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. |
Electronic properties of dopants and defects in diamane thin films
Electronic structure of the nitrogen-vacancy center in diamond
Stability and mechanical properties of amorphous and nanocrystalline carbon
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. |
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. |
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. |
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. |
Last Modified Dec 23, 2009 |