Exciton spin dynamics and photoluminescence polarization of CdSe/CdS dot-in-rod nanocrystals in high magnetic fields

The exciton spin dynamics and polarization properties of the related emission are investigated in colloidal CdSe/CdS dot-in-rod (DiR) and spherical core/shell nanocrystal (NC) ensembles by magneto-optical photoluminescence (PL) spectroscopy in magnetic fields up to 15 T. It is shown that the degree of circular polarization (DCP) of the exciton emission induced by the magnetic field is affected by the NC geometry as well as the exciton fine structure and can provide information on nanorod orientation. A theory to describe the circular and linear polarization properties of the NC emission in magnetic field is developed. It takes into account phonon mediated coupling between the exciton fine structure states as well as the dielectric enhancement effect resulting from the anisotropic shell of DiR NCs. This theoretical approach is used to model the experimental results and allows us to explain most of the measured features. The spin dynamics of the dark excitons is investigated in magnetic fields by time-resolved photoluminescence. The results highlight the importance of confined acoustic phonons in the spin relaxation of dark excitons. The bare core surface as well as the core/shell interface give rise to an efficient spin relaxation channel, while the surface of core/shell NCs seems to play only a minor role.Comment: 18 pages, 15 figure

Eulerian CFD modeling of nozzle geometry effects on ECN Sprays A and D: assessment and analysis

This is the author's version of a work that was accepted for publication in International Journal of Engine Research. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published as https://doi.org/10.1177/1468087419882500.[EN] Diesel spray modeling is a multi-scale problem with complex interactions between different flow regions, that is, internal nozzle flow, near-nozzle region and developed spray, including evaporation and combustion. There are several modeling approaches that have proven particularly useful for some spray regions although they have struggled at other areas, while Eulerian modeling has shown promise in dealing with all characteristics at a reasonable computational effort for engineering calculations. In this work, the sigma -Y single-fluid diffuse-interface model, based on scale separation assumptions at high Reynolds and Weber numbers, is used to simulate the engine combustion network Sprays A and D within a Reynolds-averaged Navier-Stokes turbulence modeling approach. The study is divided into two parts. First of all, the larger diameter Spray D is modeled from the nozzle flow till evaporative spray conditions, obtaining successful prediction of numerous spray metrics, paying special attention to the near-nozzle region where spray dispersion and interfacial surface area can be validated against measurements conducted at the Advanced Photon Source at Argonne National Laboratory, including both the ultra-small-angle X-ray scattering and the X-ray radiography. Afterwards, an analysis of the modeling predictions is made in comparison with previous results obtained for Spray A, considering the nozzle geometry effects in the modeling behavior.The authors thank the freely shared X-ray radiography and ultra-small-angle X-ray scattering measurements performed at Argonne National Laboratory by the following authors: Daniel J. Duke, Jan Ilavsky, Katarzyna E. Matusik., Brandon A. Sforzo., Alan L. Kastengren and Christopher F. Powell. They also thankfully acknowledge the computer resources at Picasso and the technical support provided by Universidad de Malaga (UMA; RES-FI-2018-1-0039).Pandal, A.; García-Oliver, JM.; Pastor Enguídanos, JM. (2020). Eulerian CFD modeling of nozzle geometry effects on ECN Sprays A and D: assessment and analysis. International Journal of Engine Research. 