IL4. The Molecular Science Software Institute

The Molecular Sciences Software Institute (MolSSI) is a nexus for science, education, and cooperation serving the worldwide community of computational molecular scientists — a broad field including of biomolecular simulation, quantum chemistry, and materials science. The Institute, which was recently funded by the National Science Foundation as part of the White House’s National Strategic Computing Initiative, will spur significant ad-vances in software infrastructure, education, standards, and best-practices that are needed to enable the molecular science community to open new windows on the next generation of scientific Grand Challenges, ranging from the simulation of intrinsically disordered proteins associated with a range of diseases to the design of new catalysts vital to the global chemical industry and climate change. The MolSSI will enable the computational molecular science community to work together to leverage its diverse capabilities that will reduce or eliminate the gulf that currently delays by years the practical realization of theoretical innovations. Ultimately, the Institute will enable computational scientists to tackle problems that are orders of magnitude larger and more complex than those currently within our grasp. This lecture will provide an overview of the Institute’s structure, goals, and vision. T. Daniel Crawford, Virginia Polytechnic and State University Cecilia Clementi, Rice University Robert J. Harrison, Stony Brook University Teresa L. Head-Gordon, University of California at Berkeley Shantenu Jha, Rutgers University Anna I. Krylov, University of Southern California, Los Angeles Vijay S. Pande, Stanford University Theresa L. Windus, Iowa State Universit

The Possible Interstellar Anion CH2CN-: Spectroscopic Constants, Vibrational Frequencies, and Other Considerations

It is hypothesized that the A ^1B_1 <- X ^1A' excitation into the dipole-bound state of the cyanomethyl anion (CH2CN-) is proposed as the carrier for one diffuse interstellar band. However, this particular molecular system has not been detected in the interstellar medium even though the related cyanomethyl radical and the isoelectronic ketenimine molecule have been found. In this study we are employing the use of proven quartic force fields and second-order vibrational perturbation theory to compute accurate spectroscopic constants and fundamental vibrational frequencies for ^1A' CH2CN- in order to assist in laboratory studies and astronomical observations

Predation by Amphibians and Small Mammals on the Spruce Budworm (Lepidoptera: Tortricidae)

Stomach-content analyses of pitfall-trapped amphibians and small mammals showed that the eastern American toad, Bujo americanus americanus, and the wood frog, Rana sylvatica, preyed on late instars and moths of the spruce budworm, Choristoneura fumiferana. The spotted salamander, Ambystoma maculatum, and the masked shrew, Sorex cinereus, also preyed on late instars of the spruce budworm

Diagrammatic Coupled Cluster Monte Carlo

We propose a modified coupled cluster Monte Carlo algorithm that stochastically samples connected terms within the truncated Baker--Campbell--Hausdorff expansion of the similarity transformed Hamiltonian by construction of coupled cluster diagrams on the fly. Our new approach -- diagCCMC -- allows propagation to be performed using only the connected components of the similarity-transformed Hamiltonian, greatly reducing the memory cost associated with the stochastic solution of the coupled cluster equations. We show that for perfectly local, noninteracting systems, diagCCMC is able to represent the coupled cluster wavefunction with a memory cost that scales linearly with system size. The favorable memory cost is observed with the only assumption of fixed stochastic granularity and is valid for arbitrary levels of coupled cluster theory. Significant reduction in memory cost is also shown to smoothly appear with dissociation of a finite chain of helium atoms. This approach is also shown not to break down in the presence of strong correlation through the example of a stretched nitrogen molecule. Our novel methodology moves the theoretical basis of coupled cluster Monte Carlo closer to deterministic approaches.Comment: 31 pages, 6 figure

Challenges in the use of quantum computing hardware-efficient Ansatze in electronic structure theory

Advances in quantum computation for electronic structure, and particularly heuristic quantum algorithms, create an ongoing need to characterize the performance and limitations of these methods. Here we discuss some potential pitfalls connected with the use of hardware-efficient Ansatze in variational quantum simulations of electronic structure. We illustrate that hardware-efficient Ansatze may break Hamiltonian symmetries and yield non-differentiable potential energy curves, in addition to the well-known difficulty of optimizing variational parameters. We discuss the interplay between these limitations by carrying out a comparative analysis of hardware-efficient Ansatze versus unitary coupled cluster and full configuration interaction, and of second- and first-quantization strategies to encode fermionic degrees of freedom to qubits. Our analysis should be useful in understanding potential limitations and in identifying possible areas of improvement in hardware-efficient Ansatze.Comment: 16 pages, 9 figures, supplemental information included as an ancillary fil

Vibrational Frequencies and Spectroscopic Constants for 1(sup 3)A' HNC and 1(sup 3)A' HOC+ from High-Accuracy Quartic Force Fields

