Research projects

Brief description

Our research work is focused on the interface of materials science and biophysical phenomena and belongs to the field of computational physics. Applications of this work can be purely technological, like MEMS/NEMS coatings and spin qubits or biotechnological, like ultra-fast DNA sequencing and biosensing.

Currently, our research deals with the integration of biomolecules and materials and their interaction, modified surfaces, 2D materials, DNA biophysical processes, such as DNA translocation though narrow pores, as well as the mechanical and electronic properties of Carbon nanostructures with defects and dopants. Our work is purely computational, for which a variety of methodologies are used, ranging from classical (Monte-Carlo schemes within empirical potential approaches), semi-empirical (parametrized tight-binding schemes), quantum mechanical (implementations of the density functional theory w/o the non-equilibrium Greens functions approach for quantum transport), classical (Molecular Dynamics), and multiscale schemes (coupled Langevin molecular-dynamics and lattice-Boltzmann method for modeling molecular motion in a fluid solvent). Our simulations allow for a bottom-up approach of materials and biophysical systems, their structural, mechanical, electronic, and transport properties.

Biosensing

  1. Functionalized nanopores for detecting and identifying DNA

  2. Interaction of materials with biomolecules: Hydrogen bonding of diamondoids and DNA

Modified surfaces

  1. Self-assembled diamondoid surfaces

  2. Biologically modified surfaces

Two-dimensional materials

  1. Exploring the polymorphicity of transition metal dicholgenides

Biophysics:

  1. Multiscale modeling of DNA translocation though a nanopore

  2. Electronic behavior in stretched and unstretched DNA

  3. An ab initio based potential for double-stranded DNA/RNA

Chemical Physics:

  1. Optimization of ionic force fields for Molecular Dynamics simulations of ionic solutions

Condensed matter physics:

  1. Functionalized diamondoids

  2. Electronic properties of dopants and defects in diamane thin films

  3. Assembly of Carbon onions

  4. Electronic structure of the nitrogen-vacancy center in diamond

  5. Stability and mechanical properties of amorphous and nanocrystalline carbon


  1. Functionalized electrodes for detecting and identifying DNA

  2. A computational modeling of functionalized electrodes for sensing biomolecules, such as DNA, reveals all the inherent details involved in this sensing. The structural, electronic, and transport properties are evaluated together in order to understand the read-out properties of the functionalized electrode break-junction. The type of the functionalization molecule, its specific chemistry, and its adsorption on the electrodes significantly influences the whole structure. These characteristics can be tuned in order to enhance the biosensitivity of the functionalized break-junction.
    Snapshot of functionalized gold electrodes which detect a nucleotide (A) placed in between.
  1. Hydrogen bonding of diamondoids and DNA

  2. Understanding the interaction of biomolecules with materials is essential in view of the variety of the potential applications these complexes can realize. To this end, we investigate the interaction of DNA molecules with diamondoids. The latter are a wide family of tiny hydrogen-terminated diamond clusters which have recently shown high technological potential. We probe this interaction through quantum-mechanical computer simulations. Focus is given on the hydrogen bonding possibilities of the different DNA nucleobases with the lower diamondoids. The bonding strength with respect to the relative distance and orientation of a nucleobase and a diamondoid is evaluated. Our aim is to investigate ways to promote the binding between these two units. Accordingly, we functionalize the diamondoids by replacing one of its hydrogens with atomic groups, such as amine groups, and study the respective binding probabilities of these two molecules. We probe this interaction through the binding energy and the electronic structure of the nucleobase-diamondoid material and reveal the specific details of their association. In the end, we discuss the relevance of our results in view of realizing a diamondoid functionalized nanopore for electrically reading out the human genome.
    Snapshot of amine-diamondoid interacting through hydrogen bonds with a nucleobase.
top
  1. Self-assembled diamondoid Surfaces

