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At least 289 records · Page 16

Weak Gravity Conjecture, Black Hole Entropy, and Modular Invariance

In recent literature, it has been argued that a mild form of the Weak Gravity Conjecture (WGC) is satisfied by wide classes of effective field theories in which higher-derivative corrections can be shown to shift the charge-to-mass ratios of extremal black holes to larger values. However, this mild form does not directly constrain low-energy physics because the black holes satisfying the WGC have masses above the cutoff of the effective theory. In this note, we point out that in string theory modular invariance can connect a light superextremal state to heavy superextremal states; the latter collapse into black holes at small string coupling. In the context of heterotic string theory, we show that these states are black holes that have α'-exact charge-to-mass ratios exceeding the classical extremality bound. This suggests that modular invariance of the string partition function can be used to relate the existence of a light superextremal particle to the positive shift in charge-to-mass ratio of extremal black holes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

CosmoSIS: Modular cosmological parameter estimation

Cosmological parameter estimation is entering a new era. Large collaborations need to coordinate high-stakes analyses using multiple methods; furthermore such analyses have grown in complexity due to sophisticated models of cosmology and systematic uncertainties. In this paper we argue that modularity is the key to addressing these challenges: calculations should be broken up into interchangeable modular units with inputs and outputs clearly defined. Here we present a new framework for cosmological parameter estimation, CosmoSIS, designed to connect together, share, and advance development of inference tools across the community. We describe the modules already available in CosmoSIS, including CAMB, Planck, cosmic shear calculations, and a suite of samplers. Lastly, we illustrate it using demonstration code that you can run out-of-the-box with the installer available at http://bitbucket.org/joezuntz/cosmosis

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Modular performance prediction for scientific workflows using Machine Learning

Scientific workflows provide an opportunity for declarative computational experiment design in an intuitive and efficient way. A distributed workflow is typically executed on a variety of resources, and it uses a variety of computational algorithms or tools to achieve the desired outcomes. Such a variety imposes additional complexity in scheduling these workflows on large scale computers. As computation becomes more distributed, insights into expected workload that a workflow presents become critical for effective resource allocation. In this paper, we present a modular framework that leverages Machine Learning for creating precise performance predictions of a workflow. The central idea is to partition a workflow in such a way that makes the task of forecasting each atomic unit manageable and gives us a way to combine the individual predictions efficiently. We recognize a combination of an executable and a specific physical resource as a single module. This gives us a handle to characterize workload and machine power as a single unit of prediction. Overall, our modular technique of creating atomic modules and deployment of longest-path approach to estimate workflow performance, allows the framework to adapt to highly complex nested directed acyclic workflows and scale to new scenarios, since it does not make assumptions of underlying workflow structure. We present performance estimation results of independent workflow modules executed on the XSEDE SDSC Comet cluster using various Machine Learning algorithms. The results provide insights into the behavior and effectiveness of different algorithms in the context of scientific workflow performance prediction.

97 MATHEMATICS AND COMPUTING↗

Modular total absorption spectrometer

The design and performance of the Modular Total Absorption Spectrometer built and commissioned at the Oak Ridge National Laboratory is presented here. The active volume of the detector is approximately one ton of NaI(Tl), which results in very high full γ energy peak efficiency of 71% at 6 MeV and nearly flat efficiency of around 81.5% for low energy γ-rays between 300 keV and 1 MeV. In addition to the high peak efficiency, the modular construction of the detector permits the use of a γ-coincidence technique in data analysis as well as β-delayed neutron observation.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Interface Nucleus Templating of Modular Intermetallic Morphologies: Chemical Pressure Complementarity, Columnar Domains, and Complex Disorder in Y 13 Ag 42.7 Zn 29.7

One element of the diversity of intermetallic phases is the formation of complex structures from the assembly of fragments of simpler structures. Recently, we devised the Interface Nuclear Approach as a model for understanding such modular arrangements, in which the intergrowth of different structures is driven by chemical pressure (CP) relief at shared motifs at the domain interfaces, referred to as interface nuclei. In this Article, we present the synthesis, crystal structure, and CP analysis of a new compound that expands on this theme, Y 13 Ag 42.7 Zn 29.7 . Its hexagonal structure contains interpenetrating domains based on the CaPd 5+x and EuMg 5 types. The CaPd 5+x -based regions are reminiscent of the lamellar intergrowth structures previously observed in the Y−Ag−Zn system. In Y 13 Ag 42.7 Zn 29.7 , however, the domains have a different morphology, forming columns that adopt a hexagonal rod-packing. The geometrical features of the remaining spaces are assigned, using the program GrowDomain, to the cores of trigonal units of the EuMg 5 type, while layers of disordered atoms occur at heights along z where the parent structures are mismatched. At the CaPd 5+x -type/EuMg 5 -type interfaces, simple interface nucleus motifs with strong CP-complementarity can be identified, while their distribution within the parent structures supports the notion of templated architectures in modular intermetallics.

