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No One Size Fits All: Semiconductor Nanocrystal Sizing Curves
Although colloidal quantum dots or nanocrystals (NCs) are now long past their infancy, there remain basic issues that must be addressed to fully establish their fundamental, size-dependent properties. This is especially true for model systems such as CdSe where confinement effects are responsible for changes in their optical response and where significant effort has been invested in developing theories of their underlying electronic structure. Surprisingly, there still appears to be a lack of consensus on one of the most fundamental metrics for NCs, their sizing curves. As shown here, these are empirical functions that link the size of isotropically shaped semiconductor NCs (such as the diameter, d, for spherical NCs and edge length, l, for cube-shaped ones) to corresponding changes in optical response.
Are Terrestrial Biosphere Models Fit for Simulating the Global Land Carbon Sink?
The Global Carbon Project estimates that the terrestrial biosphere has absorbed about one-third of anthropogenic CO 2 emissions during the 1959–2019 period. This sink-estimate is produced by an ensemble of terrestrial biosphere models and is consistent with the land uptake inferred from the residual of emissions and ocean uptake. The purpose of our study is to understand how well terrestrial biosphere models reproduce the processes that drive the terrestrial carbon sink. One challenge is to decide what level of agreement between model output and observation-based reference data is adequate considering that reference data are prone to uncertainties. To define such a level of agreement, we compute benchmark scores that quantify the similarity between independently derived reference data sets using multiple statistical metrics. Models are considered to perform well if their model scores reach benchmark scores. Our results show that reference data can differ considerably, causing benchmark scores to be low. Model scores are often of similar magnitude as benchmark scores, implying that model performance is reasonable given how different reference data are. While model performance is encouraging, ample potential for improvements remains, including a reduction in a positive leaf area index bias, improved representations of processes that govern soil organic carbon in high latitudes, and an assessment of causes that drive the inter-model spread of gross primary productivity in boreal regions and humid tropics. The success of future model development will increasingly depend on our capacity to reduce and account for observational uncertainties.
Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape
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Epistasis shapes the fitness landscape of an allosteric specificity switch
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The interplay of additivity, dominance, and epistasis on fitness in a diploid yeast cross
In diploid species, genetic loci can show additive, dominance, and epistatic effects. To characterize the contributions of these different types of genetic effects to heritable traits, we use a double barcoding system to generate and phenotype a panel of ~200,000 diploid yeast strains that can be partitioned into hundreds of interrelated families. This experiment enables the detection of thousands of epistatic loci, many whose effects vary across families. Here, we show traits are largely specified by a small number of hub loci with major additive and dominance effects, and pervasive epistasis. Genetic background commonly influences both the additive and dominance effects of loci, with multiple modifiers typically involved. The most prominent dominance modifier in our data is the mating locus, which has no effect on its own. Our findings show that the interplay between additivity, dominance, and epistasis underlies a complex genotype-to-phenotype map in diploids.
Self-driving laboratories to autonomously navigate the protein fitness landscape
Abstract Protein engineering has nearly limitless applications across chemistry, energy and medicine, but creating new proteins with improved or novel functions remains slow, labor-intensive and inefficient. Here we present the Self-driving Autonomous Machines for Protein Landscape Exploration (SAMPLE) platform for fully autonomous protein engineering. SAMPLE is driven by an intelligent agent that learns protein sequence–function relationships, designs new proteins and sends designs to a fully automated robotic system that experimentally tests the designed proteins and provides feedback to improve the agent’s understanding of the system. We deploy four SAMPLE agents with the goal of engineering glycoside hydrolase enzymes with enhanced thermal tolerance. Despite showing individual differences in their search behavior, all four agents quickly converge on thermostable enzymes. Self-driving laboratories automate and accelerate the scientific discovery process and hold great potential for the fields of protein engineering and synthetic biology.
Filling the gap with a bulky diaryl boron group: fluorinated and non-fluorinated copper pyrazolates fitted with a dimesityl boron moiety on the backbone
Successful synthesis has been reported of 4-Mes 2 B-3,5-(CF 3 ) 2 PzH and 4-Mes 2 B-3,5-(CF 3 ) 2 PzH bearing sterically demanding diarylboron moieties at the pyrazole ring 4-position, and their corresponding copper(I) pyrazolate complexes. They show visible blue photoluminescence in solution. The X-ray crystal structures revealed that the fluorinated {[4-BMes 2 -3,5-(CF 3 ) 2 Pz]Cu} 3 crystallizes as discrete trinuclear molecules whereas as the non-fluorinated {[4-BMes 2 -3,5-(CH 3 ) 2 Pz]Cu} 3 forms dimers of trimers with two close inter-trimer Cu···Cu separations. The solid {[4-BMes 2 -3,5-(CF 3 ) 2 Pz]Cu} 3 featuring a sterically confined Cu 3 N 6 core displays bright blue phosphorescence while {[4-BMes 2 -3,5-(CH 3 ) 2 Pz]Cu} 3 , which is a dimer of a trimer, is a red phosphor at room temperature. Here, this work illustrates the modulation of photo-physical properties of metal pyrazolates by adjusting the supporting ligand steric features and introducing secondary diarylboron luminophores. Computational analysis of the structures and photophysical properties of copper complexes are also presented.
