arXiv subjects

Efthimios Kaxiras

Publications and source records attributed to Efthimios Kaxiras.

At least 163 records · Page 9Linked to original sources

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

Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore

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 Lattice-Boltzmann (LB) method for the solvent dynamics. A unique feature of the present approach is that hydrodynamic interactions between the solute macromolecule and the aqueous solvent are handled explicitly, and yet in a computationally tractable way due to the dual particle-field nature of the LB solver. The suitability of the present LB-MD multiscale approach is demonstrated for the problem of polymer fast translocation through a nanopore. We also provide an interpretation of our results in the context of DNA translocation through a nanopore, a problem that has attracted much theoretical and experimental attention recently.

physics.bio-ph↗

arXiv2005

From Electrons to Finite Elements: A Concurrent Multiscale Approach for Metals

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 particular useful for systems where chemical interactions in a small region can affect the macroscopic properties of a material. We discuss how the coupling across different scales can be accomplished efficiently, and we apply the method to multiscale simulations of an edge dislocation in aluminum in the absence and presence of H impurities.

cond-mat.mtrl-sci↗

arXiv2005

Hydrogen Embrittlement of Aluminum: the Crucial Role of Vacancies

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 ductile solid. Our studies of hydrogen-induced vacancy superabundant formation and vacancy clusterization in aluminum lead to the conclusion that a large number of H atoms (up to twelve) can be trapped at a single vacancy, which over-compensates the energy cost to form the defect. In the presence of trapped H atoms, three nearest-neighbor single vacancies which normally would repel each other, aggregate to form a trivacancy on the slip plane of Al, acting as embryos for microvoids and cracks and resulting in ductile rupture along the these planes.

cond-mat.mtrl-sci↗

arXiv2004

Superconducting and charge-density wave instabilities in ultrasmall-radius carbon nanotubes

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 3.9, 4.7, and 6.8 Årespectively. The large curvature of the (5,0) CNTs makes them metallic with a large density of states at the Fermi energy. The density of states is also strongly enhanced for the (6,0) CNTs compared to the results obtained from the zone-folding method. For the (5,5) CNTs the electron-phonon interaction is dominated by the in-plane optical phonons, while for the ultrasmall (5,0) and (6,0) CNTs the main coupling is to the out-of-plane optical phonon modes. We calculate electron-phonon interaction strengths for all three types of CNTs and analyze possible instabilities toward superconducting and charge-density wave phases. For the smallest (5,0) nanotube, in the mean-field approximation and neglecting Coulomb interactions, we find that the charge-density wave transition temperature greatly exceeds the superconducting one. When we include a realistic model of the Coulomb interaction we find that the charge-density wave is suppressed to very low temperatures, making superconductivity dominant with the mean-field transition temperature around one K. For the (6,0) nanotube the charge-density wave dominates even with the inclusion of Coulomb interactions and we find the mean-field transition temperature to be around five Kelvin. We find that the larger radius (5,5) nanotube is stable against superconducting and charge-density wave orders at all realistic temperatures.

cond-mat.mes-hall↗

arXiv2004

Electron-phonon interaction in ultrasmall-radius carbon nanotubes

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 zone-folding method and the electron-phonon interaction is too small to support either a charge-density wave or superconductivity at realistic temperatures. For ultra-small (5,0) and (6,0) nanotubes we find that the large curvature makes these tubes metallic with a large density of states at the Fermi energy and leads to unusual electron-phonon interactions, with the dominant coupling coming from the out-of-plane phonon modes. By combining the frozen-phonon approximation with the RPA analysis of the giant Kohn anomaly in 1d we find parameters of the effective Frölich Hamiltonian for the conduction electrons. Neglecting Coulomb interactions, we find that the (5,5) CNT remains stable to instabilities of the Fermi surface down to very low temperatures while for the (5,0) and (6,0) CNTs a CDW instability will occur. When we include a realistic model of Coulomb interaction we find that the charge-density wave remains dominant in the (6,0) CNT with $T_{\rm CDW}$ around 5 K while the charge-density wave instability is suppressed to very low temperatures in the (5,0) CNT, making superconductivity dominant with transition temperature around one Kelvin.

cond-mat.supr-con↗

arXiv2004

Multiscale simulations in simple metals: a density-functional based methodology

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 multiscale simulations in which the part of the system requiring quantum-mechanical treatment is spatially confined to a small region. Such situations often arise in physical systems where chemical interactions in a small region can affect the macroscopic mechanical properties of a metal. We describe how this coupled treatment can be accomplished efficiently, and we present a coupled simulation for a bulk aluminum system.

cond-mat.mtrl-sci↗

arXiv2004

An Overview of Multiscale Simulations of Materials

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 status of multiscale simulations of materials. We categorize the different approaches in the spatial regime into sequential and concurrent, and we discuss in some detail representative methods in each category. We classify the multiscale modeling approaches that deal with the temporal scale into three different categories, and we discuss representative methods pertaining to the each of these categories. Finally, we offer some views on the strength and weakness of the multiscale approaches that are discussed, and touch upon some of the challenging multiscale modeling problems that need to be addressed in the future.

