state. The results have important implications on the decoherence of the electron spin which is crucial in realizing the spin qubits in diamond.

#### Nanostructured amorphous carbon

Using Monte Carlo and tight-binding Molecular Dynamics simulations we have investigated nanostructured amorphous carbon materials. These are composites, which consist of a crystalline carbon inclusion embedded in an amorphous carbon matrix. The inclusion may range from pure diamond nanocrystals and sp^{3} crystalline structures to sp^{2} conformations and carbon nanotubes. We have looked at the stability, elastomechanical and fracture properties of such materials. These properties can be tuned by an optimal choice of the type and radius of the inclusion, as well as the density of the matrix.

### Force field development

#### A potential for DNA nucleotides

Using an *ab initio* scheme we have generated a coarse grain potential for DNA bases and base-pairs. The interactions take into account base and sequence specificity, and are decomposed into physically distinct contributions that include hydrogen bonding, stacking interactions, backbone, and backbone-base interactions. Within this model, each nucleotide is reduced into two sites, the DNA base site and the sugar-phosphate site. This model is not derived from experimental data, yet it successfully reproduces properties of the stable B-DNA. It may be used to realistically
probe dynamics of DNA strands in various environments at the μs time scale and the μm length scale.

#### Classical force fields for ions in water

We use classical Molacular Dynamics simulations to model ionic solutions in water. Starting from the free energy of solvation of the single ions, perform a parameter scan and try to tune the thermodynamic properties of the respective salt solutions. A good optimized force field is the one that reproduces the relevant experimental data. For some of the ions finding a "good" force fields was not possible. We could overcome this, by also scaling the ion-pair mixing rules that are taken into account in this methodology. We have applied this approach to monovalent, as well as divalent salt solutions.

## Publications

[Selected publications; for a complete list and reprints, please vitit http://www.icp.uni-stuttgart.de/~mfyta/publ.html]

C.W. Hsu, M. Fyta, G. Lakatos, S. Melchionna, and E. Kaxiras, *Ab initio* determination of coarse-grained interactions in double-stranded DNA, J. Chem. Phys. 137(10), 105102 (2012).

M. Fyta, Structural and technical details of the Kirkwood-Buff integrals from the optimization of ionic force fields: focus on fluorides, Europ. J. Phys. E. 35, 21 (2012).

M. Fyta and R.R. Netz, Ionic force field optimization based on single-ion and ion-pair solvation properties: going beyond standard mixing rules, J. Chem. Phys. 136(12), 124103 (2012).

M.Fyta, S. Melchionna, and S. Succi,Translocation of biomolecules through solid-state nanopores: theory meets experiments, J. Polym. Sci. B, 49, 985 (2011).

A. Gali, M. Fyta, and E. Kaxiras, Ab initio supercell calculations on nitrogen-vacancy center in diamond: its electronic structure and hyperfine tensors, Phys. Rev. B, 77 155206 (2008).

R. L. Barnett, P. Maragakis, A. Turner, M. Fyta, and E. Kaxiras, Multiscale model of electronic behavior and localization in stretched dry DNA, J. Mater. Sci., 42 8894 (2007).

M. G. Fyta, I. N. Remediakis, P. C. Kelires, and D. A. Papaconstantopoulos, Insights into the strength and fracture mechanisms of amorphous and nanocomposite carbon, Phys. Rev. Lett. 96, 185503 (2006).

M. G. Fyta and P. C. Kelires, Simulations of composite carbon films with nanotube inclusions, Appl. Phys. Lett. 86, 191916 (2005),