Difference between revisions of "Maria Fyta"

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{{Person
 
{{Person
 
|name=Fyta, Maria
 
|name=Fyta, Maria
−
|title=Dr.
+
|title=apl.Prof. Dr.
−
|status=Junior Professor
+
|status=Group leader
−
|category=holm
 
−
|phone=63935
 
−
|room=203
 
 
|email=mfyta
 
|email=mfyta
−
|image=mfyta.png
+
|researcherid=F-8562-2013
 +
|image=Maria_fyta.jpg
 +
|category=fyta
 +
|topical=nanopore
 +
|topical2=sampling
 +
|ordering=1
 
}}
 
}}
 +
 +
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{{Infobox | The group has moved to the RWTH-Aachen University. Click here [https://rwth-aachen.de/go/id/suhwq] to visit the new website. }}
 +
 +
{{Infobox| A PhD or PostDoc position is available in the group. For additional inquiries and applications (a CV, a research statement, and a list of 3 references) please send an e-mail to Maria Fyta (mfyta_at_icp.uni-stuttgart.de).}}
 +
 +
<b>Personal webpage: http://www2.icp.uni-stuttgart.de/~mfyta</b>
 +
 +
== Profile ==
 +
 +
My profile at [https://scholar.google.de/citations?user=Zf0fPicAAAAJ&hl=en Scholar Google].
 +
 +
My ResearcherID: F-8562-2013.
 +
{{#widget:ResearcherId|id=F-8562-2013 }}
 +
<!--span id='badgeCont822833' style='width:26px'><script src='http://labs.researcherid.com/mashlets?el=badgeCont822833&mashlet=badge&showTitle=false&className=a&rid=F-8562-2013&size=small'></script></span-->
 +
 +
My ORCID:  0000-0002-5425-7907.
 +
 +
[https://www.researchgate.net/profile/Maria_Fyta?cp=shp Follow me on ResearchGate]
 +
<!--[https://www.researchgate.net/profile/Maria_Fyta?cp=shp [[Image:https://www.researchgate.net/images/public/profile_share_badge.png|Follow me on ResearchGate]]] -->
 +
<!--a title="Follow me on ResearchGate" href="https://www.researchgate.net/profile/Maria_Fyta?cp=shp"><img src="https://www.researchgate.net/images/public/profile_share_badge.png" alt="Follow me on ResearchGate" /></a-->
 +
 +
A short CV can be found here: http://www.icp.uni-stuttgart.de/~mfyta/cv_mfyta_short.html
 +
<!--A detailed CV can be found [[Media:cv.pdf|here]].-->
 +
 +
=== Research Keywords ===
 +
 +
* Nanopores
 +
* 2D materials
 +
* Carbon materials
 +
* Defects
 +
* DNA
 +
* Surfaces
 +
* Mechanical properties
 +
* Electronic properties
 +
* Quantum transport
  
 
== Open positions ==
 
== 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 are currently two open HiWi positions related to the Simulation Methods in Physics course.
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Typesetting a course script: The first opening concerns a HiWi position for typesetting the course script in LaTeX and in English. There is already a hand-written version of the script.
 +
 
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Preparing problem sets: The task of the second HiWi job is the preparation and testing of new exercises for the course. For this computational skills are needed.
 +
<!--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]).-->
 +
 
 +
<!-- Eine HiWi Stelle zur Unterstützung der Modellierung von biologisch modifizierten Materialien ist frei. Interessenten bitte eine E-mail an [[Maria Fyta]] (mfyta_at_icp.uni-stuttgart.de) schicken.
 +
 
 +
There is currently an opening for a HiWi (student assistant) in the field of computer simulations of modified surfaces (molecules adsorbed on surfaces).
 +
-->
 +
 
 +
<!--There are currently no open positions. -->
 +
In case you are interested in bachelor or master projects, please contact [[Maria Fyta]] (mfyta_at_icp.uni-stuttgart.de).
  
 
== Research interests ==
 
== Research interests ==
Line 19: Line 70:
 
within empirical potential approaches, Molecular Dynamics), semi-empirical
 
within empirical potential approaches, Molecular Dynamics), semi-empirical
 
(parametrized tight-binding schemes), quantum mechanical
 
(parametrized tight-binding schemes), quantum mechanical
−
(implementations of the density functional theory),
+
(implementations of the density functional theory also in conjunction with non-equilibrium Greens functions for quantum transport),
 
and multiscale methodologies (coupled Langevin molecular-dynamics
 
and multiscale methodologies (coupled Langevin molecular-dynamics
 
and lattice-Boltzmann method for modeling molecular
 
and lattice-Boltzmann method for modeling molecular
−
motion in a fluid solvent).
+
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 ===
+
=== Biosensing ===
 +
 
