|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
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.
Coarse grained interactions between DNA nucleotides
An optimized intermolecular potential is derived from accurate density-functional-theory based simulations on DNA bases and base-pairs. Hydrogen bonding energy is calculated as a function of the horizontal distance between bases, and the stacking energies between two base-pairs are calculated as a function of their twisting angle and vertical separation. The stability of all 10 Watson-Crick nearest-neighbors and the contribution to the energy from the sugar backbone are also taken into account. All results have been fitted to analytical formulae, whose parameters show a large sequence-dependent variability. Construction of such an intermolecular potential for dry double-stranded DNA, based on the combination of all these fitted functionals, aims at unraveling the conformational variability of DNA. This variability remains a problem of significant importance, especially in view of recent experimental studies of DNA translocation through solid nanopores and DNA interaction with other nanostructures such as carbon nanotubes. For efficient simulation of these systems, a coarse-grained model of DNA, like the one constructed here is desirable.
Ionic solutions in water
Using classical Molacular Dynamics simulations we have modeled a variety of ionic solutions in water. These simulations 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). We investigate strategies to optimize ionic force fields based on single-ion and ion-pair thermodynamic properties simultaneously. We have concluded that a modification of the ion-pair combination rules is often necessary in order to obtain well optimized ionic force fields. We further aim to optimize the ionic force fields and test their applicability in more complex systems.
[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).