The symmetric quasi-classical model using on-the-fly time-dependent density functional theory within the Tamm-Dancoff approximation

The primary computational challenge when simulating nonadiabatic ab initio molecular dynamics is the unfavorable compute costs of electronic structure calculations with molecular size. Simple electronic structure theories, like time-dependent density functional theory within the Tamm-Dancoff approximation (TDDFT/TDA), alleviate this cost for moderately sized molecular systems simulated on realistic time scales. Although TDDFT/TDA does have some limitations in accuracy, an appealing feature is that, in addition to including electron correlation through the use of a density functional, the cost of calculating analytic nuclear gradients and nonadiabatic coupling vectors is often computationally feasible even for moderately-sized basis sets. In this work, some of the benefits and limitations of TDDFT/TDA are discussed and analyzed with regard to its applicability as a "back-end" electronic structure method for the symmetric quasi-classical Meyer-Miller model (SQC/MM). In order to investigate the benefits and limitations of TDDFT/TDA, SQC/MM is employed to predict and analyze a prototypical example of excited-state hydrogen transfer in gas-phase malonaldehyde. Then, the ring-opening dynamics of selenophene are simulated which highlight some of the deficiencies of TDDFT/TDA. Additionally, some new algorithms are proposed that speed up the calculation of analytic nuclear gradients and nonadiabatic coupling vectors for a set of excited electronic states.Comment: 35 pages, 8 figures, 2 table

DECIPHERING THE EXCITED-STATE VIBRATIONAL SIGNATURES OF THE WATER-IODIDE BINARY COMPLEX THROUGH QUANTUM SIMULATIONS.

The water-iodide monomer (I$^{-}$H$_{2}$O), nominally the simplest of the halide-water complexes, challenges our current understanding of ion hydration. Most notably, this seemingly simple complex displays multiple resonant vibrational transitions, a low tunneling barrier, and a strong transition dipole moment along the bound OH-I coordinate. These effects combine to yield spectroscopic signatures that deviate strongly from traditional harmonic analyses and are even difficult to qualitatively reproduce with anharmonic methodologies. Among these signatures is a quartet of peaks in the 3300 – 3500 cm-1 range that is unexplained using traditional single-photon spectroscopy. Challenging both experiment and theory alike, this situation required the interpretation of newly developed IR-IR 2-color photodissociation spectroscopy that probes well below the dissociation threshold. In this work, we use both exact eigensolver techniques and a newly developed vibrationally adiabatic model, along with a new potential energy surface$^a$ to computationally explore the excited-state spectra. The resulting analyses identify the source of the strength of the resonant transitions, directly assign the vibrational and rotational spectroscopic signatures, and discern the electronic origin of these surprising effects in this fundamental model of ion hydration. $^a$Bajaj, P. Gotz, A.W., Paesani, F. Journal of Chemical Theory and Computation, 2016, 12 (6), 2698-2705

A Declarative Specification for Authoring Metrics Dashboards

Despite their ubiquity, authoring dashboards for metrics reporting in modern data analysis tools remains a manual, time-consuming process. Rather than focusing on interesting combinations of their data, users have to spend time creating each chart in a dashboard one by one. This makes dashboard creation slow and tedious. We conducted a review of production metrics dashboards and found that many dashboards contain a common structure: breaking down one or more metrics by different dimensions. In response, we developed a high-level specification for describing dashboards as sections of metrics repeated across the same dimensions and a graphical interface, Quick Dashboard, for authoring dashboards based on this specification. We present several usage examples that demonstrate the flexibility of this specification to create various kinds of dashboards and support a data-first approach to dashboard authoring.Comment: To appear at Visual Data Science (VDS) Symposium at IEEE VIS 202

My patient is short of breath: is there pleural fluid, and will PoCUS help drain it safely?

Pathological pleural fluid is common in patients presenting to the emergency department, occurring in as many as 17% of patients presenting with shortness of breath, and as many as 20% of patients with blunt thoracic trauma. A typical chest X-ray may fail to identify as much as 175 mL of pleural fluid in the erect position, and as much as 500 mL in the supine position. Point-of-care ultrasound (PoCUS) on the other hand can detect as little as 20 mL of pleural fluid, and has consistently been shown to have sensitivities and specificities for the detection of pleural fluid close to 100% in both the trauma and critically ill populations. In addition, ultrasound identifies pleural fluid more rapidly than chest X-ray. PoCUS can be used to guide thoracentesis, resulting in improved success rates with decreased complications. Here we describe the evidence supporting the use of PoCUS in the management of pleural fluid collections