The spectroscopic constants and vibrational frequencies for the 1(sup 3)A' states of HNC, DNC, HOC+, and DOC+ are computed and discussed in this work. The reliable CcCR quartic force field based on high-level coupled cluster ab initio quantum chemical computations is exclusively utilized to provide the anharmonic potential. Then, second order vibrational perturbation theory and vibrational configuration interaction methods are employed to treat the nuclear Schroedinger equation. Second-order perturbation theory is also employed to provide spectroscopic data for all molecules examined. The relationship between these molecules and the corresponding 1(sup 3)A' HCN and HCO+ isomers is further developed here. These data are applicable to laboratory studies involving formation of HNC and HOC+ as well as astronomical observations of chemically active astrophysical environments

Speciation in Duckweeds (Lemnaceae): Phylogenetic and Ecological Inferences

Species of duckweeds (Letnnaceae) that were resolved as sister taxa in a phylogeny based on combined molecular and non-molecular data were compared for morphological, physiological, and ecological attributes to infer factors important in the initial divergence leading to speciation. The ability to survive extreme conditions such as desiccation and cold temperatures is the most common difference identified between species. Two morphological characters facilitating survival in extreme environments are production of special resting buds called turions and increased seed production. The prevalent geographic pattern for species pairs consists of one restricted species occurring on the periphery of a more widespread taxon; this pattern indicates that divergence of peripheral isolates is a common geographical mode of speciation in duckweeds. Other species differ in optimal environmental conditions for growth, and these species are largely sympatric. In only one instance does it appear that divergence and speciation occurred following long-distance dispersal. Sympatric species pairs have the lowest molecular divergence; widespread primarily allopatric, and distantly allopatric species have the highest molecular divergence. Despite infrequent sexual reproduction, some degree of detectable variation (molecular, physiological, etc.) occurs within populations and among populations of the same species. Molecular evidence indicates that variation within duckweeds extends from the population and intraspecific levels to very different levels of divergence among recognized species. Contrary to the appearance of morphological and ecological uniformity implied by their reduced morphology and restricted occurrence in fresh water habitats, duckweeds are not a group in evolutionary stasis. Rather, these smallest of all flowering plants are dynamic evolutionarily, and comprise a model system for studying plant evolution and speciation

Diagrammatic Coupled Cluster Monte Carlo.

We propose a modified coupled cluster Monte Carlo algorithm that stochastically samples connected terms within the truncated Baker-Campbell-Hausdorff expansion of the similarity-transformed Hamiltonian by construction of coupled cluster diagrams on the fly. Our new approach-diagCCMC-allows propagation to be performed using only the connected components of the similarity-transformed Hamiltonian, greatly reducing the memory cost associated with the stochastic solution of the coupled cluster equations. We show that for perfectly local, noninteracting systems diagCCMC is able to represent the coupled cluster wavefunction with a memory cost that scales linearly with system size. The favorable memory cost is observed with the only assumption of fixed stochastic granularity and is valid for arbitrary levels of coupled cluster theory. Significant reduction in memory cost is also shown to smoothly appear with dissociation of a finite chain of helium atoms. This approach is also shown not to break down in the presence of strong correlation through the example of a stretched nitrogen molecule. Our novel methodology moves the theoretical basis of coupled cluster Monte Carlo closer to deterministic approaches.Sims Fun

An investigation into the reliability of a mobile app designed to assess orthodontic treatment need and severity.

Aim To investigate reliability of the Easy IOTN app between clinicians with different levels of experience in determining Index of Orthodontic Treatment Need (IOTN) Dental Health Component (DHC) and Aesthetic Component (AC) scores from study models. The accuracy of each clinician in discriminating treatment need using the app against the 'gold standard' conventional assessment at the threshold of treatment acceptance criteria was also explored.Materials and methods In total, 150 sets of pre-treatment study models were assessed by six clinicians using the app on two separate occasions (T1 and T2). A single IOTN-calibrated clinician also scored the models using the conventional technique. Clinician scores for both intra- and inter-rater reliability were assessed using Cohen's Kappa. The performance of each clinician in discriminating treatment need using the app against the conventional assessment method at the threshold of treatment acceptance criteria was also assessed using the area under the curve-receiver operating characteristic.Results The intra-rater agreement for the clinician undertaking the conventional assessment of the models was 1.0. Intra-rater agreement scores for clinicians using the Easy IOTN app ranged between 0.37-0.87 (DHC) and 0.22-0.44 (AC). Inter-rater agreement scores at T2 were 0.59 (DHC) and 0.23 (AC). Based on the IOTN DHC, all clinicians displayed an excellent level of accuracy in determining malocclusions qualifying for treatment (range 81.7-90.0%). Based on the IOTN AC, all clinicians showed an acceptable level of accuracy in determining malocclusions qualifying for treatment (range 71.9-79.2%).Conclusions The Easy IOTN app was shown to have moderate inter-rater reliability. Variation in the intra-rater reliability was evident between clinicians of different grades/level of experience. Importantly, the diagnostic accuracy of the app to discriminate between malocclusions that qualify for NHS treatment was rated as excellent (IOTN DHC) and acceptable (IOTN AC) and independent of clinician grade or level of experience