Orbital eigenchannel analysis for ab-initio quantum transport calculations

We show how to extract the orbital contribution to the transport eigenchannels from a first-principles quantum transport calculation in a nanoscopic conductor. This is achieved by calculating and diagonalizing the first-principles transmission matrix reduced to selected scattering cross-sections. As an example, the orbital nature of the eigenchannels in the case of Ni nanocontacts is explored, stressing the difficulties inherent to the use of non-orthogonal basis sets and first-principles Hamiltonians.Comment: 5 pages, 5 figurs; replaced with final version, introduction revised; to be published in PR

Creation of macroscopic superpositions of flow states with Bose-Einstein condensates

We present a straightforward scheme for creating macroscopic superpositions of different superfluid flow states of Bose-Einstein condensates trapped in optical lattices. This scheme has the great advantage that all the techniques required are achievable with current experiments. Furthermore, the relative difficulty of creating cats scales favorably with the size of the cat. This means that this scheme may be well-suited to creating superpositions involving large numbers of particles. Such states may have interesting technological applications such as making quantum-limited measurements of angular momentum.Comment: 9 pages, 7 figure

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein-ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0

Magnetic and orbital blocking in Ni nanocontacts

We address the fundamental question of whether magneto-resistance (MR) of atomic-sized contacts of Nickel is very large because of the formation of a domain wall (DW) at the neck. Using {\em ab initio} transport calculations we find that, as in the case of non-magnetic electrodes, transport in Ni nanocontacts depends very much on the orbital nature of the electrons. Our results are in agreement with several experiments in the average value of the conductance. On the other hand, contrary to existing claims, DW scattering does {\em not} account for large MR in Ni nanocontacts.Comment: 5 pages, 3 Figure

Realizable Hamiltonians for Universal Adiabatic Quantum Computers

It has been established that local lattice spin Hamiltonians can be used for universal adiabatic quantum computation. However, the 2-local model Hamiltonians used in these proofs are general and hence do not limit the types of interactions required between spins. To address this concern, the present paper provides two simple model Hamiltonians that are of practical interest to experimentalists working towards the realization of a universal adiabatic quantum computer. The model Hamiltonians presented are the simplest known QMA-complete 2-local Hamiltonians. The 2-local Ising model with 1-local transverse field which has been realized using an array of technologies, is perhaps the simplest quantum spin model but is unlikely to be universal for adiabatic quantum computation. We demonstrate that this model can be rendered universal and QMA-complete by adding a tunable 2-local transverse XX coupling. We also show the universality and QMA-completeness of spin models with only 1-local Z and X fields and 2-local ZX interactions.Comment: Paper revised and extended to improve clarity; to appear in Physical Review

Transport in magnetically ordered Pt nanocontacts

Pt nanocontacts, like those formed in mechanically controlled break junctions, are shown to develop spontaneous local magnetic order. Our density functional calculations predict that a robust local magnetic order exists in the atoms presenting low coordination, i. e., those forming the atom-sized neck. In contrast to previous work, we thus find that the electronic transport can be spin-polarized, although the net value of the conductance still agrees with available experimental information. Experimental implications of the formation of this new type of nanomagnet are discussed.Comment: 4 pages, 3 figure

A Deformable Model for Magnetic Vortex Pinning

A two-parameter analytical model of the magnetic vortex in a thin disk of soft magnetic material is constructed. The model is capable of describing the change in evolution of net vortex state magnetization and of core position when the vortex core interacts with a magnetic pinning site. The model employs a piecewise, physically continuous, magnetization distribution obtained by the merger of two extensively used one-parameter analytical models of the vortex state in a disk. Through comparison to numerical simulations of ideal disks with and without pinning sites, the model is found to accurately predict the magnetization, vortex position, hysteretic transitions, and 2-D displacement of the vortex in the presence of pinning sites. The model will be applicable to the quantitative determination of vortex pinning energies from measurements of magnetization.Comment: 27 pages, 7 figures, including supplementary information, ancillary files:3 supplementary movie