ML Track Fitting in Nuclear Physics
Charged particle tracking represents the largest consumer of CPU resources in high data volume Nuclear Physics (NP) experiments. An effort is underway to develop machine learning (ML) networks that will reduce the resources required for charged particle tracking. Tracking in NP experiments represent some unique challenges compared to high energy physics (HEP). In particular, track finding typically represents only a small fraction of the overall tracking problem in NP. This presentation will outline the differences and similarities between NP and HEP charged particle tracking and areas where ML learning may provide a benefit. The status of the specific effort taking place at Jefferson Lab will also be shown.
Interchange, Extension and Validation of R-matrix fits for gamma production
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Automated Fitting of a Semi-empirical Multiphase Equation of State for Carbon
The equation of state (EOS) of carbon is important in high explosive, geophysical, and inertial confinement fusion applications. Within the semi-empirical Sesame framework, the EOS of each phase is represented by a sum of cold, vibrational, and thermal electronic Helmholtz free energy contributions. Each phase has ~5-10 independent parameters that are adjusted to reproduce single-phase data (e.g., thermal expansion, isothermal compression) as well as experimentally- and computationally- derived phase boundaries. Manual calibration of the full multiphase EOS is arduous. We present our progress in development of automated EOS parameterization based on minimization of an objective function. Here, this function encodes deviation of model EOS results from experimental/computational benchmarks. Optimization is implemented as a combination of global (particle swarm) and local optimization techniques.
Mutational fitness landscapes reveal genetic and structural improvement pathways for a vaccine-elici
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PICAR: An Efficient Extendable Approach for Fitting Hierarchical Spatial Models
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A new class of multivariate goodness of fit tests for multivariate normal mixtures
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Case study: Accounting for response measurement error in fitting a regression model
This article presents a case study motivated by a plot of data that suggested an emerging trend that the authors were faced with explaining. When the measurement error of the data is accounted for, it turns out there was no real trend. Furthermore, this article shows how to use a Bayesian modeling approach to account for the measurement error.
Simulations of Heat Transfer Using Tight-Fitting Twisted Tape Inserts for First Wall Cooling in Molten Salt Breeder Blankets
One of the major components in fusion energy systems is the fusion blanket, which has a vacuum vessel to contain the plasma. As part of the fusion blanket/vacuum vessel, the first wall and plasma-facing components require sufficient cooling to prevent material degradation during operation from the superheated plasma. Most fusion blanket concepts involve first wall and divertor coolant channels with heat transfer enhancements (HTEs) that are intended to withstand the incident high heat fluxes of 1 to 5 MW/m 2 . Twisted tape inserts are a proposed HTE that have been investigated previously for first wall cooling and monoblock divertor cooling channels and in other nonfusion heat transfer components. By inserting twisted tapes into straight pipes, the amount of turbulence in the system can be increased at lower Reynolds numbers by swirling the flow. This results in better heat transfer characteristics with marginal increases in frictional pressure losses. In particular, simulations of high-Prandtl-number fluids such as the proposed molten salt FLiBe in twisted tapes, which is prototypic to liquid immersion blankets, have not been previously explored. Here, in this study, we simulate various Prandtl numbers in pipes with twisted tape inserts using large eddy simulations to determine the effects of increasing Prandtl numbers on heat transfer performance. The quantities of particular interest are the Nusselt number and the friction factor, which were recovered using data reduction techniques to determine impacts on heat transfer and pressure losses. This work serves as a starting point for determining the feasibility of twisted tape inserts for liquid immersion blanket concepts.
PLATO hare-and-hounds exercise: asteroseismic model fitting of main-sequence solar-like pulsators
ABSTRACT Asteroseismology is a powerful tool to infer fundamental stellar properties. The use of these asteroseismic-inferred properties in a growing number of astrophysical contexts makes it vital to understand their accuracy. Consequently, we performed a hare-and-hounds exercise where the hares simulated data for six artificial main-sequence stars and the hounds inferred their properties based on different inference procedures. To mimic a pipeline such as that planned for the PLATO mission, all hounds used the same model grid. Some stars were simulated using the physics adopted in the grid, others a different one. The maximum relative differences found (in absolute value) between the inferred and true values of the mass, radius, and age were 4.32, 1.33, and 11.25 per cent, respectively. The largest systematic differences in radius and age were found for a star simulated assuming gravitational settling, not accounted for in the model grid, with biases of −0.88 per cent (radius) and 8.66 per cent (age). For the mass, the most significant bias (−3.16 per cent) was found for a star with a helium enrichment ratio outside the grid range. Moreover, an ∼7 per cent dispersion in age was found when adopting different prescriptions for the surface corrections or shifting the classical observations by ±1σ. The choice of the relative weight given to the classical and seismic constraints also impacted significantly the accuracy and precision of the results. Interestingly, only a few frequencies were required to achieve accurate results on the mass and radius. For the age the same was true when at least one l = 2 mode was considered.