Driving forces for transmembrane alpha-helix oligomerization.

We present what we believe to be a novel statistical contact potential based on solved structures of transmembrane (TM) alpha-helical bundles, and we use this contact potential to investigate the amino acid likelihood of stabilizing helix-helix interfaces. To increase statistical significance, we have reduced the full contact energy matrix to a four-flavor alphabet of amino acids, automatically determined by our methodology, in which we find that polarity is a more dominant factor of group identity than is size, with charged or polar groups most often occupying the same face, whereas polar/apolar residue pairs tend to occupy opposite faces. We found that the most polar residues strongly influence interhelical contact formation, although they occur rarely in TM helical bundles.

An implicit solvent coarse-grained lipid model with correct stress profile.

We develop a coarse-grained parametrization strategy for lipid membranes that we illustrate for a dipalmitoylphosphatidylcholine bilayer. Our coarse-graining approach eliminates the high cost of explicit solvent but maintains more lipid interaction sites. We use a broad attractive tail-tail potential and extract realistic bonded potentials of mean force from all-atom simulations, resulting in a model with a sharp gel to fluid transition, a correct bending modulus, and overall very reasonable dynamics when compared with experiment.

Predicting accurate electronic excitation transfer rates via marcus theory with Boys or Edmiston-Ruedenberg localized diabatization.

We model the triplet-triplet energy-transfer experiments from the Closs group [ Closs , G. L. ; et al.

Hartree-Fock exchange computed using the atomic resolution of the identity approximation.

In this work, we apply the atomic resolution of the identity (ARI) fitting approximation to the computation of Hartree-Fock exchange. The ARI approximation is a local modification of the RI approximation that produces an energy which is differentiable with respect to nuclear motion, unlike other local applications of RI. We justify empirically the use of locality and present timing comparisons of ARI, RI, and exact computation for one-, two-, and three-dimensional carbon systems.

The limits of local correlation theory: electronic delocalization and chemically smooth potential energy surfaces.

Local coupled-cluster theory provides an algorithm for measuring electronic correlation quickly, using only the spatial locality of localized electronic orbitals. Previously, we showed [J. Subotnik et al.

Localized orbital theory and ammonia triborane.

In a previous paper [J. Subotnik, Y. Shao and W.

Linear scaling density fitting.

Two modifications of the resolution of the identity (RI)/density fitting (DF) approximations are presented. First, we apply linear scaling and J-engine techniques to speed up traditional DF. Second, we develop an algorithm that produces local, accurate fits with effort that scales linearly with system size.

A near linear-scaling smooth local coupled cluster algorithm for electronic structure.

We demonstrate near linear scaling of a new algorithm for computing smooth local coupled-cluster singles-doubles (LCCSD) correlation energies of quantum mechanical systems. The theory behind our approach has been described previously, [J. Subotnik and M.

A Fast Implementation of Perfect Pairing and Imperfect Pairing Using the Resolution of the Identity Approximation.

We present an efficient implementation of the perfect pairing and imperfect pairing coupled-cluster methods, as well as their nuclear gradients, using the resolution of the identity approximation to calculate two-electron integrals. The perfect pairing and imperfect pairing equations may be solved rapidly, making integral evaluation the bottleneck step. The method's efficiency is demonstrated for a series of linear alkanes, for which we show significant speed-ups (of approximately a factor of 10) with negligible error.

Unrestricted perfect pairing: the simplest wave-function-based model chemistry beyond mean field.

The perfect pairing (PP) approximation from generalized valence bond theory is formulated in an unrestricted fashion for both closed- and open-shell systems using a coupled cluster ansatz. In the model chemistry proposed here, active electron pairs are correlated, but the unpaired or radical electrons remain uncorrelated, leading to a linear number of decoupled cluster amplitudes which can be solved for analytically. The alpha and beta spatial orbitals are variationally optimized independently.

Auxiliary basis expansions for large-scale electronic structure calculations.

One way to reduce the computational cost of electronic structure calculations is to use auxiliary basis expansions to approximate four-center integrals in terms of two- and three-center integrals, usually by using the variationally optimum Coulomb metric to determine the expansion coefficients. However, the long-range decay behavior of the auxiliary basis expansion coefficients has not been characterized. We find that this decay can be surprisingly slow.