Using SCF metadynamics to extend density matrix embedding theory to excited states.

A new framework based on density matrix embedding theory (DMET) capable of directly targeting excited electronic states is proposed and implemented. DMET has previously been shown to be an effective method of calculating the ground state energies of systems exhibiting strong static correlation but has never been applied to calculate excited state energies. In this work, the Schmidt decomposition is applied directly on excited states, approximated by higher lying self-consistent field solutions. The DMET prescription is applied following this Schmidt decomposition allowing for a direct embedding of excited states. Initial results are obtained for a system of multiple hydrogen dimers and the lithium hydride dissociation. We analyze the nature of each part of the excited state DMET calculation and identify challenges. These challenges to the implementation of excited state DMET are discussed, and potential suggestions moving forward are recommended

Long-range interactions from the many-pair expansion: A different avenue to dispersion in DFT

One of the several problems that plague majority of density functional theory calculations is their inability to properly account for long-range correlations giving rise to dispersion forces. The recently proposed many-pair expansion (MPE) [T. Zhu et al., Phys. Rev. B 93, 201108(R) (2016)] is a hierarchy of approximations that systematically corrects any deficiencies of an approximate functional to finally converge to the exact energy. This is achieved by decomposing the total density into a sum of two-electron densities and accounting for successive two-, four-, six-,… electron interactions. Here, we show that already low orders of MPE expansion recover the dispersion energy accurately. To this end, we employ the Pariser-Parr-Pople Hamiltonian and study the behavior of long-range interactions in trans-polyacetylene as well as stacks of ethylene and benzene molecules. We also show how convergence of the expansion is affected by electron conjugation and the choice of the density partitioning.National Science Foundation (U.S.) (Grant CHE-1464804

An extension of the coupled-cluster method: A variational formalism

A general quantum many-body theory in configuration space is developed by extending the traditional coupled cluter method (CCM) to a variational formalism. Two independent sets of distribution functions are introduced to evaluate the Hamiltonian expectation. An algebraic technique for calculating these distribution functions via two self-consistent sets of equations is given. By comparing with the traditional CCM and with Arponen's extension, it is shown that the former is equivalent to a linear approximation to one set of distribution functions and the later is equivalent to a random-phase approximation to it. In additional to these two approximations, other higher-order approximation schemes within the new formalism are also discussed. As a demonstration, we apply this technique to a quantum antiferromagnetic spin model.Comment: 15 pages. Submitted to Phys. Rev.

Spin Resolution of the Electron-Gas Correlation Energy: Positive same-spin contribution

The negative correlation energy per particle of a uniform electron gas of density parameter $r_s$ and spin polarization $\zeta$ is well known, but its spin resolution into up-down, up-up, and down-down contributions is not. Widely-used estimates are incorrect, and hamper the development of reliable density functionals and pair distribution functions. For the spin resolution, we present interpolations between high- and low-density limits that agree with available Quantum Monte Carlo data. In the low-density limit for $\zeta = 0$, we find that the same-spin correlation energy is unexpectedly positive, and we explain why. We also estimate the up and down contributions to the kinetic energy of correlation.Comment: new version, to appear in PRB Rapid Communicatio

TDR Targets: a chemogenomics resource for neglected diseases

The TDR Targets Database (http://tdrtargets.org) has been designed and developed as an online resource to facilitate the rapid identification and prioritization of molecular targets for drug development, focusing on pathogens responsible for neglected human diseases. The database integrates pathogen specific genomic information with functional data (e.g. expression, phylogeny, essentiality) for genes collected from various sources, including literature curation. This information can be browsed and queried using an extensive web interface with functionalities for combining, saving, exporting and sharing the query results. Target genes can be ranked and prioritized using numerical weights assigned to the criteria used for querying. In this report we describe recent updates to the TDR Targets database, including the addition of new genomes (specifically helminths), and integration of chemical structure, property and bioactivity information for biological ligands, drugs and inhibitors and cheminformatic tools for querying and visualizing these chemical data. These changes greatly facilitate exploration of linkages (both known and predicted) between genes and small molecules, yielding insight into whether particular proteins may be druggable, effectively allowing the navigation of chemical space in a genomics context

Solution structure of an arsenate reductase-related protein, YffB, from Brucella melitensis, the etiological agent responsible for brucellosis

B. melitensis is a NIAID Category B microorganism that is responsible for brucellosis and is a potential agent for biological warfare. Here, the solution structure of the 116-residue arsenate reductase-related protein Bm-YffB (BR0369) from this organism is reported