# Difference between revisions of "Maria Fyta"

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=== DNA translocation through narrow pores === | === 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. | + | 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. |

+ | <!--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 === | === Optoelectronic and mechanical properties of carbon nanostructures === |

## Revision as of 11:48, 15 November 2012

**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

## Open positions

There are currently no open positions.

## 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

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.

## Publications

[Selected publications; for a complete list, 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).

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),