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The valine-activation domain-encoding portion of the srfA locus (srfA-d4) is not only involved in the non-ribosomal synthesis of surfactin, but is also required for the regulation of competence development. In this study we show that impairment of the adenylation activity of the valine-activating domain did not affect competence development. Deletion(More)
SH3 domains are small protein modules of 60–85 amino acids that bind to short proline-rich sequences with moderate-to-low affinity and specificity. Interactions with SH3 domains play a crucial role in regulation of many cellular processes (some are related to cancer and AIDS) and have thus been interesting targets in drug design. The decapeptide APSYSPPPPP(More)
The random phase approximation (RPA) is an increasingly popular post-Kohn-Sham correlation method, but its high computational cost has limited molecular applications to systems with few atoms. Here we present an efficient implementation of RPA correlation energies based on a combination of resolution of the identity (RI) and imaginary frequency integration(More)
The basis set convergence of energy differences obtained from the random phase approximation (RPA) to the correlation energy is investigated for a wide range of molecular interactions. For dispersion bound systems the basis set incompleteness error is most pronounced, as shown for the S22 benchmark [P. Jurecka et al., Phys. Chem. Chem. Phys. 8, 1985(More)
We present a formally exact van der Waals inclusive electronic structure theory, called FDE-vdW, based on the Frozen Density Embedding formulation of subsystem Density-Functional Theory. In subsystem DFT, the energy functional is composed of subsystem additive and non-additive terms. We show that an appropriate definition of the long-range correlation(More)
Restricted and unrestricted forms of time-dependent Hartree-Fock theory have been implemented and used to study the electronic dynamics of ethene, benzene, and the formaldehyde cation subjected to both weak and strong oscillating electric fields. Absorption spectra and frequency-dependent polarizabilities are calculated via the instantaneous dipole moment(More)
Henk Eshuis, Julian Yarkony, and Filipp Furche Department of Chemistry, University of California, Irvine, CA 92697, USA (Dated: February 23, 2010) Abstract The random phase approximation (RPA) is an increasingly popular method to compute postKohn-Sham correlation energies, but its high computational cost has limited molecular applications to systems with(More)
Performance of the random phase approximation (RPA) is tested for thermochemistry and geometries of transition-metal chemistry using various benchmarks obtained either computationally or experimentally. Comparison is made to popular (semi)local meta- and hybrid density functionals as well as to the second-order Møller-Plesset perturbation theory (MP2) and(More)
The random phase approximation (RPA) is an increasingly popular method for computing molecular ground-state correlation energies within the adiabatic connection fluctuation-dissipation theorem framework of density functional theory. We present an efficient analytical implementation of first-order RPA molecular properties and nuclear forces using the(More)
In this work we address the influence of the initial state on electron transfer dynamics by comparing two different ways of setting up the initial state, namely by taking an electron from the HOMO of a DFT ground state, or by using constrained DFT to self-consistently create the initial state. We solve the TDKS equations for the benzyl-pentafluorobenzene(More)
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