cond-mat.mtrl-sci↗

arXiv2003

Fast method for force computations in electronic structure calculations

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 forces, and the electron-ion contribution to the stress tensor. The present methods are applicable to calculations in which the electronic charge density is represented on a uniform grid in real space. They are particularly well-suited for metallic extended systems, where other O(N) methodologies are not readily applicable. Based on a fast algorithm for determining the atomic structure factor, originally developed by Essmann et al. (U. Essmann, L. Perera, et al.,J. Chem. Phys. v.103, p.8577 (1995)) for fast Ewald energy and force computation, the present methods involve approximations that can be systematically improved. The methods are tested on a representative metallic system (bulk Al),and their ability to simultaneously achieve high accuracy and efficiency is demonstrated.

cond-mat.mtrl-sci↗

arXiv2002

Electronic structure of overstretched DNA

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 ongoing experimental and theoretical efforts to characterize the conducting properties of DNA wires. We present quantum mechanical calculations for acidic, dry, poly(CG).poly(CG) DNA which has undergone elongation of up to 90 % relative to its natural length, along with a method for visualizing the effects of stretching on the electronic eigenstates. We find that overstretching leads to a drastic drop of the hopping matrix elements between localized occupied electronic states suggesting a dramatic decrease in the conductivity through holes.

cond-mat.mtrl-sci↗

arXiv2002

Can vacancies lubricate dislocation motion in aluminum?

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 theoretically the so-called vacancy lubrication effect on dislocation motion in Al, a discovery that can settle a long-standing controversy in dislocation theory for fcc metals. We provide insights on the lubrication effect by exploring the connection between dislocation mobility and its core width. We predict an increased dislocation splitting in the presence of vacancy. We find that on average there is a weak repulsion between vacancies and dislocations which is independent of dislocation character.

cond-mat.mtrl-sci↗

arXiv2001

Kinetic energy density functionals for non-periodic systems

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 problems associated with the application of widely used kinetic energy functionals to non-periodic systems. We develop a method that circumvents this difficulty and allows the kinetic energy to be evaluated entirely in real space. We demonstrate that the method is efficient [O(N)] and accurate by comparing the results of our real-space formulation to calculations performed in reciprocal space, and to calculations using traditional approaches based on electronic states.

cond-mat↗

arXiv2001

Energetics of hydrogen impurities in aluminum and their effect on mechanical properties

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 concentration of the stacking fault energy, the cleavage energy, the Al/H surface energy and the Al/H/Al interface formation energy. The results indicate a strong dependence of the slip energy barrier in the $[\bar 211]$ direction the cleavage energy in the [111] direction and the Al/H/Al interface formation energy, on H concentration and on tension. The dependence of the Al/H surface energy on H coverage is less pronounced, while the optimal H coverage is $\leq 0.25$ monolayer. The calculated activation energy for diffusion between high symmetry sites in the bulk and on the surface is practically the same, 0.167 eV. From these results, we draw conclusions about the possible effect of H impurities on mechanical properties, and in particular on their role in embrittlement of Al.

cond-mat.mtrl-sci↗

arXiv2001

Variational finite-difference representation of the kinetic energy operator

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 origin of this feature is the systematic underestimation of the kinetic energy by the finite difference representation of the Laplacian operator. We present an alternative representation that provides a rigorous upper bound estimate of the true kinetic energy and we illustrate its properties with a harmonic oscillator potential. For a more realistic application, we study the convergence of the total energy of bulk silicon using a real-space-grid density-functional code and employing both the conventional and the alternative representations of the kinetic energy operator.

cond-mat.mtrl-sci↗

arXiv2001

Hydrogen-enhanced local plasticity in aluminum: an ab initio study

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 dislocation emission from the crack tip but also enhances dislocation mobility dramatically, leading to macroscopically softening and thinning of the material ahead of the crack tip. We observe strong binding between H and dislocation cores, with the binding energy depending on dislocation character. This dependence can directly affect the mechanical properties of Al by inhibiting dislocation cross-slip and developing slip planarity.

cond-mat.mtrl-sci↗

arXiv2000

HARES: an efficient method for first-principles electronic structure calculations of complex systems

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 functional theory. This improved version which we call HARES (for High-performance-fortran Adaptive grid Real-space Electronic Structure) aims at making the method widely applicable and efficient, using high performance Fortran on parallel architectures. The scaling of various parts of a HARES calculation is analyzed and compared to that of plane-wave based methods. The new developments that lead to enhanced performance, and their parallel implementation, are presented in detail. We illustrate the application of HARES to the study of elemental crystalline solids, molecules and complex crystalline materials, such as blue bronze and zeolites.

cond-mat.mtrl-sci↗

arXiv2000

Thermodynamics of C incorporation on Si(100) from ab initio calculations

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 the important lowest energy structures, and a classical effective Hamiltonian which is employed to represent the long-range strain effects and incorporate the thermodynamic aspects. We determine the equilibrium phase diagram in temperature and C chemical potential, which allows us to predict the mesoscopic structure of the system that should be observed under experimentally relevant conditions.

cond-mat.mtrl-sci↗