arXiv subjects

Maria Fyta

Publications and source records attributed to Maria Fyta.

17 recordsLinked to original sources

arXiv2024

In silico design and prediction of metastable quaternary phases in Cu-Ni-Si-Cr alloys

Quaternary phases formed in copper alloys are investigated through a combination of quantum-mechanical and classical computer simulations and active machine learning. Focus is given on nickel, silicon, and chromium impurities in a copper matrix. The analysis of the formation enthalpies of candidate quaternary structures leads to the prediction of two novel quaternary phases and the assessment of their stability. For the predicted two phases, machine learned atomistic potentials are developed using active learning with a quantum-mechanical accuracy. Use of these potentials in atomistic simulations further elucidates the structure, temperature-dependent dynamics, and elastic behavior of the predicted quaternary phases in copper alloys. The combined in silico approach is thus proven highly efficient in both designing materials and elucidating their properties and potential combining different spatiotemporal scales. In the case of alloys, this computational scheme significantly reduces the effort in searching the huge chemical space of possible phases, enhancing the efficiency in synthesizing novel alloys with pre-defined properties.

cond-mat.mtrl-sci↗

arXiv2017

Electrokinetic Lattice Boltzmann solver coupled to Molecular Dynamics: application to polymer translocation

We develop a theoretical and computational approach to deal with systems that involve a disparate range of spatio-temporal scales, such as those comprised of colloidal particles or polymers moving in a fluidic molecular environment. Our approach is based on a multiscale modeling that combines the slow dynamics of the large particles with the fast dynamics of the solvent into a unique framework. The former is numerically solved via Molecular Dynamics and the latter via a multi-component Lattice Boltzmann. The two techniques are coupled together to allow for a seamless exchange of information between the descriptions. Being based on a kinetic multi-component description of the fluid species, the scheme is flexible in modeling charge flow within complex geometries and ranging from large to vanishing salt concentration. The details of the scheme are presented and the method is applied to the problem of translocation of a charged polymer through a nanopores. In the end, we discuss the advantages and complexities of the approach.

cond-mat.soft↗

arXiv2011

Carbon-based nanostructured composite films: elastic, mechanical and optoelectronic properties derived from computer simulations

In this review, we present our recent computational work on carbon-based nanostructured composites. These materials consist of carbon crystallites embedded in an amorphous carbon matrix and are modeled here through classical and semi-empirical quantum-mechanical simulations. We investigate the energetics, mechano-elastic, and optoelectronic properties of these materials. Once the stability of the composites is discussed, we move on to the calculation of their elastic moduli and constants, their anisotropy and elastic recovery. At a next step, we focus on diamond composites, which were found to be the most stable among the composites studied, and went beyond the elastic regime to investigate their ideal fracture. Finally, for these materials, the electronic density of states, dielectric function, and optical response were calculated and linked to the disorder in the structures. Our findings unveil the high potential of these materials in nanotechnological applications, especially as ultlra-hard coatings.

cond-mat.mtrl-sci↗

arXiv2009

Ionic force field optimization based on single-ion and ion-pair solvation properties

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). In this paper 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 $\{\sigma,\epsilon\}$ 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.

physics.chem-ph↗

arXiv2009

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

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. Large-scale simulation with 10^5 atoms is realized by using the ' order-N' simulation code 'ELSES' (http://www.elses.jp). The simulation starts with a diamond structure that contains initial structural defects and results in a mixture of graphite(sp^2)-like and diamond(sp^3)-like regions as nano-meter-scale domains. We speculate that the domains are metastable and are possible candidates of the precursor structures.

cond-mat.mtrl-sci↗

arXiv2009

Quantized biopolymer translocation through nanopores: departure from simple scaling

We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds through multi-folded configurations characterized by a well-defined integer number of folds. As a consequence, the translocation time acquires a dependence on the average folding number, which results in a deviation from the single-exponent power-law characterizing single-file translocation through narrow pores. The mechanism of folding quantization allows polymers above a threshold length (approximately $1,000$ persistence lengths for double-stranded DNA) to exhibit cooperative behavior and as a result to translocate noticeably faster.

physics.bio-ph↗

arXiv2009

Numerical simulation of conformational variability in biopolymer translocation through wide nanopores

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 mesoscopic fluid solvent. Thousands of events of long polymers (up to 8000 monomers) are monitored as they pass through nanopores. Comparison between the different pore sizes shows that wide pores can host a larger number of multiple biopolymer segments, as compared to smaller pores. The simulations provide clear evidence of folding quantization in the translocation process as the biopolymers undertake multi-folded configurations, characterized by a well-defined integer number of folds. Accordingly, the translocation time is no longer represented by a single-exponent power law dependence on the length, as it is the case for single-file translocation through narrow pores. The folding quantization increases with the biopolymer length, while the rate of translocated beads at each time step is linearly correlated to the number of resident beads in the pore. Finally, analysis of the statistics over the translocation work unravels the importance of the hydrodynamic interactions in the process.

physics.bio-ph↗

arXiv2008

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

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 surrounding solvent. The simulations confirm that the coupling of the correlated molecular motion to hydrodynamics results in significant acceleration of the translocation process. Based on these results, we construct a phenomenological model which incorporates the statistical and dynamical features of the translocation process and predicts a power law dependence of the translocation time on the polymer length with an exponent $α$ $\approx 1.2$. The actual value of the exponent from the simulations is $α= 1.28 \pm 0.01$, which is in excellent agreement with experimental measurements of DNA translocation through a nanopore, and is not sensitive to the choice of parameters in the simulation. The mechanism behind the emergence of such a robust exponent is related to the interplay between the longitudinal and transversal dynamics of both translocated and untranslocated segments. The connection to the macroscopic picture involves separating the contributions from the blob shrinking and shifting processes, which are both essential to the translocation dynamics.

