Biomedical subjects

S T Pantelides

Publications and source records attributed to S T Pantelides.

At least 19 recordsLinked to original sources

PubMed2006

Selective nontemplated adsorption of organic molecules on nanofacets and the role of bonding patterns.

A key element of functionalizing nanocrystals with organic molecules is the nontemplated selective adsorption of different molecules on different facets. Here we report scanning-tunneling-microscopy images of perylene-3,4,9,10-tetracarboxylic-dianhydride and 2,5-dimethyl-N,N'-dicyanoquinonediimine on silver, demonstrating selective adsorption on different facets. We also report first-principles calculations that account for the data and show that bonding, which controls selectivity, occurs via the end atoms, while the molecule's midregion arches away from the substrate. The results are also consistent with data that have been interpreted in terms of bonding via the midregion.

Journal Article↗

PubMed2006

Oxygen migration, agglomeration, and trapping: key factors for the morphology of the Si-SiO(2) interface.

The measured activation energies for oxide growth rates at the initial and late stages of oxidation of Si are 2 and 1.2 eV, respectively. These values imply that oxidation can proceed at temperatures much smaller than the 800 degrees C normally used to obtain devices with exceptionally smooth Si-SiO2 interfaces. Here, we use first-principles calculations to identify the atomic-scale mechanisms of the 2 eV process and of additional processes with higher barriers that control the interface morphology and ultimately provide for smooth layer-by-layer oxide growth, as observed at high temperatures.

Journal Article↗

PubMed2005

First-principles mobility calculations and atomic-scale interface roughness in nanoscale structures.

Calculations of mobilities have so far been carried out using approximate methods that suppress atomic-scale detail. Such approaches break down in nanoscale structures. Here we report the development of a method to calculate mobilities using atomic-scale models of the structures and density functional theory at various levels of sophistication and accuracy. The method is used to calculate the effect of atomic-scale roughness on electron mobilities in ultrathin double-gate silicon-on-insulator structures. The results elucidate the origin of the significant reduction in mobility observed in ultrathin structures at low electron densities.

Journal Article↗

PubMed2005

Enhanced current transport at grain boundaries in high-T(c) superconductors.

Large-scale applications of high-transition-temperature (high-T(c)) superconductors, such as their use in superconducting cables, are impeded by the fact that polycrystalline materials (the only practical option) support significantly lower current densities than single crystals. The superconducting critical current density (J(c)) across a grain boundary drops exponentially if the misorientation angle exceeds 2 degrees -7 degrees. Grain texturing reduces the average misorientation angle, but problems persist. Adding impurities (such as Ca in YBa2Cu3O7-delta; YBCO) leads to increased J(c) (refs 9, 10), which is generally attributed to excess holes introduced by Ca2+ substituting for Y3+ (ref. 11). However, a comprehensive physical model for the role of grain boundaries and Ca doping has remained elusive. Here we report calculations, imaging and spectroscopy at the atomic scale that demonstrate that in poly-crystalline YBCO, highly strained grain-boundary regions contain excess O vacancies, which reduce the local hole concentration. The Ca impurities indeed substitute for Y, but in grain-boundary regions under compression and tension they also replace Ba and Cu, relieving strain and suppressing O-vacancy formation. Our results demonstrate that the ionic radii are more important than their electronic valences for enhancing J(c).

Journal Article↗

PubMed2005

Charging of molecules during transport.

The possibility that a single molecule can acquire charge during steady-state transport is an open issue. We report first-principles calculations in a range of configurations of certain molecules and conclude the following. When a molecule is strongly coupled to the electrodes, charging is not sustainable. On the other hand, by using variable-length tunnel barriers (insulating tethers) one can enable and control charging. In particular, by using different combinations of "tethers", we demonstrate the possibility of charging by a single electron, sustainable over a wide bias range, and also the possibility of continuous linear charging when a gate voltage is applied.

Biopolymers↗

PubMed2003

Role of electronic versus atomic relaxations in Stokes shifts at defects in solids.