21(1):73-88. https://doi.org/10.1177/1468087419882500S7388211PAYRI, R., GARCIA, J., SALVADOR, F., & GIMENO, J. (2005). 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M., Pastor, J. M., Pandal, A., Baldwin, E., & Schmidt, D. P. (2016). Coupled/decoupled spray simulation comparison of the ECN spray a condition with the -Y Eulerian atomization model. International Journal of Multiphase Flow, 80, 89-99. doi:10.1016/j.ijmultiphaseflow.2015.12.002Garcia-Oliver, J. M., Pastor, J. M., Pandal, A., Trask, N., Baldwin, E., & Schmidt, D. P. (2013). DIESEL SPRAY CFD SIMULATIONS BASED ON THE Σ-Υ EULERIAN ATOMIZATION MODEL. Atomization and Sprays, 23(1), 71-95. doi:10.1615/atomizspr.2013007198Navarro-Martinez, S. (2014). Large eddy simulation of spray atomization with a probability density function method. International Journal of Multiphase Flow, 63, 11-22. doi:10.1016/j.ijmultiphaseflow.2014.02.013Pandal, A., Pastor, J. M., García-Oliver, J. M., Baldwin, E., & Schmidt, D. P. (2016). A consistent, scalable model for Eulerian spray modeling. International Journal of Multiphase Flow, 83, 162-171. doi:10.1016/j.ijmultiphaseflow.2016.04.003Pandal, A., Payri, R., García-Oliver, J. M., & Pastor, J. M. (2017). Optimization of spray break-up CFD simulations by combining Σ-Y Eulerian atomization model with a response surface methodology under diesel engine-like conditions (ECN Spray A). Computers & Fluids, 156, 9-20. doi:10.1016/j.compfluid.2017.06.022Pandal, A., García-Oliver, J. M., Novella, R., & Pastor, J. M. (2018). A computational analysis of local flow for reacting Diesel sprays by means of an Eulerian CFD model. International Journal of Multiphase Flow, 99, 257-272. doi:10.1016/j.ijmultiphaseflow.2017.10.010Payri, R., Ruiz, S., Gimeno, J., & Martí-Aldaraví, P. (2015). Verification of a new CFD compressible segregated and multi-phase solver with different flux updates-equations sequences. Applied Mathematical Modelling, 39(2), 851-861. doi:10.1016/j.apm.2014.07.011Salvador, F. J., Gimeno, J., Pastor, J. M., & Martí-Aldaraví, P. (2014). Effect of turbulence model and inlet boundary condition on the Diesel spray behavior simulated by an Eulerian Spray Atomization (ESA) model. International Journal of Multiphase Flow, 65, 108-116. doi:10.1016/j.ijmultiphaseflow.2014.06.003Demoulin, F.-X., Beau, P.-A., Blokkeel, G., Mura, A., & Borghi, R. (2007). A NEW MODEL FOR TURBULENT FLOWS WITH LARGE DENSITY FLUCTUATIONS: APPLICATION TO LIQUID ATOMIZATION. Atomization and Sprays, 17(4), 315-345. doi:10.1615/atomizspr.v17.i4.20Pandal, A., Pastor, J. M., Payri, R., Kastengren, A., Duke, D., Matusik, K., … Schmidt, D. (2017). Computational and Experimental Investigation of Interfacial Area in Near-Field Diesel Spray Simulation. SAE International Journal of Fuels and Lubricants, 10(2), 423-431. doi:10.4271/2017-01-0859Weller, H. G., Tabor, G., Jasak, H., & Fureby, C. (1998). A tensorial approach to computational continuum mechanics using object-oriented techniques. 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Analyzing the Structure and Function of Novel Cytochromes from a Natural Microbial Community

