Unconstrained Global Optimization of Molecules on Surfaces: From globally optimized structures to scanning-probe data

The adsorption of molecules on a surface plays a vital role in heterogeneous catalysis. For a proper unterstanding of the reaction mechanisms involved, the adsorption ge ometry of the molecules on the surface needs to be known. So far, experimental data from tunneling microscopes and spectroscopy, such as STM and IRAS are the main ways to obtain such knowledge. Due to the vast search space of adsorption geometries, especially for oligomers, optimizations using ab initio methods can be used to confirm the experimental data only if good initial guesses are available. Global optimization can serve two purposes in these situations. On the one hand it allows for a thorough investigation of the given search space, which can provide good initial guesses for subsequent high-level structural refinements. On the other hand, given a known reaction mechanism, it could also be used to find catalysts that influence e.g. the relevant bonds. With respect to this idea the topic of this thesis is to find a local optimization method cheap enough such that the total computational cost of global optimization does not exceed availability and yet good enough that the results are meaningful to the problem at hand. With this in mind multiple force field and semiempirical methods have been tested and evaluated mainly on benzene, acetophenone and ethyl pyruvate on Pt(111) surfaces. Some other adsorbates have also been tested shortly. In addition to these global optimization results, DFT geometry optimizations of ethyl pyruvate on Pt(111) have been performed and the structures of the best adsorption geometry from global optimization and from DFT are compared. Furthermore, from the DFT data STM images have been calculated that are compared to experimental results. The theoretical and experimental STM images agree well

2018 Annual Report

In 2018, the Museum of Southwestern Biology (MSB) has continued to improve its profile and impacts, both on the University of New Mexico campus and in the international scientific community. Its collections serve as scientific infrastructure that enhances research, teaching, community service, and public outreach. The MSB is part of the UNM Department of Biology, and the missions of the MSB and the Department are synergistic. MSB houses extensive and rapidly growing collections representing biodiversity of world, primarily from the last halfcentury. MSB has outstanding collections from New Mexico and western North America, but it also has substantial holdings from five other continents around the world. MSB consists of eight divisions, and one special program (the Natural Heritage Program New Mexico). MSB also manages the large federal collection of the US Geological Survey collection, second only the Smithsonian Institution in size among federal collections. The collections enrich education by allowing for scientists, educators, public health professionals, and natural resource managers to investigate climate change, environmental quality, emerging diseases, invasive species, ecology, genomics, and evolution. The databases associated with the MSB\u27s eight collections constitute a significant, accessible informatics resource that grows in value each time scientific research is done using the collections. In these ways, MSB contributes to understanding life on earth, its origins, diversity, function, and relationships with human society and public health. MSB annual reports are archived and accessible via UNM\u27s internet repository: (http://repository.unm.edu/handle/1928/24433).https://digitalrepository.unm.edu/msb_annual_reports/1012/thumbnail.jp

Rates of molecular evolution and their application to neotropical avian biogeography

The tempo of evolution and the causes of rate variation among lineages are central foci of evolutionary biology. I evaluated two hypothesized sources of variation in molecular evolutionary rate, and I applied a variable molecular clock to estimate the timescale of diversification in three families of Neotropical birds. First, I examined the phylogenetic evidence for molecular punctuated equilibrium, the hypothesis that speciation drives accelerated molecular evolution. Recent findings that rates of DNA evolution and speciation are linked implicate molecular punctuated equilibrium as an important cause of rate variation among lineages. I used phylogenetic simulations to test this reported link, and I found that it was entirely attributable to a methodological artifact. In a review of the topic, I found no unequivocal empirical evidence for molecular punctuated equilibrium and I concluded that its predicted phylogenetic consequences are theoretically implausible. Second, I tested the metabolic rate hypothesis, which holds that mutation rate in mtDNA is correlated with mass-specific metabolic rate. This hypothesis predicts that small-bodied lineages should evolve rapidly. Previous studies verified this prediction, but none utilized adequately large samples of independent contrasts among appropriate taxa. The use of many such contrasts from bird mtDNA sequences conspicuously failed to corroborate the link between metabolic and mtDNA rates. On the contrary, high rates of nonsynonymous substitution were associated with large body mass, implicating population size as a pervasive cause of evolutionary rate variation. Third, I developed molecular phylogenies for puffbirds, jacamars, and motmots to test hypothesized area relationships in the Neotropics. I used penalized likelihood to estimate node times while accommodating significant rate variation under a set of biologically realistic assumptions. Phylogenetic patterns in each family were consistent with expansion following the formation of the Central American Landbridge and subsequent vicariance across the Andes. I applied a calibration based on the final uplift of the Isthmus of Panama, 3.1 Ma. Average estimated rates were close to the commonly cited 2% sequence divergence/Myr. Concordant area relationships were found among co-distributed species complexes; however, the timescale of divergence was variable, suggesting that common dispersal corridors rather than common vicariant events may be driving co-phylogenetic patterns