Redshifts of luminescence relative to optical absorption bands (Stokes shifts) of molecules and of defects in solids are universally attributed to slow atomic relaxations on the grounds that electronic transitions are fast (Franck-Condon principle). Here we report a novel phenomenon that can occur only in the solid state: Stokes shifts caused by slow electronic relaxations. We demonstrate that the phenomenon occurs in the nonbridging oxygen defect in amorphous SiO2. We predict that another defect (OH group), which can exist in either crystalline or amorphous SiO2, has a similar Stokes shift, but it arises from a mix of lattice and electronic relaxations with manifest differences in the two phases.

Journal Article↗

PubMed2003

Nucleation of single-walled carbon nanotubes.

The nucleation pathway for single-wall carbon nanotubes on a metal surface is demonstrated by a series of total energy calculations using density functional theory. Incorporation of pentagons at an early stage of nucleation is energetically favorable as they reduce the number of dangling bonds and facilitate curvature of the structure and bonding to the metal. In the presence of the metal surface, nucleation of a closed cap or a capped single-wall carbon nanotube is overwhelmingly favored compared to any structure with dangling bonds or to a fullerene.

Journal Article↗

PubMed2002

Structure, properties, and dynamics of oxygen vacancies in amorphous SiO2.

Oxygen vacancies in SiO2 have long been regarded as bistable, forming a Si-Si dimer when neutral and a puckered configuration when positively charged. We report first-principles calculations of O vacancies in amorphous SiO2 supercells that unveil significantly more complex behavior. We find that the vast majority of O vacancies do not pucker after capture of a hole, but are shallow traps. The remaining vacancies exhibit two distinct types of puckering. Upon capturing an electron, one type forms a metastable dipole, while the other collapses to a dimer. A statistical distribution of O vacancies is obtained, and the implications for charge transport and trapping in SiO2 are discussed.

Journal Article↗

PubMed2002

Island shape selection in Pt(111) submonolayer homoepitaxy with or without CO as an adsorbate.

The microscopic selection mechanisms of single-layer island shapes in Pt(111) homoepitaxy with or without minute amounts of CO adsorbate have been investigated theoretically. For clean growth, only triangular islands of a fixed orientation are obtained within a wide range of growth temperatures, with the orientation uniquely determined by a disparity in the rates of atom supply to an island corner site from the two island edges defining the corner. This novel picture is further corroborated by growth predictions in the presence of CO, whose preferential decoration of one type of the island edges reverses the intrinsic rate disparity for atom supply, thereby inverting the island orientation.

Journal Article↗

PubMed2002

The role of the nanoscale in surface reactions: CO2 on CdSe.

Cd-rich CdSe nanocrystals below a critical size, under illumination, catalyze CO2 fixation, but bulk CdSe surfaces do not. We report first-principles calculations in which we determine the roles of faceting, deviations from stoichiometry, photoexcitation, and electron confinement, and the specific physics of the nanoscale. We further establish that catalysis does not occur at the nanocrystal surface; instead, neutral molecules adsorb, desorb negatively charged, and react elsewhere. Finally, we predict that n-type doped CdSe nanocrystals would be effective catalysts without photoexcitation.

Journal Article↗

PubMed2002

Diffusion mechanism of hydrogen in amorphous silicon: ab initio molecular dynamics simulation.

The mechanism of H migration in amorphous Si has remained an unresolved problem. The main issue is the small activation energy (1.5 eV) relative to the known strength of Si-H bonds (2-3.5 eV). We report first-principles finite-temperature simulations which demonstrate vividly that H is not released spontaneously, as proposed by most models, but awaits the arrival of a floating bond (FB). The "migrating species" is an FB-H complex, with H jumping from Si to Si and the FB literally floating around it. Migration stops when the FB veers away.

Journal Article↗

PubMed2002

Reactions and diffusion of water and oxygen molecules in amorphous SiO2.

