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Hoang K.,North Dakota State University | Johannes M.D.,Center for Computational Materials Science
Journal of Materials Chemistry A | Year: 2014

We report a comprehensive first-principles study of the thermodynamics and transport of intrinsic point defects in layered oxide cathode materials LiMO2 (M = Co, Ni), using density-functional theory and the Heyd-Scuseria-Ernzerhof screened hybrid functional. We find that LiCoO 2 has a complex defect chemistry; different electronic and ionic defects can exist under different synthesis conditions, and LiCoO2 samples free of cobalt antisite defects can be made under Li-excess (Co-deficient) environments. A defect model for lithium over-stoichiometric LiCoO2 is also proposed, which involves negatively charged lithium antisites and positively charged small (hole) polarons. In LiNiO2, a certain amount of Ni3+ ions undergo charge disproportionation and the concentration of nickel ions in the lithium layers is high. Tuning the synthesis conditions may reduce the nickel antisites but would not remove the charge disproportionation. In addition, we find that LiMO2 cannot be doped n- or p-type; the electronic conduction occurs via hopping of small polarons and the ionic conduction occurs via migration of lithium vacancies, either through a monovacancy or divacancy mechanism, depending on the vacancy concentration. © 2014 the Partner Organisations.

Kim Y.C.,Center for Computational Materials Science | Mittal J.,Lehigh University
Physical Review Letters | Year: 2013

A statistical mechanical theory is presented to predict the effects of macromolecular crowding on protein association equilibria, accounting for both excluded volume and attractive interactions between proteins and crowding molecules. Predicted binding free energies are in excellent agreement with simulation data over a wide range of crowder sizes and packing fractions. It is shown that attractive interactions between proteins and crowding agents counteract the stabilizing effects of excluded volume interactions. A critical attraction strength, for which there is no net effect of crowding, is approximately independent of the crowder packing fraction. © 2013 American Physical Society.

Ott F.D.,ETH Zurich | Spiegel L.L.,ETH Zurich | Norris D.J.,ETH Zurich | Erwin S.C.,Center for Computational Materials Science
Physical Review Letters | Year: 2014

Although poorly understood, cation-exchange reactions are increasingly used to dope or transform colloidal semiconductor nanocrystals (quantum dots). We use density-functional theory and kinetic Monte Carlo simulations to develop a microscopic theory that explains structural, optical, and electronic changes observed experimentally in Ag-cation-exchanged CdSe nanocrystals. We find that Coulomb interactions, both between ionized impurities and with the polarized nanocrystal surface, play a key role in cation exchange. Our theory also resolves several experimental puzzles related to photoluminescence and electrical behavior in CdSe nanocrystals doped with Ag. © 2014 American Physical Society.

Kim Y.C.,Center for Computational Materials Science | Hummer G.,U.S. National Institute of Diabetes and Digestive and Kidney Diseases
Biochimica et Biophysica Acta - Bioenergetics | Year: 2012

Cytochrome c oxidase is an efficient energy transducer that reduces oxygen to water and converts the released chemical energy into an electrochemical membrane potential. As a true proton pump, cytochrome c oxidase translocates protons across the membrane against this potential. Based on a wealth of experiments and calculations, an increasingly detailed picture of the reaction intermediates in the redox cycle has emerged. However, the fundamental mechanism of proton pumping coupled to redox chemistry remains largely unresolved. Here we examine and extend a kinetic master-equation approach to gain insight into redox-coupled proton pumping in cytochrome c oxidase. Basic principles of the cytochrome c oxidase proton pump emerge from an analysis of the simplest kinetic models that retain essential elements of the experimentally determined structure, energetics, and kinetics, and that satisfy fundamental physical principles. The master-equation models allow us to address the question of how pumping can be achieved in a system in which all reaction steps are reversible. Whereas proton pumping does not require the direct modulation of microscopic reaction barriers, such kinetic gating greatly increases the pumping efficiency. Further efficiency gains can be achieved by partially decoupling the proton uptake pathway from the active-site region. Such a mechanism is consistent with the proposed Glu valve, in which the side chain of a key glutamic acid shuttles between the D channel and the active-site region. We also show that the models predict only small proton leaks even in the absence of turnover. The design principles identified here for cytochrome c oxidase provide a blueprint for novel biology-inspired fuel cells, and the master-equation formulation should prove useful also for other molecular machines. This article is part of a Special Issue entitled: Respiratory Oxidases. © 2011 Elsevier B.V. All rights reserved.

Young S.M.,Center for Computational Materials Science | Kane C.L.,University of Pennsylvania
Physical Review Letters | Year: 2015

Graphene is famous for being a host of 2D Dirac fermions. However, spin-orbit coupling introduces a small gap, so that graphene is formally a quantum spin Hall insulator. Here we present symmetry-protected 2D Dirac semimetals, which feature Dirac cones at high-symmetry points that are not gapped by spin-orbit interactions and exhibit behavior distinct from both graphene and 3D Dirac semimetals. Using a two-site tight-binding model, we construct representatives of three possible distinct Dirac semimetal phases and show that single symmetry-protected Dirac points are impossible in two dimensions. An essential role is played by the presence of nonsymmorphic space group symmetries. We argue that these symmetries tune the system to the boundary between a 2D topological and trivial insulator. By breaking the symmetries we are able to access trivial and topological insulators as well as Weyl semimetal phases. © 2015 American Physical Society.

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