Biomedical subjects

Efthimios Kaxiras

Publications and source records attributed to Efthimios Kaxiras.

13 recordsLinked to original sources

PubMed2007

DNA nucleoside interaction and identification with carbon nanotubes.

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 nucleosides on CNTs based on measurement of electronic features through a local probe such as scanning tunneling spectroscopy. We demonstrate through quantum mechanical calculations that these measurements can achieve 100% efficiency in identifying DNA bases. Our results support the practicality of ultrafast DNA sequencing using electrical measurements.

DNA↗

PubMed2006

Structural model of eumelanin.

Melanin is a ubiquitous pigment in living organisms with multiple important functions, yet its structure is not well understood. We propose a structural model for eumelanin protomolecules, consisting of 4 or 5 of the basic molecular units (hydroquinone, indolequinone, and its tautomers), in arrangements that contain an inner porphyrin ring. We use time-dependent density functional theory to calculate the optical absorption spectrum of the structural model, which reproduces convincingly the main features of the experimental spectrum of eumelanin. Our model also reproduces accurately other important properties of eumelanin, including x-ray scattering data, its ability to capture and release metal ions, and the characteristic size of the protomolecules.

Animals↗

PubMed2006

Rich coordination chemistry of Au adatoms in gold sulfide monolayer on Au(111).

The rich chemistry of Au nanoparticles and ions has attracted tremendous interest, in part because the surfaces of bulk Au have traditionally been considered to be chemically inert. On the other hand, large-scale mass transport and the formation of vacancy islands have been observed on the Au(111) surface following the deposition of adsorbates, such as sulfur and thiols, that can interact strongly with the Au surface. In this work, we revisit the structure and chemistry of an ordered incommensurate AuS adlayer that forms on Au(111) following the deposition of sulfur and annealing to 450 K. A structural model of this AuS surface phase has not yet been determined experimentally due to the complexity of the system. Here, we use state-of-the-art density functional theory to develop an atomic-scale model that is consistent with the previously reported Au-S stoichiometry. In particular, we introduce theoretical techniques to take into account the charge transfer in an incommensurate system. Our model reproduces convincingly STM images and is remarkably robust. Bonding analysis based on Wannier functions shows that the model exhibits rich coordination chemistry corresponding to different Au oxidation states. The extraordinary stability and rich chemistry of this structure have implications for related S-Au interfaces and previously reported surface features of this system.

Letter↗

PubMed2006

Tuning solid surfaces from hydrophobic to superhydrophilic by submonolayer surface modification.

Molecular-scale understanding and manipulation of the wetting behavior of water on solids remains a fundamental challenge. Using diamond as a model system, we show that the naturally hydrophobic behavior of a hydrogen-terminated C(111) surface can be manipulated by replacing the H termination with a monolayer of adsorbate. In particular, a mixed monolayer of 1/3 Na and 2/3 F atoms leads to superhydrophilic behavior, as shown by first-principles calculations. The physical origin of the superhydrophilic behavior is attributed to the ionic nature of the Na adatoms, which mediate the right degree of binding strength between water molecules and the substrate.

Journal Article↗

PubMed2006

The nature of contact between Pd leads and semiconducting carbon nanotubes.

The contact between semiconducting single-wall carbon nanotubes (SWCNTs) and metallic leads is of central importance to potential electronic device applications. We investigate the nature of the contact of SWCNTs with Pd leads in a fully covered geometry that closely resembles experimental setups. We employ first-principles calculations within density functional theory to obtain the equilibrium structure for representative semiconducting SWCNTs embedded in Pd and analyze their electronic structure features, charge-transfer effects, electrostatic potentials, and Fermi level alignment at the interfaces with the metal contact. We find that there is no electrostatic or Schottky-type barrier to electron transfer between the metal and the nanotube.

Nanotubes, Carbon↗

PubMed2005

Orbital-free density functional theory applied to NaAlH4.

