Domain-specific ChatBots for Science using Embeddings

Large language models (LLMs) have emerged as powerful machine-learning systems capable of handling a myriad of tasks. Tuned versions of these systems have been turned into chatbots that can respond to user queries on a vast diversity of topics, providing informative and creative replies. However, their application to physical science research remains limited owing to their incomplete knowledge in these areas, contrasted with the needs of rigor and sourcing in science domains. Here, we demonstrate how existing methods and software tools can be easily combined to yield a domain-specific chatbot. The system ingests scientific documents in existing formats, and uses text embedding lookup to provide the LLM with domain-specific contextual information when composing its reply. We similarly demonstrate that existing image embedding methods can be used for search and retrieval across publication figures. These results confirm that LLMs are already suitable for use by physical scientists in accelerating their research efforts.Comment: 12 pages, 5 figure

Advances in Kriging-Based Autonomous X-Ray Scattering Experiments.

Autonomous experimentation is an emerging paradigm for scientific discovery, wherein measurement instruments are augmented with decision-making algorithms, allowing them to autonomously explore parameter spaces of interest. We have recently demonstrated a generalized approach to autonomous experimental control, based on generating a surrogate model to interpolate experimental data, and a corresponding uncertainty model, which are computed using a Gaussian process regression known as ordinary Kriging (OK). We demonstrated the successful application of this method to exploring materials science problems using x-ray scattering measurements at a synchrotron beamline. Here, we report several improvements to this methodology that overcome limitations of traditional Kriging methods. The variogram underlying OK is global and thus insensitive to local data variation. We augment the Kriging variance with model-based measures, for instance providing local sensitivity by including the gradient of the surrogate model. As with most statistical regression methods, OK minimizes the number of measurements required to achieve a particular model quality. However, in practice this may not be the most stringent experimental constraint; e.g. the goal may instead be to minimize experiment duration or material usage. We define an adaptive cost function, allowing the autonomous method to balance information gain against measured experimental cost. We provide synthetic and experimental demonstrations, validating that this improved algorithm yields more efficient autonomous data collection

Investigation of photomechanical surface patterning in azobenzene materials

Detailed modeling and experiments were conducted in order to elucidate the nature of photo-induced surface patterning in azobenzene materials. Using a cellular automaton simulation, it was established that both the absolute temperature rise, and the thermal gradient, in a film during patterning are negligibly small. These results, confirmed experimentally by patterning samples on substrates of differing thermal conductivity, eliminate purely thermal mechanisms as candidate explanations for mass transport. The length-scale of patterning was probed by monitoring the formation and thermal erasure of gratings as a function of film thickness. In both cases, film dynamics deviate from bulk behavior when film thickness decreases below ~150 nm. Moreover, mass transport is completely hindered below 40 nm. This deviation of polymer dynamics implies that photo-induced mass transport involves the coordinated motion of many polymer chains in the depth of the material, and not merely surface diffusion of individual chains.Neutron reflectometry was applied to measure in detail the photomechanical response of azobenzene materials. A significant photo-expansion effect, up to 17%, was observed at 25°C, attributed to the molecular free volume requirement of azo isomerization. Above a well-defined crossover temperature, which occurs at ~50°C for poly(disperse red 1 acrylate), the material response is inverted. At these elevated temperatures, photo-contraction effects, of more than -15%, were instead measured. In this case the combination of photo-induced motion and thermally-enabled mobility enables aggregation, aromatic stacking, and crystallization of the azobenzene dipoles. Using localized surface patterning experiments, it was confirmed that the mass transport phenomenon exhibits the same trend and phase relationship as the photomechanical effect. It is argued that the fundamental origin of surface mass transport in azo materials is in fact this newly identified photomechanical effect. This suggestion enables explanation of a variety of previously contradictory results in the literature

Evidence of stratification in binary colloidal films from microbeam X-ray scattering: Toward optimizing the evaporative assembly processes for coatings

Colloidal films have many important applications where a layered configuration is desirable, including flexible electronics, anti-reflective coatings, and anti-microbial paints. We report stratification during evaporative film formation in binary colloidal dispersion, probed using a novel microbeam small-angle X-ray scattering (SAXS) technique. To our knowledge, SAXS approaches have not been used to experimentally obtain quantitative data of concentration profiles in multicomponent colloidal films. We measured the local scattering of a film at different vertical locations using a microfocused X-ray beam and determined particle concentrations at different film depths using a linear combination analysis of the mixed film and pure film scattering data. Using small particle size ratios ranging from 2.55 to 1.25, we experimentally observed and quantify three distinct stratification configurations: inverted small on- top, large-on-top, and no stratification. Our results show some agreement with a previously proposed stratification state diagram, although there are some limitations. Experimental verification of these stratification phenomena is critical to fully understanding the physics of particle movement and structure development during film formation, which is crucial for optimizing evaporative assembly processes for coatings.Financial support for this work was provided by the National Science Foundation through award CBET-1335787 and a Department of Education Graduate Assistance in Areas of National Need (GAANN) fellowship for A. J. C., Award P200A160163. This research used beamline 11-BM, CMS, of the National Synchrotron Light Source II, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Brookhaven National Laboratory under Contract No. DE-SC0012704