The Richmond mine in Iron Mountain, California, provides an unusual ecosystem suitable for the growth of microbial biofilms which produce many unique proteins. Through iron oxidation, these proteins facilitate acid mine drainage (AMD). Because this habitat is extremely acidic, survival is an extraordinary feat and the process of environmental selection is rare. In order to understand the mechanisms by which these organisms oxidize iron and gain electrons for energy, biochemical studies were applied. More specifically, column chromatography, spectrophotometry, and gel electrophoresis were used to determine the proteins present in different biofilms. Two specific locations of the mine researched were the AB drift and Ultraback C (UBC), which were both found to contain at least five different types of protein and a large amount of heme-bound cytochromes. Another application of these methods was to investigate proteins playing a major role within the community; one protein selected was cytochrome 579 (Cyt{sub 579}) due to its abundance in the biofilm, iron oxidizing potential, and signature absorbance of 579nm. The structure and function of Cyt{sub 579} could be characterized by the isolation of its heme, which was completed using column chromatography; however, one of the challenges has been liberating the heme from the column. Further research, including acid-base and temperature profiling of Cyt{sup 579} should help elucidate its structural changes within alternate environments and metabolism within the community

08-ERD-071 Final Report: New Molecular Probes and Catalysts for Bioenergy Research

A major thrust in bioenergy research is to develop innovative methods for deconstructing plant cell wall polymers, such as cellulose and lignin, into simple monomers that can be biologically converted to ethanol and other fuels. Current techniques for monitoring a broad array of cell wall materials and specific degradation products are expensive and time consuming. To monitor various polymers and assay their breakdown products, molecular probes for detecting specific carbohydrates and lignins are urgently needed. These new probes would extend the limited biochemical techniques available, and enable realtime imaging of ultrastructural changes in plant cells. Furthermore, degradation of plant biomass could be greatly accelerated by the development of catalysts that can hydrolyze key cell wall polysaccharides and lignin. The objective of this project was to develop cheap and efficient DNA reagents (aptamers) used to detect and quantify polysaccharides, lignin, and relevant products of their breakdown. A practical goal of the research was to develop electrochemical aptamer biosensors, which could be integrated into microfluidic devices and used for high-throughput screening of enzymes or biological systems that degrade biomass. Several important model plant cell wall polymers and compounds were targeted for specific binding and purification of aptamers, which were then tested by microscopic imaging, circular dichroism, surface plasmon resonance, fluorescence anisotropy, and electrochemical biosensors. Using this approach, it was anticiated that we could provide a basis for more efficient and economically viable biofuels, and the technologies established could be used to design molecular tools that recognize targets sought in medicine or chemical and biological defense projects

Advances in field-based high-throughput photosynthetic phenotyping

Gas exchange techniques revolutionized plant research and advanced understanding, including associated fluxes and efficiencies, of photosynthesis, photorespiration, and respiration of plants from cellular to ecosystem scales. These techniques remain the gold standard for inferring photosynthetic rates and underlying physiology/biochemistry, although their utility for high-throughput phenotyping (HTP) of photosynthesis is limited both by the number of gas exchange systems available and the number of personnel available to operate the equipment. Remote sensing techniques have long been used to assess ecosystem productivity at coarse spatial and temporal resolutions, and advances in sensor technology coupled with advanced statistical techniques are expanding remote sensing tools to finer spatial scales and increasing the number and complexity of phenotypes that can be extracted. In this review, we outline the photosynthetic phenotypes of interest to the plant science community and describe the advances in high-throughput techniques to characterize photosynthesis at spatial scales useful to infer treatment or genotypic variation in field-based experiments or breeding trials. We will accomplish this objective by presenting six lessons learned thus far through the development and application of proximal/remote sensing-based measurements and the accompanying statistical analyses. We will conclude by outlining what we perceive as the current limitations, bottlenecks, and opportunities facing HTP of photosynthesis

Laboratory Focus on Improving the Culture of Biosafety: Statewide Risk Assessment of Clinical Laboratories That Process Specimens for Microbiologic Analysis

The Wisconsin State Laboratory of Hygiene challenged Wisconsin laboratories to examine their biosafety practices and improve their culture of biosafety. One hundred three clinical and public health laboratories completed a questionnaire-based, microbiology-focused biosafety risk assessment. Greater than 96% of the respondents performed activities related to specimen processing, direct microscopic examination, and rapid nonmolecular testing, while approximately 60% performed culture interpretation. Although they are important to the assessment of risk, data specific to patient occupation, symptoms, and travel history were often unavailable to the laboratory and, therefore, less contributory to a microbiology-focused biosafety risk assessment than information on the specimen source and test requisition. Over 88% of the respondents complied with more than three-quarters of the mitigation control measures listed in the survey. Facility assessment revealed that subsets of laboratories that claim biosafety level 1, 2, or 3 status did not possess all of the biosafety elements considered minimally standard for their respective classifications. Many laboratories reported being able to quickly correct the minor deficiencies identified. Task assessment identified deficiencies that trended higher within the general (not microbiology-specific) laboratory for core activities, such as packaging and shipping, direct microscopic examination, and culture modalities solely involving screens for organism growth. For traditional microbiology departments, opportunities for improvement in the cultivation and management of highly infectious agents, such as acid-fast bacilli and systemic fungi, were revealed. These results derived from a survey of a large cohort of small- and large-scale laboratories suggest the necessity for continued microbiology-based understanding of biosafety practices, vigilance toward biosafety, and enforcement of biosafety practices throughout the laboratory setting