Chemical structure↗

Heterologous Gene Expression of N -Terminally Truncated Variants of LipPks1 Suggests a Functionally Critical Structural Motif in the N -terminus of Modular Polyketide Synthase

Streptomyces genomes have a high G + C content and typically use an ATG or GTG codon to initiate protein synthesis. Although gene-finding tools perform well in low GC genomes, it is known that the accuracy in predicting a translational start site (TSS) is much less for high GC genomes. LipPks1 is a Streptomyces-derived, well-characterized modular polyketide synthase (PKS). Here, using this enzyme as a model, we experimentally investigated the effects of alternative TSSs using a heterologous host, Streptomyces venezuelae. One of the TSSs employed boosted the protein level by 59-fold and the product yield by 23-fold compared to the originally annotated start codon. Interestingly, a structural model of the PKS indicated the presence of a structural motif in the N-terminus, which may explain the observed different protein levels together with a proline and arginine-rich sequence that may inhibit translational initiation. Lastly, this structure was also found in six other modular PKSs that utilize noncarboxylated starter substrates, which may guide the selection of optimal TSSs in conjunction with start-codon prediction software.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Biochemical and Structural Basis for Controlling Chemical Modularity in Fungal Polyketide Biosynthesis

Modular collaboration between iterative fungal polyketide synthases (IPKSs) is an important mechanism for generating structural diversity of polyketide natural products. Inter-PKS communication and substrate channeling are controlled in large by the starter unit acyl carrier protein transacylase (SAT) domain found in the accepting IPKS module. Here in this study, we reconstituted the modular biosynthesis of the benzaldehyde core of the chaetoviridin and chaetomugilin azaphilone natural products using the IPKSs CazF and CazM. Our studies revealed a critical role of CazM’s SAT domain in selectively transferring a highly reduced triketide product from CazF. In contrast, a more oxidized triketide that is also produced by CazF and required in later stages of biosynthesis of the final product is not recognized by the SAT domain. The structural basis for the acyl unit selectivity was uncovered by the first X-ray structure of a fungal SAT domain, highlighted by a covalent hexanoyl thioester intermediate in the SAT active site. Finally, the crystal structure of SAT domain will enable protein engineering efforts aimed at mixing and matching different IPKS modules for the biosynthesis of new compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Bio-based production of fuels and industrial chemicals by repurposing antibiotic-producing type I modular polyketide synthases: opportunities and challenges

Complex polyketides comprise a large number of natural products that have broad application in medicine and agriculture. They are produced in bacteria and fungi from large enzyme complexes named type I modular polyketide synthases (PKSs) that are composed of multifunctional polypeptides containing discrete enzymatic domains organized into modules. The modular nature of PKSs has enabled a multitude of efforts to engineer the PKS genes to produce novel polyketides of predicted structure. Finally, we have repurposed PKSs to produce a number of short-chain mono- and di-carboxylic acids and ketones that could have applications as fuels or industrial chemicals.

Yuzawa, Satoshi↗

Development and flight-testing of modular autonomous cultivation systems for biological plastics upcycling aboard the ISS

Cultivation of microorganisms in space has enormous potential to enable in-situ resource utilization (ISRU) Here, we develop an autonomous payload with fully programmable serial passaging and sample preservation, termed the Modular Open Biological Platform (MOBP), and flight-test the MOBP aboard the International Space Station (ISS) by conducting enzymatic and microbial plastics upcycling experiments. The MOBP is a compact, modular bioreactor system that allows for sustained microbial growth via automated media transfers, such as those for sample collection and storage for terrestrial analyses, and precise data monitoring from integrated sensors. The MOBP was flight-tested with two experiments designed to evaluate biological upcycling of the plastic poly(ethylene terephthalate) (PET). The bioproduct βKA can be polymerized into a nylon-6,6 analog with improved properties for use in the production of a variety of materials. We posit the MOBP will aid in democratizing the execution of synthetic biology in spaceflight towards enabling ISRU.

09 BIOMASS FUELS↗

Bond-centric modular design of protein assemblies

Directional interactions that generate regular coordination geometries are a powerful means of guiding molecular and colloidal self-assembly, but implementing such high-level interactions with proteins remains challenging due to their complex shapes and intricate interface properties. Here we describe a modular approach to protein nanomaterial design inspired by the rich chemical diversity that can be generated from the small number of atomic valencies. We design protein building blocks using deep learning-based generative tools, incorporating regular coordination geometries and tailorable bonding interactions that enable the assembly of diverse closed and open architectures guided by simple geometric principles. Experimental characterization confirms the successful formation of more than 20 multicomponent polyhedral protein cages, two-dimensional arrays and three-dimensional protein lattices, with a high (10%–50%) success rate and electron microscopy data closely matching the corresponding design models. Due to modularity, individual building blocks can assemble with different partners to generate distinct regular assemblies, resulting in an economy of parts and enabling the construction of reconfigurable networks for designer nanomaterials.