Self-assembly of a silicon-containing side-chain liquid crystalline block copolymer in bulk and in thin films: kinetic pathway of a cylinder to sphere transition

The self-assembly of a high-χ silicon-containing side-chain liquid crystalline block copolymer (LC BCP) in bulk and in thin films is reported, and the structural transition process from the hexagonally packed cylinder (HEX) to the body-centered cubic structure (BCC) in thin films was examined by both reciprocal and real space experimental methods. The block copolymer, poly(dimethylsiloxane-b-11-(4′-cyanobiphenyl-4-yloxy)undecylmethacrylate) (PDMS-b-P(4CNB11C)MA) with a molecular weight of 19.5 kg mol−1 and a volume fraction of PDMS 27% self-assembled in bulk into a hierarchical nanostructure of sub-20 nm HEX cylinders of PDMS with the P(4CNB11C)MA block exhibiting a smectic LC phase with a 1.61 nm period. The structure remained HEX as the P(4CNB11C)MA block transformed to an isotropic phase at ∼120 °C. In the thin films, the PDMS cylindrical microdomains were oriented in layers parallel to the substrate surface. The LC block formed a smectic LC phase which transformed to an isotropic phase at ∼120 °C, and the microphase-separated nanostructure transformed from HEX to BCC spheres at ∼160 °C. The hierarchical structure as well as the dynamic structural transition of the thin films were characterized using in situ grazing-incidence small-angle X-ray scattering and grazing-incidence wide-angle X-ray scattering. The transient morphologies from the HEX to BCC structure in thin films were captured by scanning electron microscopy and atomic force microscopy, and the transition pathway was described.National Science Foundation (U.S.) (DMR-1606911)National Natural Science Foundation (China) (Grant 51403132)National Natural Science Foundation (China) (Grant 51773124

Autonomous Materials Discovery Driven by Gaussian Process Regression with Inhomogeneous Measurement Noise and Anisotropic Kernels

A majority of experimental disciplines face the challenge of exploring large and high-dimensional parameter spaces in search of new scientific discoveries. Materials science is no exception; the wide variety of synthesis, processing, and environmental conditions that influence material properties gives rise to particularly vast parameter spaces. Recent advances have led to an increase in efficiency of materials discovery by increasingly automating the exploration processes. Methods for autonomous experimentation have become more sophisticated recently, allowing for multi-dimensional parameter spaces to be explored efficiently and with minimal human intervention, thereby liberating the scientists to focus on interpretations and big-picture decisions. Gaussian process regression (GPR) techniques have emerged as the method of choice for steering many classes of experiments. We have recently demonstrated the positive impact of GPR-driven decision-making algorithms on autonomously steering experiments at a synchrotron beamline. However, due to the complexity of the experiments, GPR often cannot be used in its most basic form, but rather has to be tuned to account for the special requirements of the experiments. Two requirements seem to be of particular importance, namely inhomogeneous measurement noise (input dependent or non-i.i.d.) and anisotropic kernel functions, which are the two concepts that we tackle in this paper. Our synthetic and experimental tests demonstrate the importance of both concepts for experiments in materials science and the benefits that result from including them in the autonomous decision-making process

Quaternary Organic Solar Cells Enhanced by Cocrystalline Squaraines with Power Conversion Efficiencies >10%

The incorporation of multiple donors into the bulk-heterojunction layer of organic polymer solar cells (PSCs) has been demonstrated as a practical and elegant strategy to improve photovoltaics performance. However, it is challenging to successfully design and blend multiple donors, while minimizing unfavorable interactions (e.g., morphological traps, recombination centers, etc.). Here, a new Förster resonance energy transfer-based design is shown utilizing the synergistic nature of three light active donors (two small molecules and a high-performance donor–acceptor polymer) with a fullerene acceptor to create highly efficient quaternary PSCs with power conversion efficiencies (PCEs) of up to 10.7%. Within this quaternary architecture, it is revealed that the addition of small molecules in low concentrations broadens the absorption bandwidth, induces cocrystalline molecular conformations, and promotes rapid (picosecond) energy transfer processes. These results provide guidance for the design of multiple-donor systems using simple processing techniques to realize single-junction PSC designs with unprecedented PCEs

Quaternary Organic Solar Cells Enhanced by Cocrystalline Squaraines with Power Conversion Efficiencies >10%