 +
With the aid of quantum transport simulations we are able to reveal the electron transmission and conductance across functionalized metal electrodes. We are investigating the efficiency of such a device to detect and identify biological molecules. The specific interaction of these molecules with the functionalzation unit of the electrodes plays an important role for the sensing mechanism.
 +
 
 +
=== Two dimensional 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
+
2D materials, the transition metal dicholgenides (TMDs), are being investigated. These are single monolayers which can be made of a variety of chemical elements and can form metallic as well as semiconducting phases. Our studies aim to explore the polymorphicity of these materials in view of a number of potential applications in nano electronics. We directly connect the structural characteristics of materials based on the TMDs to their electronic and transport properties.
−
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 ===
 
=== 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.-->
 +
 
 +
=== Adsorption of molecules on surfaces ===
 +
 
 +
The interaction of molecules with metallic and diamond surfaces is investigated. The bonding characteristics are revealed as well as the morphology of the modified surfaces. STM images and the charge redistribution due to the adsorption are studied and can give a clear insight into the underlying physics of these materials.
  
 
=== Optoelectronic and mechanical properties of carbon nanostructures ===
 
=== 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.
+
A high interest on carbon-based nanomaterials has led us to a variety of relevant studies, some of which are outlined here:
 +
 
 +
==== Diamondoids ====
 +
 
 +
We turn our interest to nanocage diamond structures, named diamondoids and investigate their properties by means of ''ab initio'' and Molecular Dynamics approaches. We focus on the free standing crystallites, try to tune the properties through functionalization and doping. Electronic and transport properties are of a high interest. We have also shown that stable diamondoids can also be formed using boron and nitrogen instead of carbon.
 +
 
 +
==== Nitrogen-vacancy defect centers in diamond ====
  
−
=== Coarse grained interactions between DNA nucleotides ===
+
Density-functional theory based calculations have allowed us to take a closer look into the negatively charged NV center in diamond. We give an estimate of the energy sequence of the excited state and calculate the hyperfine tensors in the ground state. The results have important implications on the decoherence of the electron spin which is crucial in realizing the spin qubits in diamond.
  
−
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.
+
==== Nanostructured amorphous carbon ====
  
−
=== Ionic solutions in water ===
+
Using Monte Carlo and tight-binding Molecular Dynamics simulations we have investigated nanostructured amorphous carbon materials. These are composites, which consist of a crystalline carbon inclusion embedded in an amorphous carbon matrix. The inclusion may range from pure diamond nanocrystals and sp<sup>3</sup> crystalline structures to sp<sup>2</sup> conformations and carbon nanotubes. We have looked at the stability, elastomechanical and fracture properties of such materials. These properties can be tuned by an optimal choice of the type and radius of the inclusion, as well as the density of the matrix.
  
−
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.
+
=== Integration of biomolecules and materials ===
  
 +
Using a variety of computational schemes ranging from density-functional-theory-based calculations to coarse-grained approaches we model biologically modified materials. 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.
  
−
[More details will come soon...]
+
=== Homology Recognition ===
  
−
== Education ==
+
The differences in the energetics between matched (Watson-Crick) and mismatched DNA base-pairs are indicative of the mechanism according to which the RecA protein reads a DNA molecule. Our work is based on quantum mechanical calculations.
 +
 
 +
=== Force field development ===
 +
 
 +
==== A potential for DNA nucleotides ====
 +
 
 +
Using an <i>ab initio</i> scheme we have generated a coarse grained 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. We are currently extending the coarse grained model for double-stranded RNA in both its A- and B-helix forms.
 +
<!--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.-->
 +
 
 +
==== 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.
 +
 
 +
<!--== 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]  
Line 80: Line 160:
 
1998 : 2nd Price at the Summer school on Advanced Physics, UoC - Foundation for Research and Technology Hellas (FORTH)  
 
1998 : 2nd Price at the Summer school on Advanced Physics, UoC - Foundation for Research and Technology Hellas (FORTH)  
  
−
1996, 1997 : Consecutive awards from the National Scholarships Foundation, Greece for undergraduate study  
+
1996, 1997 : Consecutive awards from the National Scholarships Foundation, Greece for undergraduate study -->
  
 
== Publications ==
 
== Publications ==
  
−
[Selected publications]
+
<!-- Full list
 +
<bibentry>
 +
smiatek17a,
 +
</bibentry>
 +
-->
  
−
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).
+
[Selected publications; for a complete list and reprints, please vitit http://www.icp.uni-stuttgart.de/~mfyta/publ.html]
  
