Difference between revisions of "Maria Fyta"
(→A potential for DNA nucleotides)
(→A potential for DNA nucleotides)
Revision as of 14:35, 23 November 2016
|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
Personal webpage: http://www.icp.uni-stuttgart.de/~mfyta
- 1 Profile
- 2 Open positions
- 3 Research interests
- 3.1 Biosensing
- 3.2 Two dimensional materials
- 3.3 DNA translocation through narrow pores
- 3.4 Adsorption of molecules on surfaces
- 3.5 Optoelectronic and mechanical properties of carbon nanostructures
- 3.6 Integration of biomolecules and materials
- 3.7 Homology Recognition
- 3.8 Force field development
- 4 Publications
My profile at "Scholar Google".
My ResearcherID: F-8562-2013.
My ORCID: 0000-0002-5425-7907.
A short CV can be found here: http://www.icp.uni-stuttgart.de/~mfyta/cv_mfyta_short.html
- 2D materials
- Carbon materials
- Mechanical properties
- Electronic properties
- Quantum transport
In case you are interested in bachelor or master projects, please contact Maria Fyta (mfyta_at_icp.uni-stuttgart.de).
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
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:
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.
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.
[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).