|Phone:||+49 711 685-63935|
|Fax:||+49 711 685-63658|
|Email:||mfyta _at_ icp.uni-stuttgart.de|
|Address:||Junior Prof Maria Fyta|
Institute for Computational Physics
There is an opening for a PhD student working on the multiscale modeling of biologically modified materials, as well as a position for a student (studentische Hilfskraft) (more details).
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).
Integration of biomolecules and materials
Computational modeling can provide an additional view into biophysical systems and processes studied also through experiments. These often provide insight into time and length scales not easily accessible by experimental setups. Such an insight would be essential when integrating biomolecules and materials to make biofunctional materials. These have a high potential to lead to a variety of innovative biotechnological applications, ranging from bio-sensors to templates for programmable self-assembly. Biofunctionalized electrodes are expected to be essential also in the field of ultra-fast sequencing DNA through buffers which are able to electrophoretically translocate polyelectrolytes. Apart from their bionanotechnological interest, an in depth understanding of the complex behavior of biopolymers on materials and its connection to the biomaterial's properties is lacking. In order to unravel the mechanisms that underlie these complex materials, resort to a theoretical investigation based on sequential and concurrent atomistic and coarse-grained simulations scannning a wide range of spatial and temporal scales will be attempted. The focus of the proposed research are biomolecules (from a single nucleotide to a short sequence of do uble-stranded and single-stranded DNA, and short peptides) grafted on surfaces, metallic or semiconducting. A comparative study of these materials will unravel those, which have the higher potential to be used in future relevant applications. For these, the effect of factors, like mechanical or thermal deformations occurring on the biomolecule or the surface, as well as the effect of the surrounding fluid solvent and ionic concentration will be studied. The aim is not only to computationally shed light into the understanding of the structure and properties of biofunctionalized surfaces, but potentially also guide the experiments towards their search for potential biotechnological applicati
DNA translocation through narrow pores
A multiscale approach is applied to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the solvent dynamics, explicitly taking into account the interactions of the molecule with the surrounding fluid. This coupling proceeds seamlessy in time and only requires standard interpolation/extrapolation for information transfer in physical space. Both dynamical and statistical aspects of the translocation process are investigated, by simulating polymers of various initial configurations and lengths. The translocation time obeys a scaling law with respect to the length of the chain with an exponent that is in very good agreement with experimental observations. A mean-field hydrodynamics analysis can be applied throughout the translocation, although deviations from the mean field picture are also observed. We explore the connection between the generic polymers modeled in the simulation and DNA, for which interesting recent experimental results are available.
Optoelectronic and mechanical properties of carbon nanostructures
Ionic solutions in water
[More details will come soon...]
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).
M. Fyta, I. Kalcher, L. Vrbka, J. Dzubiella, and R.R. Netz, Force field optimization of electrolyte solutions based on their thermodynamic properties , J. Chem. Phys, 132, 024911 (2010).
S. Melchionna, M. Bernaschi, M. Fyta, E. Kaxiras, and S. Succi, Quantized biopolymer translocation through nanopores: departure from simple scaling, Phys. Rev. E, 79 030901(R) (2009).
M. Fyta, Simone Melchionna, Efthimios Kaxiras, and Sauro Succi, Multiscale Simulation of Nanobiological flows, Computing in Science and Engineering, 10 10 (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, S. Melchionna, E. Kaxiras, and S. Succi, Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore, Multiscale Modeling and Simulation, 5, 1156 (2006).
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),
M. G. Fyta, I. N. Remediakis and P. C. Kelires, Energetics and stability of nanostructured amorphous carbon, Phys. Rev. B 67, 035423 (2003).