A review of the status and distribution of the Bornean Bristlehead

We compiled all documented records of Bornean Bristlehead Pityriasis gymnocephata to determine what is known about the life-history and distribution of this enigmatic species. Pityriasis is a relict cracticid, related to the Australian magpies and butcherbirds. It is a highly social species and widespread throughout Borneo in forests below 1000m elevation, but rarely encountered

The status of Abbott's Babbler in Borneo

We reviewed the occurrence of Abbott's Babbler Trichastoma abbotti on Borneo as a first step towards understanding why this species, which is common in most of its range, is so rare on the island. We were able to find only 21 documented Bornean records, most of which derived from areas of scrub habitat at low altitudes, especially near the coast

Needs Assessment: Northeast Philly Opioid Epidemic

Introduction: Philadelphia has the 3rd highest rate of opioid-related overdoses in the nation. This crisis is worsening in Northeast Philadelphia and the Department of Public Health lacks necessary information to intervene in an informed manner. Objective: This study aims to better understand the crisis in this community and to provide key information to guide future harm reduction interventions in the Northeast Philadelphia region. Methods: Using a designed discussion guide, qualitative interviews were completed with key stakeholders and community members. Information regarding personal experiences and opinions about the epidemic was gathered and interviews were analyzed using narrative analysis. In addition, needle counts were completed in public spaces. These counts were used to measure the free needle burden in this community. The findings of this study will be reported to the Department of Public Health. Results: Community member and stakeholder interviews produced a spectrum of opinions surrounding this issue. Major themes include the need for better access to needle exchange services and the idea that the harm reduction needed in this community differs from what would be accepted by its community members. The needle counts reveal that there is not a serious burden in the community, suggesting little need for further needle disposal kiosks in the area. Conclusion: In conclusion, future interventions should be centered around increasing needle exchange services and improving access and visibility of treatment centers in this community. Furthermore, further action should be taken to address the stigma of substance abuse in this community

Tactile Network Resource Allocation enabled by Quantum Annealing based on ILP Modeling

Agile networks with fast adaptation and reconfiguration capabilities are required for on-demand provisioning of various network services. We propose a new methodical framework for short-time network optimization based on quantum computing (QC) and integer linear program (ILP) models, which has the potential of realizing a real-time network automation. We define methods to map a nearly real-world ILP model for resource provisioning to a quadratic unconstrained binary optimization (QUBO) problem, which is solvable on quantum annealer (QA). We concentrate on the three-node network to evaluate our approach and its obtainable quality of solution using the state-of-the-art quantum annealer D-Wave Advantage 5.2/5.3. By studying the annealing process, we find annealing configuration parameters that obtain feasible solutions close to the reference solution generated by the classical ILP-solver CPLEX. Further, we studied the scaling of the network problem and provide estimations on quantum annealer's hardware requirements to enable a proper QUBO problem embedding of larger networks. We achieved the QUBO embedding of networks with up to 6 nodes on the D-Wave Advantage. According to our estimates a real-sized network with 12 to 16 nodes require a QA hardware with at least 50000 qubits or more.Comment: 10 pages, 9 figures. Submitted to "IEEE Quantum Week 2023". The data of the work are available on https://jugit.fz-juelich.de/qnet-public/home