−
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).
+
S. Cruz Leon, M. Prentiss, and M. Fyta,
 +
Binding energies of nucleobase complexes: Relevance to homology recognition of DNA, Phys. Rev. E 93, 062410 (2016).
 +
 
 +
G. Sivaraman, R.G. Amorim, R.H. Scheicher, and M. Fyta,
 +
Diamondoid-functionalized gold nanogaps as sensors for natural, mutated, and epigenetically modified DNA nucleotides</font>, Nanoscale, DOI: 10.1039/C6NR00500D (2016).
 +
 
 +
B. Adhikari, S. Meng, and M. Fyta,
 +
Carbene-mediated self-assembly of diamondoids on metal surfaces, Nanoscale , (2016) DOI: 10.1039/C5NR08709K.
 +
 
 +
M. Fyta,
 +
Threading DNA through nanopores for biosensing applications, J. Phys.: Cond. Matter 27, 273101 (2015).
 +
 
 +
B. Adhikari and M. Fyta,
 +
Towards double-functionalized small diamondoids: selective electronic band-gap tuning, Nanotechnology 26, 035701 (2015).
 +
 
 +
M. Fyta,
 +
Stable boron nitride diamondoids as nanoscale materials", Nanotechnology 25, 365601 (2014).
  
−
M.Fyta, S. Melchionna, and S. Succi,Translocation of biomolecules through solid-state nanopores: theory meets experiments, J. Polym. Sci. B, 49, 985 (2011).
+
G. Sivaraman and M. Fyta, Derivatives of small diamondoids as biosensors for DNA nucleobases, Nanoscale 6, 4225 (2014).
  
−
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).
+
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).
  
−
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 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, Simone Melchionna, Efthimios Kaxiras, and Sauro Succi,
+
M.Fyta, S. Melchionna, and S. Succi,Translocation of biomolecules through solid-state nanopores: theory meets experiments, J. Polym. Sci. B, 49, 985 (2011).
−
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,  
+
A. Gali, M. Fyta, and E. Kaxiras,
−
Multiscale model of electronic behavior and localization in stretched dry DNA,  
+
Ab initio supercell calculations on nitrogen-vacancy center in diamond: its electronic structure and hyperfine tensors,
−
J. Mater. Sci., 42 8894 (2007).
+
Phys. Rev. B, 77 155206 (2008).
  
−
M.G. Fyta, S. Melchionna, E. Kaxiras, and S. Succi,  
+
M. Fyta, S. Melchionna, S. Succi, and E. Kaxiras,
−
Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore,
+
Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations, Phys. Rev. E 78, 036704 (2008).
−
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,  
Line 113: Line 211:
 
M. G. Fyta and P. C. Kelires,
 
M. G. Fyta and P. C. Kelires,
 
Simulations of composite carbon films with nanotube inclusions,  
 
Simulations of composite carbon films with nanotube inclusions,  
−
Appl. Phys. Lett. 86, 191916 (2005),
+
Appl. Phys. Lett. 86, 191916 (2005).
 +
 
  
−
M. G. Fyta, I. N. Remediakis and P. C. Kelires,
+
<!--
−
Energetics and stability of nanostructured amorphous carbon,
+
== Multimedia ==
−
Phys. Rev. B 67, 035423 (2003).
+
* '''Ab initio molecular dynamics simulations of ectoine in aqueous solution (together with Frank Uhlig)'''
 +
{{#widget:YouTube|id=14jzoeCES18|width=670|height=500}}
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-->

Latest revision as of 14:37, 30 January 2023

Maria fyta.jpg
apl.Prof. Dr. Maria Fyta
Group leader
Fax:+49 711 685-63658
Email:mfyta _at_ icp.uni-stuttgart.de
Address:apl.Prof. Dr. Maria Fyta
Institute for Computational Physics
Universität Stuttgart
Allmandring 3
70569 Stuttgart
Germany


Information icon-40x40.png The group has moved to the RWTH-Aachen University. Click here [1] to visit the new website.
Information icon-40x40.png A PhD or PostDoc position is available in the group. For additional inquiries and applications (a CV, a research statement, and a list of 3 references) please send an e-mail to Maria Fyta (mfyta_at_icp.uni-stuttgart.de).

Personal webpage: http://www2.icp.uni-stuttgart.de/~mfyta

Profile

My profile at Scholar Google.

My ResearcherID: F-8562-2013.

My ORCID: 0000-0002-5425-7907.

