CheMPS2: a free open-source spin-adapted implementation of the density matrix renormalization group for ab initio quantum chemistry

The density matrix renormalization group (DMRG) has become an indispensable numerical tool to find exact eigenstates of finite-size quantum systems with strong correlation. In the fields of condensed matter, nuclear structure and molecular electronic structure, it has significantly extended the system sizes that can be handled compared to full configuration interaction, without losing numerical accuracy. For quantum chemistry (QC), the most efficient implementations of DMRG require the incorporation of particle number, spin and point group symmetries in the underlying matrix product state (MPS) ansatz, as well as the use of so-called complementary operators. The symmetries introduce a sparse block structure in the MPS ansatz and in the intermediary contracted tensors. If a symmetry is non-abelian, the Wigner-Eckart theorem allows to factorize a tensor into a Clebsch-Gordan coefficient and a reduced tensor. In addition, the fermion signs have to be carefully tracked. Because of these challenges, implementing DMRG efficiently for QC is not straightforward. Efficient and freely available implementations are therefore highly desired. In this work we present CheMPS2, our free open-source spin-adapted implementation of DMRG for ab initio QC. Around CheMPS2, we have implemented the augmented Hessian Newton-Raphson complete active space self-consistent field method, with exact Hessian. The bond dissociation curves of the 12 lowest states of the carbon dimer were obtained at the DMRG(28 orbitals, 12 electrons, D$_{\mathsf{SU(2)}}$=2500)/cc-pVDZ level of theory. The contribution of $1s$ core correlation to the $X^1\Sigma_g^+$ bond dissociation curve of the carbon dimer was estimated by comparing energies at the DMRG(36o, 12e, D$_{\mathsf{SU(2)}}$=2500)/cc-pCVDZ and DMRG-SCF(34o, 8e, D$_{\mathsf{SU(2)}}$=2500)/cc-pCVDZ levels of theory.Comment: 16 pages, 13 figure

Matrix product states and their uses in quantum chemistry

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Longitudinal static optical properties of hydrogen chains: finite field extrapolations of matrix product state calculations

We have implemented the sweep algorithm for the variational optimization of SU(2) x U(1) (spin and particle number) invariant matrix product states (MPS) for general spin and particle number invariant fermionic Hamiltonians. This class includes non-relativistic quantum chemical systems within the Born-Oppenheimer approximation. High-accuracy ab-initio finite field results of the longitudinal static polarizabilities and second hyperpolarizabilities of one-dimensional hydrogen chains are presented. This allows to assess the performance of other quantum chemical methods. For small basis sets, MPS calculations in the saturation regime of the optical response properties can be performed. These results are extrapolated to the thermodynamic limit.Comment: Submitted to J. Chem. Phy

Wave function Monte Carlo method for polariton condensates

We present a quantum jump approach to describe coupled quantum and classical systems in the context of Bose-Einstein condensation in the solid state. In our formalism, the excitonic gain medium is described by classical rate equations, while the polariton modes are described fully quantum mechanically. We show the equivalence of our method with a master equation approach. As an application, we compute the linewidth of a single mode polariton condensate. Both the line broadening due to the interactions between polaritons and the interactions with the reservoir excitons is taken into account.Comment: 6 pages, 2 figure

Guide for the identification of archaeological sea sturgeon (<i>Acipenser sturio</i> and <i>A. oxyrinchus</i>) remains

Remains of sturgeons (Acipenser sturio and A. oxyrinchus) are regularly found on western European archaeological sites. The identification of these isolated bones should ideally be carried out with the aid of a comparative skeletal collection, consisting of modern specimens of different sizes. Because such reference material of sea sturgeons (A. sturio and A. oxyrinchus) is relatively rare and dispersed over many different museums and institutes, a practical guide is presented here as an aid to the identification of the most commonly found archaeological sturgeon remains. This guide, which is based on observations made on 64 individuals housed in 13 different natural history collections, should allow identifying most archaeological sturgeon remains from western European sites. Presented are the morphological characteristics of the bones of the skull roof and circumorbital region (posttemporal, dermopterotic, parietal, frontal, dermosphenotic, postorbital, jugal and supraorbital), bones of the braincase (parasphenoid), opercular series (subopercle and branchiostegals), the palatoquadrate and associated bones and lower jaw (palatopterygoid, dermopalatine and dentary), the hyoid and gill arches with the hyomandibula, the isolated skeletal elements from the pectoral girdle (clavicle, cleithrum and supracleithrum), the bones of the fin and fin supports (pectoral fin spine, fin rays and fulcra) and the dorsal, ventral, lateral and accessory scutes. For each element, descriptions and pictures are provided of modern and archaeological specimens. Regression equations allowing fish length reconstructions on the basis of single bone measurements are given for 14 elements and the scutes. Finally, criteria for species identification are provided. In the case of the dentary, dermopalatine and palatopterygoid, these are differences in shape of the skeletal elements, whereas for the dermal bones the external surface pattern is diagnostic when reconstructed fish length is over one meter