Fantastical Excited State Optimized Structures and Where to Find Them

The quantum chemistry community has developed analytic forces for approximate electronic excited states to enable walking on excited state potential energy surfaces (PES). One can thereby computationally characterize excited state minima and saddle points. Always implicit in using this machinery is the fact that an excited state PES only exists within the realm of the Born-Oppenheimer approximation, where the nuclear and electronic degrees of freedom separate. This work demonstrates through ab initio calculations and simple nonadiabatic dynamics that some excited state minimum structures are fantastical: they appear to exist as stable configurations only as a consequence of the PES construct, rather than being physically observable. One such case is the S2 excited state of phosphine and a second case are local minima of a number of states of tris(bipyridine)ruthenium(II). Each fantastical structure exhibits an unphysically high predicted harmonic frequency and associated force constant. This fact can serve as a valuable diagnostic of when an optimized excited state structure is non-observable. Their origin lies in the coupling between different electronic states, and the resulting avoided crossings. The upper state may exhibit a minimum very close to the crossing, where the force constant relates to the strength of the electronic coupling rather than to any characteristic excited state vibration. Nonadiabatic dynamics results using a Landau-Zener model illustrate that fantastical excited state structures have extremely short lifetimes on the order of a few femtoseconds. Their appearance in a calculation signals the presence of a nearby avoided crossing or conical intersection through which the system will rapidly cross to a lower surface.Comment: 7 pages, 4 figure

Visualization of heterogeneous data

Abstract — Both the Resource Description Framework (RDF), used in the semantic web, and Maya Viz u-forms represent data as a graph of objects connected by labeled edges. Existing systems for flexible visualization of this kind of data require manual specification of the possible visualization roles for each data attribute. When the schema is large and unfamiliar, this requirement inhibits exploratory visualization by requiring a costly up-front data integration step. To eliminate this step, we propose an automatic technique for mapping data attributes to visualization attributes. We formulate this as a schema matching problem, finding appropriate paths in the data model for each required visualization attribute in a visualization template. Index Terms—Data integration, RDF, attribute inference.

Multidecadal Climate Variability and the Florescence of Fremont Societies in Eastern Utah

Fremont societies of the Uinta Basin incorporated domesticates into a foraging lifeway over a 1,000-year period from AD 300 to 1300. Fremont research provides a unique opportunity to critically examine the social and ecological processes behind the adoption and abandonment of domesticates by hunter-gatherers. We develop and integrate a 2,115-year precipitation reconstruction with a Bayesian chronological model for the growth of Fremont societies in the Cub Creek reach of Dinosaur National Monument. Comparison of the archaeological chronology with the precipitation record suggests that the florescence of Fremont societies was an adaptation to multidecadal precipitation variability with an approximately 30-plus-year periodicity over most, but not all, of the last 2,115 years. Fremont societies adopted domesticates to enhance their resilience to periodic droughts. We propose that reduced precipitation variability from AD 750 to AD 1050, superimposed over consistent mean precipitation availability, was the tipping point that increased maize production, initiated agricultural intensification, and resulted in increased population and development of pithouse communities. Our study develops a multidecadal/multigenerational model within which to evaluate the strategies underwriting the adoption of domesticates by foragers, the formation of Fremont communities, and the inherent vulnerabilities to resource intensification that implicate the eventual dissolution of those communities. Las sociedades de Fremont de la cuenca de Uinta incorporaron a los domesticados en una forma de vida de alimentación durante un período de 1.000 años desde 300–1300 dC. La investigación de Fremont brinda una oportunidad única para examinar críticamente los procesos sociales y ecológicos detrás de la adopción y el abandono de los domésticos por parte de los cazadores-recolectores. Desarrollamos e integramos una reconstrucción de precipitación de 2.115 años con un modelo cronológico Bayesiano para el crecimiento de las sociedades de Fremont en el alcance de Cub Creek del Dinosaur National Monument. La comparación de la cronología arqueológica con el registro de precipitación sugiere que la floración de las sociedades de Fremont fue una adaptación a la variabilidad de precipitación multidecadal con una periodicidad de aproximadamente 30 años en la mayoría, pero no en todos, de los últimos 2.115 años. Las sociedades de Fremont adoptaron domesticados para mejorar su resistencia a las sequías periódicas. Proponemos que la variabilidad reducida de la precipitación desde 750–1050 dC, superpuesta sobre la disponibilidad de precipitación media constante, fue el punto de inflexión que aumentó la producción de maíz, inició la intensificación agrícola y dio como resultado un aumento de la población y el desarrollo de las comunidades de médulas. Nuestro estudio desarrolla un modelo multidecadal/multigeneracional dentro del cual evaluar las estrategias que sustentan la adopción de domesticados por parte de los recolectores, la formación de comunidades de Fremont y las vulnerabilidades inherentes a la intensificación de recursos que implican la eventual disolución de esas comunidades