Follow me on ResearchGate

A short CV can be found here: http://www.icp.uni-stuttgart.de/~mfyta/cv_mfyta_short.html

Research Keywords

  • Nanopores
  • 2D materials
  • Carbon materials
  • Defects
  • DNA
  • Surfaces
  • Mechanical properties
  • Electronic properties
  • Quantum transport

Open positions

In case you are interested in bachelor or master projects, please contact Maria Fyta (mfyta_at_icp.uni-stuttgart.de).

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 also in conjunction with non-equilibrium Greens functions for quantum transport), 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

Biosensing

With the aid of quantum transport simulations we are able to reveal the electron transmission and conductance across functionalized metal electrodes. We are investigating the efficiency of such a device to detect and identify biological molecules. The specific interaction of these molecules with the functionalzation unit of the electrodes plays an important role for the sensing mechanism.

Two dimensional materials

2D materials, the transition metal dicholgenides (TMDs), are being investigated. These are single monolayers which can be made of a variety of chemical elements and can form metallic as well as semiconducting phases. Our studies aim to explore the polymorphicity of these materials in view of a number of potential applications in nano electronics. We directly connect the structural characteristics of materials based on the TMDs to their electronic and transport properties.

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.

Adsorption of molecules on surfaces

The interaction of molecules with metallic and diamond surfaces is investigated. The bonding characteristics are revealed as well as the morphology of the modified surfaces. STM images and the charge redistribution due to the adsorption are studied and can give a clear insight into the underlying physics of these materials.

Optoelectronic and mechanical properties of carbon nanostructures

A high interest on carbon-based nanomaterials has led us to a variety of relevant studies, some of which are outlined here:

Diamondoids

We turn our interest to nanocage diamond structures, named diamondoids and investigate their properties by means of ab initio and Molecular Dynamics approaches. We focus on the free standing crystallites, try to tune the properties through functionalization and doping. Electronic and transport properties are of a high interest. We have also shown that stable diamondoids can also be formed using boron and nitrogen instead of carbon.

Nitrogen-vacancy defect centers in diamond

Density-functional theory based calculations have allowed us to take a closer look into the negatively charged NV center in diamond. We give an estimate of the energy sequence of the excited state and calculate the hyperfine tensors in the ground state. The results have important implications on the decoherence of the electron spin which is crucial in realizing the spin qubits in diamond.

Nanostructured amorphous carbon

Using Monte Carlo and tight-binding Molecular Dynamics simulations we have investigated nanostructured amorphous carbon materials. These are composites, which consist of a crystalline carbon inclusion embedded in an amorphous carbon matrix. The inclusion may range from pure diamond nanocrystals and sp3 crystalline structures to sp2 conformations and carbon nanotubes. We have looked at the stability, elastomechanical and fracture properties of such materials. These properties can be tuned by an optimal choice of the type and radius of the inclusion, as well as the density of the matrix.

Integration of biomolecules and materials

Using a variety of computational schemes ranging from density-functional-theory-based calculations to coarse-grained approaches we model biologically modified materials. 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.

Homology Recognition

The differences in the energetics between matched (Watson-Crick) and mismatched DNA base-pairs are indicative of the mechanism according to which the RecA protein reads a DNA molecule. Our work is based on quantum mechanical calculations.

Force field development

A potential for DNA nucleotides

Using an ab initio scheme we have generated a coarse grained 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. We are currently extending the coarse grained model for double-stranded RNA in both its A- and B-helix forms.

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]

S. Cruz Leon, M. Prentiss, and M. Fyta, Binding energies of nucleobase complexes: Relevance to homology recognition of DNA, Phys. Rev. E 93, 062410 (2016).

G. Sivaraman, R.G. Amorim, R.H. Scheicher, and M. Fyta, Diamondoid-functionalized gold nanogaps as sensors for natural, mutated, and epigenetically modified DNA nucleotides, Nanoscale, DOI: 10.1039/C6NR00500D (2016).

B. Adhikari, S. Meng, and M. Fyta, Carbene-mediated self-assembly of diamondoids on metal surfaces, Nanoscale , (2016) DOI: 10.1039/C5NR08709K.

M. Fyta, Threading DNA through nanopores for biosensing applications, J. Phys.: Cond. Matter 27, 273101 (2015).

B. Adhikari and M. Fyta, Towards double-functionalized small diamondoids: selective electronic band-gap tuning, Nanotechnology 26, 035701 (2015).

M. Fyta, Stable boron nitride diamondoids as nanoscale materials", Nanotechnology 25, 365601 (2014).

G. Sivaraman and M. Fyta, Derivatives of small diamondoids as biosensors for DNA nucleobases, Nanoscale 6, 4225 (2014).

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 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).

M. Fyta, S. Melchionna, S. Succi, and E. Kaxiras, Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations, Phys. Rev. E 78, 036704 (2008).

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).


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