arXiv subjects

Efthimios Kaxiras

Publications and source records attributed to Efthimios Kaxiras.

At least 145 records · Page 8Linked to original sources

arXiv2014

Identifying structural flow defects in disordered solids using machine learning methods

We use machine learning methods on local structure to identify flow defects - or regions susceptible to rearrangement - in jammed and glassy systems. We apply this method successfully to two disparate systems: a two dimensional experimental realization of a granular pillar under compression, and a Lennard-Jones glass in both two and three dimensions above and below its glass transition temperature. We also identify characteristics of flow defects that differentiate them from the rest of the sample. Our results show it is possible to discern subtle structural features responsible for heterogeneous dynamics observed across a broad range of disordered materials.

cond-mat.soft↗

arXiv2013

Topological Proximity Effects in Graphene Nanoribbon Heterostructures

Topological insulators (TI) are bulk insulators that possess robust chiral conducting states along their interfaces with normal insulators. A tremendous research effort has recently been devoted to TI-based heterostructures, in which conventional proximity effects give rise to many exotic physical phenomena. Here we establish the potential existence of "topological proximity effects" at the interface of a topological graphene nanoribbon (GNR) and a normal GNR. Specifically, we show that the location of the topological edge states exhibits versatile tunability as a function of the interface orientation, as well as the strengths of the interface coupling and spin-orbit coupling in the normal GNR. For zigzag and bearded GNRs, the topological edge state can be tuned to be either at the interface or outer edge of the normal ribbon. For armchair GNR, the potential location of the topological edge state can be further enriched to be at the edge of or within the normal ribbon, at the interface, or diving into the topological GNR. We also discuss potential experimental realization of the predicted topological proximity effects, which may pave the way for integrating the salient functionality of TI and graphene in future device applications.

cond-mat.mes-hall↗

arXiv2011

Approaching the Intrinsic Bandgap in Suspended High-Mobility Graphene Nanoribbons

We report electrical transport measurements on a suspended ultra-low-disorder graphene nanoribbon(GNR) with nearly atomically smooth edges that reveal a high mobility exceeding 3000 cm2 V-1 s-1 and an intrinsic band gap. The experimentally derived bandgap is in quantitative agreement with the results of our electronic-structure calculations on chiral GNRs with comparable width taking into account the electron-electron interactions, indicating that the origin of the bandgap in non-armchair GNRs is partially due to the magnetic zigzag edges.

cond-mat.mes-hall↗

arXiv2010

Direct correlation of crystal structure and optical properties in wurtzite/zinc-blende GaAs nanowire heterostructures

A novel method for the direct correlation at the nanoscale of structural and optical properties of single GaAs nanowires is reported. Nanowires consisting of 100% wurtzite and nanowires presenting zinc-blende/wurtzite polytypism are investigated by photoluminescence spectroscopy and transmission electron microscopy. The photoluminescence of wurtzite GaAs is consistent with a band gap of 1.5 eV. In the polytypic nanowires, it is shown that the regions that are predominantly composed of either zinc-blende or wurtzite phase show photoluminescence emission close to the bulk GaAs band gap, while regions composed of a nonperiodic superlattice of wurtzite and zinc-blende phases exhibit a redshift of the photoluminescence spectra as low as 1.455 eV. The dimensions of the quantum heterostructures are correlated with the light emission, allowing us to determine the band alignment between these two crystalline phases. Our first-principles electronic structure calculations within density functional theory, employing a hybrid-exchange functional, predict band offsets and effective masses in good agreement with experimental results.

cond-mat.mes-hall↗

arXiv2010

Properties of nitrogen-vacancy centers in diamond: group theoretic approach

We present a procedure that makes use of group theory to analyze and predict the main properties of the negatively charged nitrogen-vacancy (NV) center in diamond. We focus on the relatively low temperatures limit where both the spin-spin and spin-orbit effects are important to consider. We demonstrate that group theory may be used to clarify several aspects of the NV structure, such as ordering of the singlets in the ($e^2$) electronic configuration, the spin-spin and the spin-orbit interactions in the ($ae$) electronic configuration. We also discuss how the optical selection rules and the response of the center to electric field can be used for spin-photon entanglement schemes. Our general formalism is applicable to a broad class of local defects in solids. The present results have important implications for applications in quantum information science and nanomagnetometry.

quant-ph↗

arXiv2010

On Graphene Hydrate

Using first-principles calculations, we show that the formation of carbohydrate directly from carbon and water is energetically favored when graphene membrane is subjected to aqueous environment with difference in chemical potential across the two sides. The resultant carbohydrate is two-dimensional, where the hydrogen atoms are exclusively attached on one side of graphene while the hydroxyl groups on the other side form a herringbone reconstruction that optimizes hydrogen bonding. We show that graphene undergos semi-metal-insulator transition upon hydration which is readily detectable from the significant shift in the vibration spectrum. The hydrate form of graphene suggests new applications for graphene in electronics, either deposited on a substrate or in solution.

