|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
- 1 Open positions
- 2 Research interests
- 3 Publications
There are currently no open positions.
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
We have used Monte Carlo and empirical tight-binding Molecular Dynamics simulations to model the stability, elastic, mechanical, and optoelectronic properties of nanostructured carbon. We are interested in also implementing more accurate first principles calculations to study a variety of carbon structures ranging from carbon cages to diamondoids and nitrogen-vacancy defects in diamond we have modeled in the past. Our aim is also to investigate how the properties of these materials change when these are doped or functionalized.
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.
[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),