Topological Frustration in Graphene Nanoflakes: Magnetic Order and Spin Logic Devices (2009)
Wang, Wei L., Yazyev, Oleg V., Meng, Sheng, Kaxiras, Efthimios
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...
Theory of Spin-Conserving Excitation of the $N-V^-$ Center in Diamond (2009)
Gali, Adam, Janzén, Erik, Deák, Péter, Kresse, Georg, Kaxiras, Efthimios
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...
Chen, Hua, Zhu, Wenguang, Kaxiras, Efthimios, Zhang, Zhenyu
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...
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...
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...
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...
Effective Hamiltonian for FeAs based superconductors (2008)
Manousakis, Efstratios, Ren, Jun, Meng, Sheng, Kaxiras, Efthimios
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...
Applying the lattice Boltzmann equation to multiscale fluid problems (2008)
Olga Filippova, M Aterials, S Cience, Greg Smith, Efthimios Kaxiras
The authors discuss the theory and application of the Lattice Boltzmann equation to multiscale physics in fluids. They present two examples relevant to real-life applications: airflow around an...
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...
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...
Size limits on doping phosphorus into silicon nanocrystals (2008)
Chan, T. L., Tiago, Murilo L., Kaxiras, Efthimios, Cheikowsky, James R.
We studied the electronic properties of phosphorus-doped silicon nanocrystals using the real-space first-principles pseudopotential method. We simulated nanocrystals with a diameter of up to 6 nm and...
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...
Size limits on doping phosphorus into silicon nanocrystals (2008)
Chan, T. L., Tiago, Murilo L., Kaxiras, Efthimios, Cheikowsky, James R.
We studied the electronic properties of phosphorus-doped silicon nanocrystals using the real-space first-principles pseudopotential method. We simulated nanocrystals with a diameter of up to 6 nm and...
Graphene nanoflakes with large spin (2008)
Wang, Wei L., Meng, Sheng, Kaxiras, Efthimios
We investigate, using benzenoid graph theory and first-principles calculations, the magnetic properties of arbitrarily shaped finite graphene fragments to which we refer as graphene nanoflakes...
rials phenomena: quantum mechanics, atomistic mechanics, and continuum mechanics. Unified dynamical treatment This challenging paradigm of computational science demands a unified dynamical treatment...
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...
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...
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...
Fyta, Maria G., Melchionna, Simone, Kaxiras, Efthimios, Succi, Sauro
We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin Molecular Dynamics (MD) techniques with a mesoscopic...
DNA nucleoside interaction and identification with carbon nanotubes (2006)
Meng, Sheng, Maragakis, Paul, Papaloukas, Costas, Kaxiras, Efthimios
We investigate the interaction of individual DNA nucleosides with a carbon nanotube (CNT) in vacuum and in the presence of external gate voltage. We propose a scheme to discriminate between...
From Electrons to Finite Elements: A Concurrent Multiscale Approach for Metals (2005)
Lu, Gang, Tadmor, E. B., Kaxiras, Efthimios
We present a multiscale modeling approach that concurrently couples quantum mechanical, classical atomistic and continuum mechanics simulations in a unified fashion for metals. This approach is...
Hydrogen Embrittlement of Aluminum: the Crucial Role of Vacancies (2005)
We report first-principles calculations which demonstrate that vacancies can combine with hydrogen impurities in bulk aluminum and play a crucial role in the embrittlement of this prototypical...
Superconducting and charge-density wave instabilities in ultrasmall-radius carbon nanotubes (2004)
Barnett, Ryan, Demler, Eugene, Kaxiras, Efthimios
We perform a detailed analysis of the band structure, phonon dispersion, and electron-phonon coupling of three types of small-radius carbon nanotubes (CNTs): (5,0), (6,0), and (5,5) with diameters...
Multiscale simulations in simple metals: a density-functional based methodology (2004)
Choly, Nicholas, Lu, Gang, E, Weinan, Kaxiras, Efthimios
We present a formalism for coupling a density functional theory-based quantum simulation to a classical simulation for the treatment of simple metallic systems. The formalism is applicable to...
An Overview of Multiscale Simulations of Materials (2004)
Multiscale modeling of material properties has emerged as one of the grand challenges in material science and engineering. We provide a comprehensive, though not exhaustive, overview of the current...