We present the application of orbital-free density functional theory (OF-DFT) to NaAlH(4), a potential hydrogen storage material, and related systems. Although the simple Al and NaH structures are reproduced reasonably well by OF-DFT, the approach fails for the more complex NaAlH(4) structure. Calculations on AlH(3) show that the failure to describe the Al-H interaction is related to the kinetic energy functionals used rather than the local pseudopotentials which are required within the OF-DFT approach. Thus, systems such as NaAlH(4) present a challenge which awaits the development of more reliable orbital-free kinetic energy functionals.

Journal Article↗

PubMed2005

Kinetic pathway for the formation of fe nanowires on stepped Cu111 surfaces.

We report the discovery of a novel kinetic pathway for the formation of one-dimensional Fe nanowires of single atom width on stepped Cu(111) surfaces. This pathway, identified through extensive total-energy calculations within density functional theory, establishes that the stable structure involves a row of Fe atoms on the upper edge of a step. The formation of the surface wire is preceded by facile incorporation of an initial row of Fe atoms into the surface layer at one lateral lattice constant away from the step edge, which then acts as an attractor for the second exposed row of atoms. The resulting wire structure provides a natural interpretation of existing experimental results. We also explore the applicability of this mechanism in the formation of other related systems.

Journal Article↗

PubMed2005

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 12) can be trapped at a single vacancy, which overcompensates 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 these planes.

Journal Article↗

PubMed2005

A TDDFT study of the optical response of DNA bases, base pairs, and their tautomers in the gas phase.

We present calculations of the optical response of the DNA bases and base pairs both in their normal and tautomeric forms in the gas phase, using time-dependent density functional theory (TDDFT). These calculations are performed in real time within the adiabatic approximation with a basis of local orbitals. Our results for the individual bases are in good agreement with experiment and computationally more demanding calculations of chemical accuracy. The optical response of base pairs indicates that the differences between normal and tautomeric forms in certain cases are significant enough to provide a means of identification.

Adenine↗

PubMed2005

Carbon nanotube interaction with DNA.

We investigate a system consisting of B-DNA and an array of (10,0) carbon nanotubes periodically arranged to fit into the major groove of the DNA. We obtain an accurate electronic structure of the combined system, which reveals that it is semiconducting and that the bands on either end of the gap are derived exclusively from one of the two components. We discuss in detail how this system can be used as either an electronic switch involving transport through both components, or as a device for ultrafast DNA sequencing.

Computer Simulation↗

PubMed2004

Contrasting growth modes of Mn on Ge(100) and Ge(111) surfaces: subsurface segregation versus intermixing.

Based on first-principles total energy calculations within density functional theory, we show that a low dose of Mn on Ge(100) initiates in a novel subsurface growth mode, characterized by easy access to, and strong preference for, interstitial sites located between the two topmost Ge layers. Strikingly, such a "subsurfactant action" is preserved even during epitaxial growth of additional Ge layers, analogous to the well-known phenomenon of surfactant action. In contrast, along the [111] orientation, Mn can easily diffuse into the bulk via interstitial sites. These results are discussed within the context of dopant control in dilute magnetic semiconductors.

Journal Article↗

PubMed2003

Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis.

Parameters for the zinc ion have been developed in the self-consistent charge density functional tight-binding (SCC-DFTB) framework. The approach was tested against B3LYP calculations for a range of systems, including small molecules that contain the typical coordination environment of zinc in biological systems (cysteine, histidine, glutamic/aspartic acids, and water) and active site models for a number of enzymes such as alcohol dehydrogenase, carbonic anhydrase, and aminopeptidase. The SCC-DFTB approach reproduces structural and energetic properties rather reliably (e.g., total and relative ligand binding energies and deprotonation energies of ligands and barriers for zinc-assisted proton transfers), as compared with B3LYP/6-311+G** or MP2/6-311+G** calculations.

Alcohol Dehydrogenase↗

PubMed2002

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 into 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.

Journal Article↗