The incorporation of multiple donors into the bulk-heterojunction layer of organic polymer solar cells (PSCs) has been demonstrated as a practical and elegant strategy to improve photovoltaics performance. However, it is challenging to successfully design and blend multiple donors, while minimizing unfavorable interactions (e.g., morphological traps, recombination centers, etc.). Here, a new Förster resonance energy transfer-based design is shown utilizing the synergistic nature of three light active donors (two small molecules and a high-performance donor–acceptor polymer) with a fullerene acceptor to create highly efficient quaternary PSCs with power conversion efficiencies (PCEs) of up to 10.7%. Within this quaternary architecture, it is revealed that the addition of small molecules in low concentrations broadens the absorption bandwidth, induces cocrystalline molecular conformations, and promotes rapid (picosecond) energy transfer processes. These results provide guidance for the design of multiple-donor systems using simple processing techniques to realize single-junction PSC designs with unprecedented PCEs

The Phylogenetics and Ecology of the Orthopoxviruses Endemic to North America

The data presented herein support the North American orthopoxviruses (NA OPXV) in a sister relationship to all other currently described Orthopoxvirus (OPXV) species. This phylogenetic analysis reaffirms the identification of the NA OPXV as close relatives of “Old World” (Eurasian and African) OPXV and presents high support for deeper nodes within the Chordopoxvirinae family. The natural reservoir host(s) for many of the described OPXV species remains unknown although a clear virus-host association exists between the genus OPXV and several mammalian taxa. The hypothesized host associations and the deep divergence of the OPXV/NA OPXV clades depicted in this study may reflect the divergence patterns of the mammalian faunas of the Old and New World and reflect a more ancient presence of OPXV on what are now the American continents. Genes from the central region of the poxvirus genome are generally more conserved than genes from either end of the linear genome due to functional constraints imposed on viral replication abilities. The relatively slower evolution of these genes may more accurately reflect the deeper history among the poxvirus group, allowing for robust placement of the NA OPXV within Chordopoxvirinae. Sequence data for nine genes were compiled from three NA OPXV strains plus an additional 50 genomes collected from Genbank. The current, gene sequence based phylogenetic analysis reaffirms the identification of the NA OPXV as the nearest relatives of “Old World” OPXV and presents high support for deeper nodes within the Chordopoxvirinae family. Additionally, the substantial genetic distances that separate the currently described NA OPXV species indicate that it is likely that many more undescribed OPXV/NA OPXV species may be circulating among wild animals in North America

Multisystem Inflammatory Syndrome in Children — Initial Therapy and Outcomes

This article is made available for unrestricted research re-use and secondary analysis in any form or be any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.Background: The assessment of real-world effectiveness of immunomodulatory medications for multisystem inflammatory syndrome in children (MIS-C) may guide therapy. Methods: We analyzed surveillance data on inpatients younger than 21 years of age who had MIS-C and were admitted to 1 of 58 U.S. hospitals between March 15 and October 31, 2020. The effectiveness of initial immunomodulatory therapy (day 0, indicating the first day any such therapy for MIS-C was given) with intravenous immune globulin (IVIG) plus glucocorticoids, as compared with IVIG alone, was evaluated with propensity-score matching and inverse probability weighting, with adjustment for baseline MIS-C severity and demographic characteristics. The primary outcome was cardiovascular dysfunction (a composite of left ventricular dysfunction or shock resulting in the use of vasopressors) on or after day 2. Secondary outcomes included the components of the primary outcome, the receipt of adjunctive treatment (glucocorticoids in patients not already receiving glucocorticoids on day 0, a biologic, or a second dose of IVIG) on or after day 1, and persistent or recurrent fever on or after day 2. Results: A total of 518 patients with MIS-C (median age, 8.7 years) received at least one immunomodulatory therapy; 75% had been previously healthy, and 9 died. In the propensity-score-matched analysis, initial treatment with IVIG plus glucocorticoids (103 patients) was associated with a lower risk of cardiovascular dysfunction on or after day 2 than IVIG alone (103 patients) (17% vs. 31%; risk ratio, 0.56; 95% confidence interval [CI], 0.34 to 0.94). The risks of the components of the composite outcome were also lower among those who received IVIG plus glucocorticoids: left ventricular dysfunction occurred in 8% and 17% of the patients, respectively (risk ratio, 0.46; 95% CI, 0.19 to 1.15), and shock resulting in vasopressor use in 13% and 24% (risk ratio, 0.54; 95% CI, 0.29 to 1.00). The use of adjunctive therapy was lower among patients who received IVIG plus glucocorticoids than among those who received IVIG alone (34% vs. 70%; risk ratio, 0.49; 95% CI, 0.36 to 0.65), but the risk of fever was unaffected (31% and 40%, respectively; risk ratio, 0.78; 95% CI, 0.53 to 1.13). The inverse-probability-weighted analysis confirmed the results of the propensity-score-matched analysis. Conclusions: Among children and adolescents with MIS-C, initial treatment with IVIG plus glucocorticoids was associated with a lower risk of new or persistent cardiovascular dysfunction than IVIG alone. (Funded by the Centers for Disease Control and Prevention.)