Electron-phonon interaction in ultrasmall-radius carbon nanotubes (2003)
Barnett, Ryan, Demler, Eugene, Kaxiras, Efthimios
We perform analysis of the band structure, phonon dispersion, and electron-phonon interactions in three types of small-radius carbon nanotubes. We find that the (5,5) can be described well by the...
Electronic structure of overstretched DNA (2002)
Maragakis, Paul, Barnett, Ryan Lee, Kaxiras, Efthimios, Elstner, Marcus, Frauenheim, Thomas
Minuscule molecular forces can transform DNA into a structure that is elongated by more than half its original length. We demonstrate that this pronounced conformational transition is of relevance to...
Fast method for force computations in electronic structure calculations (2002)
Choly, Nicholas, Kaxiras, Efthimios
We present new efficient (O(N log N)) methods for computing three quantities crucial to electronic structure calculations: the ionic potential, the electron-ion contribution to the Born-Oppenheimer...
Can vacancies lubricate dislocation motion in aluminum? (2002)
The interaction of vacancy with dislocations in Al is studied using the Semidiscrete Variational Peierls-Nabarro model with ab initio determined gamma surface. For the first time, we confirm...
Kinetic energy density functionals for non-periodic systems (2001)
Choly, Nicholas, Kaxiras, Efthimios
Kinetic energy functionals of the electronic density are used to model large systems in the context of density functional theory, without the need to obtain electronic wavefunctions. We discuss the...
Energetics of hydrogen impurities in aluminum and their effect on mechanical properties (2001)
Lu, Gang, Orlikowski, Daniel, Park, Ickjin, Politano, Olivier, Kaxiras, Efthimios
The effects of hydrogen impurities in the bulk and on the surface of aluminum are theoretically investigated. Within the framework of density functional theory, we have obtained the dependence on H...
Variational finite-difference representation of the kinetic energy operator (2001)
Maragakis, P., Soler, Jose M., Kaxiras, Efthimios
A potential disadvantage of real-space-grid electronic structure methods is the lack of a variational principle and the concomitant increase of total energy with grid refinement. We show that the...
Hydrogen-enhanced local plasticity in aluminum: an ab initio study (2001)
Lu, Gang, Zhang, Qing, Kioussis, Nicholas, Kaxiras, Efthimios
Dislocation core properties of Al with and without H impurities are studied using the Peierls-Nabarro model with parameters determined by ab initio calculations. We find that H not only facilitates...
Hydrogen-Enhanced Local Plasticity in Aluminum (2001)
Kaxiras, Efthimios, Kioussis, Nicholas, Lu, Gang, Zhang, Qing
Thermodynamics of C incorporation on Si(100) from ab initio calculations (2000)
Remediakis, I. N., Kaxiras, Efthimios, Kelires, P. C.
We study the thermodynamics of C incorporation on Si(100), a system where strain and chemical effects are both important. Our analysis is based on first-principles atomistic calculations to obtain...
Waghmare, U. V., Kim, Hanchul, Park, I. J., Modine, Normand, Maragakis, P., Kaxiras, Efthimios
We discuss our new implementation of the Real-space Electronic Structure method for studying the atomic and electronic structure of infinite periodic as well as finite systems, based on density...
A Critical Reexamination of the Peierls-Nabarro Model (1999)
Lu, Gang, Kioussis, Nicholas, Bulatov, Vasily V., Kaxiras, Efthimios
We reexamine two essential issues within the Peierls-Nabarro model which are critical in obtaining accurate values for the Peierls stress. The first issue is related to the sampling scheme of the...
Generalized stacking fault energy surfaces and dislocation properties of aluminum (1999)
Lu, Gang, Kioussis, Nicholas, Bulatov, Vasily V., Kaxiras, Efthimios
We have employed the semidiscrete variational generalized Peierls-Nabarro model to study the dislocation core properties of aluminum. The generalized stacking fault energy surfaces entering the model...
The surfactant effect in semiconductor thin film growth (1999)
Kandel, Daniel, Kaxiras, Efthimios
The theoretical and experimental status of surfactant mediated semiconductor epitaxial growth is reviewed. We discuss homoepitaxy as well as heteroepitaxy, and emphasize in particular issues related...
Atomic Structure and Bonding of Boron-Induced Reconstructions on Si(001). (1998)
Wang, Yajun, Hamers, Robert J., Kaxiras, Efthimios
Scanning tunneling microscopy and tunneling spectroscopy have been used to investigate the local structural and electronic properties of boron-induced reconstructions on Si(001). Thermal...