  2. Diamondoids can form self-assembled layers (SAMs) on metal surfaces. These structures have important properties, such as a strong monochromatic emission, which make them very good properties for applications in microelectronics, as field emitting devices or in sensing. Using quantum-mechanical approaches, we investigate the adsorption possibilities of the diamondoids on metal surfaces. A way to produce SAMs of high stability is by using another molecule to mediate the adsorption of the diamondoid SAMs on metal substrates. The bonding characteristics, surface morphology, and charge re-distribution in these materials gives an important insight in view of the potential applications.
    A small diamondoid adsorbed on a metal surface through the mediation of a small aromatic molecule.
  1. Biologically modified surfaces

  2. 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 applications.
top
  • Exploring the polymorphicity in transition metal dicholgenides

  • Two dimensional transition metal dicholgenides (TMDs) are intensively investigated, as many of their properties are believed to be superior to those of graphene. The advantage of the former 2D materials are the variety of chemical compositions and phases they can assume. These can be found in a metallic (1T) or semiconducting phase (2H). This polymorphicity we study here in view of the vast variety of nanotechnological applications of TMDs. The electronic and transport properties of different TMDs and their combinations
    A snapshot of a 2D TMD slab which demonstrated the complexity and polymorphicity in these materials.
    top
  • Multiscale modeling of DNA translocation though a nanopore

  • 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.
    Snapshot of a chain of beads (in red) representing a 6 kbp double-stranded DNA, as it translocates through a 12nm size pore. The fluid velocity is shown through a 3-D representation at the vicinity of the beads and is also mapped on 2-D planes.
    top
  • Electronic behavior in stretched and unstretched DNA

  • Density Functional Theory (DFT) based simulations are performed for the interactions between base-pairs in DNA. The energetics as well as the electronic states in DNA bases and base pairs in various relative configurations in the equilibrium and stretched forms are calculated. The frontier states in the base pairs were found to be related to only one of the components of the pair and are very little affected when the two components of the base-pair are separated along the direction in which they are hydrogen-bonded. Little dependence of these states was also found in terms of the relative rotation (with respect to the DNA axis) and axial distance of two base pairs that are stacked on top of each other. These calculations will set the stage for a proper interpretation of the electronic and mechanical behavior in the stretched and unstretched DNA forms.
    The frontier states in the A-T base pair and their identification with corresponding orbitals in the isolated bases.
    top
  • An ab initio based potential for double-stranded DNA/RNA

  • 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. An extension of this model for double-stranded RNA is currently being done.
    The expression for the ab initio based potential for DNA nucleobases. The all-atom picture has been replaced by a scheme with 4 different beads for each nucleobase and 1 bead for the sugar-backbone site.
    top
  • Optimization of ionic force fields for Molecular Dynamics simulations of ionic solutions

  • Molecular dynamics simulations of ionic solutions 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 properties simultaneously. To that end, we simulate five different salt solutions, namely CsCl, KCl, NaI, KF, and CsI, at finite ion concentration. The force fields of these ions are systematically varied under the constraint that the single-ion solvation free energy matches the experimental value, which reduces the two-dimensional {σ, ε} parameter space of the Lennard Jones interaction to a one dimensional line for each ion. From the finite-concentration simulations, the pair-potential is extracted and the osmotic coefficient is calculated, which is compared to experimental data. We find a strong dependence of the osmotic coefficient on the force field, which is remarkable as the single-ion solvation free energy and the ion-water structure remain invariant under the parameter variation. Optimization of the force field is achieved for the cations Cs+ and K+, while for the anions I- and F- the experimental osmotic coefficient cannot be reached. This suggests that in the long run, additional parameters might have to be introduced into the modeling, for example by modified mixing rules.
    top
  • Functionalized diamondoids

  • Through density-functional-theory based simulations we investigate the functionalization of diamondoids, tiny hydrogen-terminated diamond clusters. We focus on their stability, as well as their electronic properties for practical applications. In a similar manner, we also look a the doping effects of these tiny nanostructures. Specifically, we choose different diamondoids and dope these with boron and nitrogen. The presence of defects in the diamondoids is also studied.
    The HOMO orbital for a nitrogen-doped diamondoid.
    top
  • Electronic properties of dopants and defects in diamane thin films