Design and experimental validation of a compact collimated Knudsen source

In this paper we discuss the design and performance of a collimated Knudsen source which has the benefit of a simple design over recirculating sources. Measurements of the flux, transverse velocity distribution and brightness at different temperatures were conducted to evaluate the performance. The scaling of the flux and brightness with the source temperature follow the theoretical predictions. The transverse velocity distribution in the transparent operation regime also agrees with the simulated data. The source was found able to produce a flux of $10^{14}$ s$^{-1}$ at a temperature of 433 K. Furthermore the transverse reduced brightness of an ion beam with equal properties as the atomic beam reads $1.7 \times 10^2$ A/(m${}^2$ sr eV) which is sufficient for our goal: the creation of an ultra-cold ion beam by ionization of a laser-cooled and compressed atomic rubidium beam

Cavity-enhanced photoionization of an ultracold rubidium beam for application in focused ion beams

A two-step photoionization strategy of an ultracold rubidium beam for application in a focused ion beam instrument is analyzed and implemented. In this strategy the atomic beam is partly selected with an aperture after which the transmitted atoms are ionized in the overlap of a tightly cylindrically focused excitation laser beam and an ionization laser beam whose power is enhanced in a build-up cavity. The advantage of this strategy, as compared to without the use of a build-up cavity, is that higher ionization degrees can be reached at higher currents. Optical Bloch equations including the photoionization process are used to calculate what ionization degree and ionization position distribution can be reached. Furthermore, the ionization strategy is tested on an ultracold beam of $^{85}$Rb atoms. The beam current is measured as a function of the excitation and ionization laser beam intensity and the selection aperture size. Although details are different, the global trends of the measurements agree well with the calculation. With a selection aperture diameter of 52 $\mu$m, a current of $\left(170\pm4\right)$ pA is measured, which according to calculations is 63% of the current equivalent of the transmitted atomic flux. Taking into account the ionization degree the ion beam peak reduced brightness is estimated at $1\times10^7$ A/(m$^2\,$sr$\,$eV).Comment: 13 pages, 9 figure

Laser application to measure vertical sea temperature and turbidity, design phase

An experiment to test a new method was designed, using backscattered radiation from a laser beam to measure oceanographic parameters in a fraction of a second. Tyndall, Rayleigh, Brillouin, and Raman scattering all are utilized to evaluate the parameters. A beam from a continuous argon ion laser is used together with an interferometer and interference filters to gather the information. The results are checked by direct measurements. Future shipboard and airborne experiments are described

Disulfides as redox switches : from molecular mechanisms to functional significance

The molecular mechanisms underlying thiol-based redox control are poorly defined. Disulfide bonds between Cys residues are commonly thought to confer extra rigidity and stability to their resident protein, forming a type of proteinaceous spot weld. Redox biologists have been redefining the role of disulfides over the last 30&ndash;40 years. Disulfides are now known to form in the cytosol under conditions of oxidative stress. Isomerization of extracellular disulfides is also emerging as an important regulator of protein function. The current paradigm is that the disulfide proteome consists of two subproteomes: a structural group and a redox-sensitive group. The redoxsensitive group is less stable and often associated with regions of stress in protein structures. Some characterized redox-active disulfides are the helical CXXC motif, often associated with thioredoxin-fold proteins; and forbidden disulfides, a group of metastable disulfides that disobey elucidated rules of protein stereochemistry. Here we discuss the role of redox-active disulfides as switches in proteins.<br /