Water and oxygen molecules determine many of the properties of amorphous SiO2 used in several technologies, but the underlying atomic-scale processes remain unresolved. We report results of first-principles calculations showing that a wide range of behavior is possible in an amorphous environment, including diffusion of the molecule as a whole and various reactions with the network. Experimental data including oxygen exchange reaction and radiation sensitivity are accounted for. The possibility of H3O+ formation as a source of positive charge is discussed.

Journal Article↗

PubMed2002

Current-induced forces in molecular wires.

We report first-principles calculations of current-induced forces in molecular wires for which experiments are available. We investigate, as an example, the effect of current-induced forces on a benzene molecule connected to two bulk electrodes via sulfur end groups. We find that the molecule twists around an axis perpendicular to its plane and undergoes a "breathing" oscillation at resonant tunneling via antibonding states. However, current-induced forces do not substantially affect the absolute value of the current for biases as high as 5 V, suggesting that molecular wires can operate at very large electric fields without current-induced breakdown.

Journal Article↗

PubMed2001

Defect generation by hydrogen at the Si- SiO(2) interface.

Hydrogen is known to passivate Si dangling bonds at the Si-SiO(2) interface, but the subsequent arrival of H(+) at the interface causes depassivation of Si-H bonds. Here we report first-principles density functional calculations, showing that, contrary to conventional assumptions, depassivation is not a two-step process, namely, neutralization of H(+) by a Si electron and subsequent formation of an H(2) molecule. Instead, we establish that H(+) is the only stable charge state at the interface and that H(+) reacts directly with Si-H, forming an H(2) molecule and a positively charged dangling bond (P(b) center). As a result, H-induced interface-trap formation does not depend on the availability of Si electrons.

Journal Article↗

PubMed2001

Interactions of hydrogen with CeO(2).

The interactions of hydrogen with ceria have been the subject of several experimental studies, but whether hydrogen atoms enter the bulk or are merely chemisorbed on the surfaces is disputed. We combine first-principles calculations with thermodynamic arguments and conclude that the uptake of small amounts of hydrogen by ceria is spontaneous below 665 K. The calculations also predict that hydrogen atoms within the bulk form hydroxyl groups and slightly expand the lattice. The predicted hydrogen content, OH vibrational frequency, and ceria lattice expansion upon hydrogen uptake are consistent with available data.

Journal Article↗

PubMed2001

Atomic-scale dynamics of the formation and dissolution of carbon clusters in SiO(2).

Oxidation of SiC produces SiO(2) while CO is released. A "reoxidation" step at lower temperatures is, however, necessary to produce high-quality SiO(2). This step is believed to cleanse the oxide of residual C without further oxidation of the SiC substrate. We report first-principles calculations that describe the nucleation and growth of O-deficient C clusters in SiO(2) under oxidation conditions, fed by the production of CO at the advancing interface, and their gradual dissolution by the supply of O under reoxidation conditions. We predict that both CO and CO(2) are released during both steps.

Journal Article↗

PubMed2001

Control of doping by impurity Cchemical potentials: predictions for p-type ZnO.

Theoretical work has so far focused on the role of host-element chemical potentials in determining defect formation energies that control doping levels in semiconductors. Here, we report on our analysis of the role of the dopant-impurity chemical potential, which depends on the source gas. We present first-principles total-energy calculations that demonstrate a wide variation in the possible effective chemical potential of N. We account in detail for the recent puzzling observations of doping ZnO using N2 and N2O and predict that the use of dilute NO or NO2 gas would resolve the long-standing problem of achieving p-type ZnO.

Journal Article↗

PubMed2001

Nonstoichiometry and the electrical activity of grain boundaries in SrTiO3.

A combination of experiments and first-principles calculations is used to show that grain boundaries in SrTiO3 are intrinsically nonstoichiometric. Total-energy calculations reveal that the introduction of nonstoichiometry into the grain boundaries is energetically favorable and results in structures that are consistent with atomic-resolution Z-contrast micrographs. Electron energy-loss spectra provide direct evidence of nonstoichiometry. These results and calculations for nonstoichiometric grain boundaries provide an explanation of the microscopic origin of the "double Schottky barriers" that dominate the electrical behavior of polycrystalline oxides.

Journal Article↗