Difference between revisions of "Maria Fyta"

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(DNA translocation through narrow pores)
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There are currently no open positions.
 
There are currently no open positions.
 
 
<!--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) ([http://www.icp.uni-stuttgart.de/~icp/Open_Positions more details]).-->
 
<!--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) ([http://www.icp.uni-stuttgart.de/~icp/Open_Positions more details]).-->
 
 
== Research interests ==
 
== Research interests ==
  
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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.
 
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 ===
+
=== Force field development ===
  
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.
+
==== A potential for DNA nucleotides ====
  
=== Ionic solutions in water ===
+
Using an <i>ab initio</i> 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.
 +
<!--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.-->
  
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.
+
==== 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.
  
<!--[More details will come soon...]
+
<!--== Education ==
 
 
== Education ==
 
  
 
Jun. 2005: PhD (Department of Physics, University of Crete, Greece), Advisor: Prof. P.C. Kelires (University of Crete) [Title:Theoretical investigation of the energetics and mechanical properties of nanostructured amorphous carbon]  
 
Jun. 2005: PhD (Department of Physics, University of Crete, Greece), Advisor: Prof. P.C. Kelires (University of Crete) [Title:Theoretical investigation of the energetics and mechanical properties of nanostructured amorphous carbon]  
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== Publications ==
 
== Publications ==
  
[Selected publications; for a complete list, please vitit http://www.icp.uni-stuttgart.de/~mfyta/publ.html]
+
[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).
 
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).
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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, 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,  
 
R. L. Barnett, P. Maragakis, A. Turner, M. Fyta, and E. Kaxiras,  
 
Multiscale model of electronic behavior and localization in stretched dry DNA,  
 
Multiscale model of electronic behavior and localization in stretched dry DNA,  
 
J. Mater. Sci., 42 8894 (2007).
 
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,  
 
M. G. Fyta, I. N. Remediakis, P. C. Kelires, and D. A. Papaconstantopoulos,  
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Appl. Phys. Lett. 86, 191916 (2005),
 
Appl. Phys. Lett. 86, 191916 (2005),
  
<!-- 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).
+
<!-- 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. 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).
 
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).

Revision as of 12:02, 15 November 2012

Mfyta.png
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.

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),