cond-mat.mes-hall↗

arXiv2009

Topological Frustration in Graphene Nanoflakes: Magnetic Order and Spin Logic Devices

Magnetic order in graphene-related structures can arise from size effects or from topological frustration. We introduce a rigorous classification scheme for the types of finite graphene structures (nano-flakes) which lead to large net spin or to antiferromagnetic coupling between groups of electron spins. Based on this scheme, we propose specific examples of structures that can serve as the fundamental (NOR and NAND) logic gates for the design of high-density ultra-fast spintronic devices. We demonstrate, using ab initio electronic structure calculations, that these gates can in principle operate at room temperature with very low and correctable error rates.

cond-mat.other↗

arXiv2009

Theory of Spin-Conserving Excitation of the $N-V^-$ Center in Diamond

The negatively charged nitrogen-vacancy defect ($N-V^-$ center) in diamond is an important atomic-scale structure that can be used as a qubit in quantum computing and as a marker in biomedical applications. Its usefulness relies on the ability to optically excite electrons between well-defined gap states, which requires clear and detailed understanding of the relevant states and excitation processes. Here we show that by using hybrid density-functional-theory calculations in a large supercell we can reproduce the zero-phonon line and the Stokes and anti-Stokes shifts, yielding a complete picture of the spin-conserving excitation of this defect.

cond-mat.mtrl-sci↗

arXiv2009

Optimization of Mn Doping in Group-IV-based Dilute Magnetic Semiconductors by Electronic Co-dopants

The percentage of substitutional doping of magnetic atoms (Mn) in group-IV-based dilute magnetic semiconductors (DMS) can be increased by co-doping with another conventional electronic dopant (e-dopant) [Zhu et al., Phys. Rev. Lett. 100, 027205 (2008)]. Here, we report extensive theoretical investigations of the kinetic and thermodynamic characteristics of several co-doped systems including bulk Si and Ge as hosts and various group-III and group-V e-dopants. The main findings are as follows: The n-p pairing of n-type e-dopants with p-type substitutional Mn is energetically stable in bulk Ge and Si. Mn atoms move from interstitial sites to substitutional sites easier in the presence of a neighboring n-type e-dopant. Magnetic coupling between two Mn atoms in bulk Ge oscillates between positive (ferromagnetic) and negative (antiferromagnetic) values with increasing Mn-Mn distance, but in Mn/As co-doped Ge the coupling parameter remains positive at all distances beyond nearest-neighbors and this qualitative difference does not change with the doping level. For Mn doped Si, all coupling values except for the nearest neighbor one are positive and do not change much upon co-doping. We find an unconventional magnetic anisotropy in the co-doped system, that is, the dependence of magnetic coupling on the relative positions of the magnetic ions and their neighboring e-dopants. We employ Monte Carlo simulations to estimate the Curie temperature (Tc). We find that in Mn doped Ge no ferromagnetic order exists for Mn concentrations ranging from 3.13% to 6%. Instead, a spin-glass phase transition occurs at ~5K at 5% Mn doping. For Mn/As co-doped Ge, Tc increases nearly linearly with the Mn concentration and reaches 264K at 5% Mn doping.

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

Effective Hamiltonian for FeAs based superconductors

The recently discovered FeAs-based superconductors show intriguing behavior and unusual dynamics of electrons and holes which occupy the Fe $d$-orbitals and As $4s$ and $4p$ orbitals. Starting from the atomic limit, we carry out a strong coupling expansion to derive an effective hamiltonian that describes the electron and hole behavior. The hopping and the hybridization parameters between the Fe $d$ and As $s$ and $p$-orbitals are obtained by fitting the results of our density-functional-theory calculations to a tight-binding model with nearest-neighbor interactions and a minimal orbital basis. We find that the effective hamiltonian, in the strong on-site Coulomb repulsion limit, operates on three distinct sub-spaces coupled through Hund's rule. The three sub-spaces describe different components (or subsystems): (a) one spanned by the $d_{x^2-y^2}$ Fe orbital; (b) one spanned by the degenerate atomic Fe orbitals $d_{xz}$ and $d_{yz}$; and (c) one spanned by the atomic Fe orbitals $d_{xy}$ and $d_{z^2}$. Each of these Hamiltonians is an extended t-t'-J-J' model and is characterized by different coupling constants and filling factors. For the case of the undoped material the second subspace alone prefers a ground state characterized by a spin-density-wave order similar to that observed in recent experimental studies, while the other two subspaces prefer an antiferromagnetic order. We argue that the observed spin-density-wave order minimizes the ground state energy of the total hamiltonian.

cond-mat.str-el↗

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↗