08-ERD-071 Final Report: New Molecular Probes and Catalysts for Bioenergy Research

A major thrust in bioenergy research is to develop innovative methods for deconstructing plant cell wall polymers, such as cellulose and lignin, into simple monomers that can be biologically converted to ethanol and other fuels. Current techniques for monitoring a broad array of cell wall materials and specific degradation products are expensive and time consuming. To monitor various polymers and assay their breakdown products, molecular probes for detecting specific carbohydrates and lignins are urgently needed. These new probes would extend the limited biochemical techniques available, and enable realtime imaging of ultrastructural changes in plant cells. Furthermore, degradation of plant biomass could be greatly accelerated by the development of catalysts that can hydrolyze key cell wall polysaccharides and lignin. The objective of this project was to develop cheap and efficient DNA reagents (aptamers) used to detect and quantify polysaccharides, lignin, and relevant products of their breakdown. A practical goal of the research was to develop electrochemical aptamer biosensors, which could be integrated into microfluidic devices and used for high-throughput screening of enzymes or biological systems that degrade biomass. Several important model plant cell wall polymers and compounds were targeted for specific binding and purification of aptamers, which were then tested by microscopic imaging, circular dichroism, surface plasmon resonance, fluorescence anisotropy, and electrochemical biosensors. Using this approach, it was anticiated that we could provide a basis for more efficient and economically viable biofuels, and the technologies established could be used to design molecular tools that recognize targets sought in medicine or chemical and biological defense projects

Juxtaposition of system dynamics and agent-based simulation for a case study in immunosenescence

Advances in healthcare and in the quality of life significantly increase human life expectancy. With the aging of populations, new un-faced challenges are brought to science. The human body is naturally selected to be well-functioning until the age of reproduction to keep the species alive. However, as the lifespan extends, unseen problems due to the body deterioration emerge. There are several age-related diseases with no appropriate treatment; therefore, the complex aging phenomena needs further understanding. It is known that immunosenescence is highly correlated to the negative effects of aging. In this work we advocate the use of simulation as a tool to assist the understanding of immune aging phenomena. In particular, we are comparing system dynamics modelling and simulation (SDMS) and agent-based modelling and simulation (ABMS) for the case of age-related depletion of naive T cells in the organism. We address the following research questions: Which simulation approach is more suitable for this problem? Can these approaches be employed interchangeably? Is there any benefit of using one approach compared to the other? Results show that both simulation outcomes closely fit the observed data and existing mathematical model; and the likely contribution of each of the naive T cell repertoire maintenance method can therefore be estimated. The differences observed in the outcomes of both approaches are due to the probabilistic character of ABMS contrasted to SDMS. However, they do not interfere in the overall expected dynamics of the populations. In this case, therefore, they can be employed interchangeably, with SDMS being simpler to implement and taking less computational resources

N-Myc-induced metabolic rewiring creates novel therapeutic vulnerabilities in neuroblastoma

N-Myc is a transcription factor that is aberrantly expressed in many tumor types and is often correlated with poor patient prognosis. Recently, several lines of evidence pointed to the fact that oncogenic activation of Myc family proteins is concomitant with reprogramming of tumor cells to cope with an enhanced need for metabolites during cell growth. These adaptions are driven by the ability of Myc proteins to act as transcriptional amplifiers in a tissue-of-origin specific manner. Here, we describe the effects of N-Myc overexpression on metabolic reprogramming in neuroblastoma cells. Ectopic expression of N-Myc induced a glycolytic switch that was concomitant with enhanced sensitivity towards 2-deoxyglucose, an inhibitor of glycolysis. Moreover, global metabolic profiling revealed extensive alterations in the cellular metabolome resulting from overexpression of N-Myc. Limited supply with either of the two main carbon sources, glucose or glutamine, resulted in distinct shifts in steady-state metabolite levels and significant changes in glutathione metabolism. Interestingly, interference with glutamine-glutamate conversion preferentially blocked proliferation of N-Myc overexpressing cells, when glutamine levels were reduced. Thus, our study uncovered N-Myc induction and nutrient levels as important metabolic master switches in neuroblastoma cells and identified critical nodes that restrict tumor cell proliferation