physics.bio-ph↗

arXiv2008

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

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 structure and other properties have not yet been explored in detail. We study the properties of the nitrogen-vacancy center in diamond through density functional theory within the local spin density approximation, using supercell calculations. While this theory is strictly applicable for ground state properties, we are able to give an estimate for the energy sequence of the excited states of this defect. We also calculate the hyperfine tensors in the ground state. The results clearly show that: (i) the spin density and the appropriate hyperfine constants are spread along a plane and unevenly distributed around the core of the defect; (ii) the measurable hyperfine constants can be found within about 7 A from the vacancy site. These results have important implications on the decoherence of the electron spin which is crucial in realizing the spin qubits in diamond.

cond-mat.other↗

arXiv2008

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

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 microscopic scale as combined with a self-consistent mesoscopic description for the solvent fluid dynamics. We report evidence for quantized current blockade depending on the folding configuration and offer detailed information on the role of hydrodynamic correlations in speeding-up the translocation process.

physics.comp-ph↗

arXiv2007

Parallel multiscale modeling of biopolymer dynamics with hydrodynamic correlations

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 Boltzmann (LB) method for the solvent dynamics, explicitly taking into account the interactions of the molecule with the surrounding fluid. We describe an efficient parallel implementation of the method which exhibits excellent scalability on the Blue Gene platform. We investigate both dynamical and statistical aspects of the translocation process by simulating polymers of various initial configurations and lengths. For a representative molecule size, we explore the effects of important parameters that enter in the simulation, paying particular attention to the strength of the molecule-solvent coupling and of the external electric field which drives the translocation process. Finally, we explore the connection between the generic polymers modeled in the simulation and DNA, for which interesting recent experimental results are available.

physics.comp-ph↗

arXiv2007

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

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 hydrodynamics. The multiscale approach is based on a simple scheme of exchange of space-time information between the atomistic and mesoscopic scales and is capable of describing self-consistent hydrodynamic effects on molecular motion at a computational cost which scales linearly with both solute size and solvent volume. For an application of our multiscale method, we consider the much studied problem of biopolymer translocation through nanopores: we find that the method reproduces with remarkable accuracy the statistical scaling behavior of the translocation process and provides valuable insight into the cooperative aspects of biopolymer and hydrodynamic motion.

physics.bio-ph↗

arXiv2007

Multiscale model of electronic behavior and localization in stretched dry DNA

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 scales, have a dramatic effect on electronic properties at the atomic scale and on electrical transport along DNA. Accordingly, a multiscale approach is necessary to capture the electronic behavior of the stretched DNA helix. To construct such a model, we begin with accurate density-functional-theory calculations for electronic states in DNA bases and base pairs in various relative configurations encountered in the equilibrium and stretched forms. These results are complemented by semi-empirical quantum mechanical calculations for the states of a small size [18 base pair poly(CG)-poly(CG)] dry, neutral DNA sequence, using previously published models for stretched DNA. The calculated electronic states are then used to parametrize an effective tight-binding model that can describe electron hopping in the presence of environmental effects, such as the presence of stray water molecules on the backbone or structural features of the substrate. These effects introduce disorder in the model hamiltonian which leads to electron localization. The localization length is smaller by several orders of magnitude in stretched DNA relative to that in the unstretched structure.

cond-mat.mtrl-sci↗

arXiv2007

Multiscale modeling of biopolymer translocation through a nanopore

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 mesoscopic lattice Boltzmann (LB) method for the solvent dynamics, explicitly taking into account the interactions of the molecule with the surrounding fluid. Both dynamical and statistical aspects of the translocation process were investigated, by simulating polymers of various initial configurations and lengths. For a representative molecule size, we explore the effects of important parameters that enter in the simulation, paying particular attention to the strength of the molecule-solvent coupling and of the external electric field which drives the translocation process. Finally, we explore the connection between the generic polymers modeled in the simulation and DNA, for which interesting recent experimental results are available.

physics.bio-ph↗

arXiv2007

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

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 into account. By generating polymers of various initial configurations and lengths we map the probability distibutions of the passage times of the DNA through the nanopore. A scaling law behavior for the most probable of these times with respect to length is derived, and shown to exhibit an exponent that is in a good agreement with the experimental findings. The essential features of the DNA dynamics as it passes through the pore are explored.

physics.bio-ph↗

arXiv2007

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

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 both materials are extremely hard, but their superb diamondlike properties are limited by their sp^2 component. In diamond composites, the sp^2 atoms are found in the matrix and far from the interface with the inclusion, and they are responsible for the softening of the material. In UNCD, the sp^2 atoms are located in the grain boundaries. They offer relaxation mechanisms which relieve the strain but, on the other hand, impose deformations that lead to softening. The higher the sp^2 component the less rigid these materials are.

cond-mat.mtrl-sci↗

arXiv2006

Stress variations near surfaces in diamond-like amorphous carbon

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 distribution of stresses and the distributions of sp^2 and sp^3 atoms as a function of depth from the surface are highly inhomogeneous. They show the same close relationship between local stress and bonding hybridization found previously in the bulk of the material. Compressive local stress favors the formation of sp^3 sites, while tensile stress favors the formation of sp^2 sites.

cond-mat.mtrl-sci↗