J. S. Spencer

The khmer software package: enabling efficient nucleotide sequence analysis

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at https://github.com/dib-lab/khmer/.

Natural Orbitals for Wave Function Based Correlated Calculations Using a Plane Wave Basis Set

We demonstrate that natural orbitals allow for reducing the computational cost of wave function based correlated calculations, especially for atoms and molecules in a large box, when a plane wave basis set under periodic boundary conditions is used. The employed natural orbitals are evaluated on the level of second-order Møller-Plesset perturbation theory (MP2), which requires a computational effort that scales as [Formula: see text](N(5)), where N is a measure of the system size. Moreover, we find that a simple approximation reducing the scaling to [Formula: see text](N(4)) yields orbitals that allow for a similar reduction of the number of virtual orbitals. The MP2 natural orbitals are applied to coupled-cluster singles and doubles (CCSD) as well as full configuration interaction Quantum Monte Carlo calculations of the H2 molecule to test our implementation. Finally, the atomization energies of the LiH molecule and solid are calculated on the level of MP2 and CCSD.

The sign problem and population dynamics in the full configuration interaction quantum Monte Carlo method

The recently proposed full configuration interaction quantum Monte Carlo method allows access to essentially exact ground-state energies of systems of interacting fermions substantially larger than previously tractable without knowledge of the nodal structure of the ground-state wave function. We investigate the nature of the sign problem in this method and how its severity depends on the system studied. We explain how cancellation of the positive and negative particles sampling the wave function ensures convergence to a stochastic representation of the many-fermion ground state and accounts for the characteristic population dynamics observed in simulations.

Dispersion interactions between semiconducting wires

The dispersion energy between extended molecular chains (or equivalently infinite wires) with nonzero band gaps is generally assumed to be expressible as a pair-wise sum of atom-atom terms which decay as

Semi-stochastic full configuration interaction quantum Monte Carlo: developments and application

{R}^{\ensuremath{-}6}

Density-matrix quantum Monte Carlo method

. Using a model system of two parallel wires with a variable band gap, we show that this is not the case. The dispersion interaction scales as

Interaction picture density matrix quantum Monte Carlo

{z}^{\ensuremath{-}5}

The effect of quantization on the full configuration interaction quantum Monte Carlo sign problem.

for large interwire separations

Developments in stochastic coupled cluster theory: The initiator approximation and application to the uniform electron gas

z

Linked coupled cluster Monte Carlo

, as expected for an insulator, but as the band gap decreases the interaction is greatly enhanced; while at shorter (but nonoverlapping) separations it approaches a power-law scaling given by