  • We use density-functional-theory based simulations to investigate the electronic structure of diamane films. These are thin diamond films of 2-3 layers, terminated with hydrogen atoms, which are expected to have exceptional mechanical, thermal, and electrical properties. To unravel and understand these properties we quantum-mechanically model double-layered diamane films and are specifically interested in the effect of dopants and defects on these properties. We use boron and nitrogen atoms as dopants and study also nitrogen-vacancy defects in diamane. These defects in crystalline diamond have enormous possibilities in quantum computing. Here, we address the question, whether these defects in diamane could enhance their potential as qubits. The way defects and dopants can be used to tune the electronic properties of diamane nanostructures is investigated in detail. The structural differences in these diamane structures are investigated and mapped to their electronic properties. The implications of our results in practical applications are discussed in terms of the differences in the electronic structure of diamane films as imposed by the presence of dopants and defects.
    top
  • Assembly of Carbon onions

  • Atomistic simulations at two levels, classical and quantum-mechanical, are used to probe the coalescence of multi-shelled concentric fullerenes, also known as 'carbon onions'. We focus on the binding behavior of adjacent carbon onions and promote their binding through the addition of vacancies, as well as doping with boron and nitrogen atoms. Molecular Dynamics simulations are used to extract the binding energy between two carbon onions and the thermal stability of the assembled structure. At a lower level, density functional theory based calculations reveal the electronic structure of the single and coalesced carbon onions. The binding at this level will be addressed in view of the electronic structure and frontier orbitals of the carbon onions. The results are evaluated with respect to the relative distance of the adjacent carbon onions, the number of fullerene shells, the number of vacancies, and the amount of doping and understand their corresponding electronic properties. We aim to optimize the conditions for assembling these nanoscale building blocks in view of their high potential in nanoengineering novel functional nanomaterials.
    Two carbon onions: C60@c240@c540
    top
  • Electronic structure of the negatively charged nitrogen-vacancy center in diamond

  • As a representative example of materials with high technological interest, we study nitrogenous defects in diamond, and focus especially on the nitrogen-vacancy (NV) center in diamond. This is a system that has been intensively studied in recent years and can be found in the neutral and the negatively (-1) charged state. Specifically, the negatively charged NV center provides the opportunity to manipulate an individual electron spin even at room temperature and coherently couple it to individual proximal 13C nuclear spins. This property renders this defective material to a good candidate for quantum information processing by promoting a long distance quantum communication with NV centers. We use DFT simulations to model the negatively charged NV center in diamond and are interested in extracting its electronic structure and especially the electronic wavefunctions. This will allow us to calculate the Fermi contact and hyperfine terms in this material and gain information about the interaction of the NV center with its environment.
    Calculated spin density isosurfaces for the 3A2 state and Ms=1. Side view relative to the <111> axis of the defect and its nearest and next nearest neighbors. The vacant site is indicated by a small pink circle and the neighboring C and N atoms by grey and cyan balls, respectively.
    top
  • Stability and mechanical properties of amorphous and nanocrystalline carbon

  • We have explored the main characteristics and properties, both structural and mechanical, of nanostructured amorphous carbon; a material with a potential to intermingle properties of carbon nanostructures with those of pure amorphous carbon. Controlling the type and size of the embedded structures opens the possibility to tailor the properties of the amorphous phase. The nanostructures are embedded in an amorphous carbon matrix and are varied both in type and size, ranging from diamond crystallites to nanotubes and concentric-shell graphitic onions bound by dispersion forces, to entirely three-dimensional sp2 covalent conformations, which include porous, open graphene structures with negative curvature. This study is based on classical and semi-empirical simulations, using Monte Carlo schemes within the empirical potential approach and tight-binding molecular dynamics utilizing two different hamiltonians. For detailed information click here.
    Representative ball and stick models of carbon nanocomposites: a diamond (left) and a carbon nanotube (right) embedded in amorphous carbon matrices. The sp3 atoms are shown in white, sp2 in black, while in grey are the atoms the crystalline inclusions.

    top

    Last Modified Dec 23, 2009