Maria Fyta

Large scale simulation of quantum-mechanical molecular dynamics for nano-polycrystalline diamond (2009)

Hoshi, Takeo, Iitaka, Toshiaki, Fyta, Maria

Quantum-mechanical molecular-dynamics simulations are carried out to explore possible precursor states of nano-polycrystalline diamond, a novel ultra-hard material produced directly from graphite....

Quantized biopolymer translocation through nanopores: departure from simple scaling (2009)

Melchionna, Simone, Bernaschi, Massimo, Fyta, Maria, Kaxiras, Efthimios, Succi, Sauro

We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding...

Numerical simulation of conformational variability in biopolymer translocation through wide nanopores (2009)

Fyta, Maria, Melchionna, Simone, Bernaschi, Massimo, Kaxiras, Efthimios, Succi, Sauro

Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a...

Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations (2008)

Fyta, Maria, Melchionna, Simone, Succi, Sauro, Kaxiras, Efthimios

We investigate the process of biopolymer translocation through a narrow pore using a multiscale approach which explicitly accounts for the hydrodynamic interactions of the molecule with the...

Quantized current blockade and hydrodynamic correlations in biopolymer translocation through nanopores: Evidence from multiscale simulations (2008)

Bernaschi, Massimo, Melchionna, Simone, Succi, Sauro, Fyta, Maria, Kaxiras, Efthimios

We present a detailed description of biopolymer translocation through a nanopore in the presence of a solvent using an innovative multiscale methodology that treats the biopolymer at the microscopic...

Ab initio supercell calculations on nitrogen-vacancy center in diamond: its electronic structure and hyperfine tensors (2008)

Gali, Adam, Fyta, Maria, Kaxiras, Efthimios

The nitrogen-vacancy center in diamond is a promising candidate for realizing the spin qubits concept in quantum information. Even though this defect is known for a long time, its electronic...

Quantized current blockade and hydrodynamic correlations in biopolymer translocation through nanopores: evidence from multiscale simulations (2008)

Bernaschi, Massimo, Melchionna, Simone, Succi, Sauro, Fyta, Maria, Kaxiras, Efthimios

We present a detailed description of biopolymer translocation through a nanopore in the presence of a solvent, using an innovative multi-scale methodology which treats the biopolymer at the...

Parallel multiscale modeling of biopolymer dynamics with hydrodynamic correlations (2007)

Fyta, Maria, Sircar, Jayanta, Kaxiras, Efthimios, Melchionna, Simone, Bernaschi, Massimo, Succi, Sauro

We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Molecular Dynamics (MD) with a mesoscopic Lattice...

Coupling Lattice Boltzmann with Atomistic Dynamics for the multiscale simulation of nano-biological flows (2007)

Fyta, Maria, Melchionna, Simone, Kaxiras, Efthimios, Succi, Sauro

We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent...

Multiscale model of electronic behavior and localization in stretched dry DNA (2007)

Barnett, Ryan, Maragakis, Paul, Turner, Ari, Fyta, Maria, Kaxiras, Efthimios

When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic...

Multiscale modeling of biopolymer translocation through a nanopore (2007)

Fyta, Maria, Melchionna, Simone, Kaxiras, Efthimios, Succi, Sauro

We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a...

Simulations on the elastic response of amorphous and nanocomposite carbon (2007)

Fyta, Maria, Kelires, P. C.

Theoretical calculations of the elastic response of carbon composites and amorphous carbon are reported. The studied composites consist of crystalline nanoinclusions, either spherical diamonds or...

Exploring DNA translocation through a nanopore via a multiscale Lattice-Boltzmann Molecular-Dynamics methodology (2007)

Melchionna, Simone, Fyta, Maria, Kaxiras, Efthimios, Succi, Sauro

A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken...

Probing the sp^2 dependence of elastic moduli in ultrahard diamond films (2007)

Fyta, Maria, Hadjisavvas, G. C., Kelires, P. C.

The structural and elastic properties of diamond nanocomposites and ultrananocrystalline diamond films (UNCD) are investigated using both empirical potentials and tight binding schemes. We find that...

Stress variations near surfaces in diamond-like amorphous carbon (2006)

Fyta, Maria, Kelires, Pantelis C.

Using Monte Carlo simulations within the empirical potential approach, we examine the effect produced by the surface environment on the atomic level stresses in tetrahedral amorphous carbon. Both the...