De Koning, M., Antonelli, A., Bazant, Martin Z., Kaxiras, Efthimios, Justo, J. F.
We calculate the free energies of unstable stacking fault (USF) configurations on the glide and shuffle slip planes in silicon as a function of temperature, using the recently developed Environment...
Interatomic Potential for Silicon Defects and Disordered Phases (1997)
Justo, Joao F., Bazant, Martin Z., Kaxiras, Efthimios, Bulatov, V. V., Yip, Sidney
We develop an empirical potential for silicon which represents a considerable improvement over existing models in describing local bonding for bulk defects and disordered phases. The model consists...
Surface reconstruction induced geometries of Si clusters (1997)
We discuss a generalization of the surface reconstruction arguments for the structure of intermediate size Si clusters, which leads to model geometries for the sizes 33, 39 (two isomers), 45 (two...
Environment Dependent Interatomic Potential for Bulk Silicon (1997)
Bazant, Martin Z., Kaxiras, Efthimios, Justo, J. F.
We use recent theoretical advances to develop a new functional form for interatomic forces in bulk silicon. The theoretical results underlying the model include a novel analysis of elastic properties...
Kaxiras, Efthimios, Joannopoulos, John, Vashishta, Priya, Kalia, Rajiv K.
Significant advances have been made recently toward understanding the properties of materials through theoretical approaches. These approaches are based either on first-principles quantum mechanical...
Juan, Yu-min, Kaxiras, Efthimios
The generalized stacking fault (GSF) energy surfaces have received considerable attention due to their close relation to the mechanical properties of solids. We present a detailed study of the GSF...
Slip energy barriers in aluminum and implications for ductile versus brittle behavior (1996)
Sun, Yuemin, Kaxiras, Efthimios
We conisder the brittle versus ductile behavior of aluminum in the framework of the Peierls-model analysis of dislocation emission from a crack tip. To this end, we perform first-principles quantum...
Modeling of Covalent Bonding in Solids by Inversion of Cohesive Energy Curves (1996)
Bazant, Martin Z., Kaxiras, Efthimios
We provide a systematic test of empirical theories of covalent bonding in solids using an exact procedure to invert ab initio cohesive energy curves. By considering multiple structures of the same...
Modine, N. A., Kaxiras, Efthimios
We study the spin-$\frac{1}{2}$ Heisenberg antiferromagnet on a series of finite-size clusters with features inspired by the fullerenes. Frustration due to the presence of pentagonal rings makes such...
Adaptive coordinate, real-space electronic structure calculations on parallel computers (1995)
Zumbach, Gil, Modine, N. A., Kaxiras, Efthimios
We present a method for electronic structure calculations that retains all of the advantages of real space and addresses the inherent inefficiency of a regular grid, which has equal precision...
Atomistic Aspects of Diffusion and Growth on the Si and Ge (111) Surfaces (1995)
The stability of interfaces and the mechanisms of thin film growth on semiconductors are issues of central importance in electronic devices. These issues can only be understood through detailed study...
Use of the Generalized Gradient Approximation in Pseudopotential Calculations of Solids (1995)
Juan, Yumin, Kaxiras, Efthimios
We present a study of the equilibrium properties of $sp$-bonded solids within the pseudopotential approach, employing recently proposed generalized gradient approximation (GGA) exchange correlation...
Zeger, Linda M., Juan, Yu-Min, Kaxiras, Efthimios, Antonelli, A.
We study a new hypothetical form of solid carbon \csc, with a unit cell which is composed of the \cs \ fullerene cluster and an additional single carbon atom arranged in the zincblende structure....
Ab Initio theory of polar surfaces of binary compound semiconductors /--by Efthimios Kaxiras. (1987)
Supervised by John D. Joannopoulos.
Theoretical Models of Eumelanin Protomolecules and their Optical Properties
Meng, Sheng, Kaxiras, Efthimios
The molecular structure of melanin, one of the most ubiquitous natural pigments in living organisms, is not known and its multifaceted biological role is still debated. We examine structural models...
Mechanisms for Ultrafast Nonradiative Relaxation in Electronically Excited Eumelanin Constituents
Meng, Sheng, Kaxiras, Efthimios
We investigate the relaxation dynamics of melanin model constituents including monomers, dimers, and tetramers, upon excitation, using state-of-the-art, time-dependent, density functional theory...