Biomaterials – proteins↗

A modular chromosomally integrated toolkit for ectopic gene expression in Vibrio cholerae

The ability to express genes ectopically in bacteria is essential for diverse academic and industrial applications. Two major considerations when utilizing regulated promoter systems for ectopic gene expression are (1) the ability to titrate gene expression by addition of an exogenous inducer and (2) the leakiness of the promoter element in the absence of the inducer. Here, we describe a modular chromosomally integrated platform for ectopic gene expression in Vibrio cholerae . We compare the broadly used promoter elements P tac and P BAD to versions that have an additional theophylline-responsive riboswitch (P tac -riboswitch and P BAD -riboswitch). These constructs all exhibited unimodal titratable induction of gene expression, however, max induction varied with P tac > P BAD > P BAD -riboswitch > P tac -riboswitch. We also developed a sensitive reporter system to quantify promoter leakiness and show that leakiness for P tac > P tac -riboswitch > P BAD ; while the newly developed P BAD -riboswitch exhibited no detectable leakiness. We demonstrate the utility of the tightly inducible P BAD -riboswitch construct using the dynamic activity of type IV competence pili in V. cholerae as a model system. The modular chromosomally integrated toolkit for ectopic gene expression described here should be valuable for the genetic study of V. cholerae and could be adapted for use in other species.

59 BASIC BIOLOGICAL SCIENCES↗

Hierarchical deep reinforcement learning reveals a modular mechanism of cell movement

Time-lapse images of cells and tissues contain rich information about dynamic cell behaviours, which reflect the underlying processes of proliferation, differentiation and morphogenesis. However, we lack computational tools for effective inference. Here we exploit deep reinforcement learning (DRL) to infer cell–cell interactions and collective cell behaviours in tissue morphogenesis from three-dimensional (3D) time-lapse images. We use hierarchical DRL (HDRL), known for multiscale learning and data efficiency, to examine cell migrations based on images with a ubiquitous nuclear label and simple rules formulated from empirical statistics of the images. When applied to Caenorhabditis elegans embryogenesis, HDRL reveals a multiphase, modular organization of cell movement. Imaging with additional cellular markers confirms the modular organization as a novel migration mechanism, which we term sequential rosettes. Furthermore, HDRL forms a transferable model that successfully differentiates sequential rosettes-based migration from others. Our study demonstrates a powerful approach to infer the underlying biology from time-lapse imaging without prior knowledge.

59 BASIC BIOLOGICAL SCIENCES↗

Modular microfluidics for point-of-care protein purifications

Biochemical separations are the heart of diagnostic assays and purification methods for biologics. On-chip miniaturization and modularization of separation procedures will enable the development of customized, portable devices for personalized health-care diagnostics and point-of-use production of treatments. In this report, we describe the design and fabrication of miniature ion exchange, size exclusion and affinity chromatography modules for on-chip clean-up of recombinantly-produced proteins. Our results demonstrate that these common separations techniques can be implemented in microfluidic modules with performance comparable to conventional approaches. We introduce embedded 3-D microfluidic interconnects for integrating micro-scale separation modules that can be arranged and reconfigured to suit a variety of fluidic operations or biochemical processes. In conclusion, we demonstrate the utility of the modular approach with a platform for the enrichment of enhanced green fluorescent protein (eGFP) from Escherichia coli lysate through integrated affinity and size-exclusion chromatography modules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A divergent synthetic route to functional copolymer libraries via modular polymers

High-throughput polymer synthesis enables rapid exploration of chemical space but remains limited by batch-to-batch inconsistencies that can obscure structure–property relationship trends. To address this challenge, we developed a synthetic approach to produce multifunctional copolymers using post-polymerization modification of activated ester modular polymers with commercially available amines. Easily derivitized parent polymers—poly(tetrafluorophenyl acrylate) and poly(tetrafluorophenyl styrene sulfonate)—were synthesized by RAFT polymerization to yield single polymer batches containing highly reactive tetrafluorophenyl esters or sulfonate esters on each repeat unit. Tuning post-polymerization modification reaction conditions enabled the addition of sub-stoichiometric amounts of amines (relative to the repeat unit) to yield partially functionalized intermediates that could then be further derivatized. Reaction monitoring by 19 F NMR spectroscopy confirmed good control over these sequential post-polymerization modifications. This synthetic route produced a variety of copolymers with defined comonomer ratios while preserving the underlying polymer structure (degree of polymerization, dispersity, tacticity) for both the acrylate and styrene sulfonate backbones. We further applied this approach in a divergent manner to create a small library of structurally distinct copolymers from a single parent batch in three synthetic steps. This modular, divergent synthesis demonstrates a general route to structurally consistent copolymer libraries that enable systematic studies of structure–property relationships and can accelerate functional materials discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modular cryogenic interconnects for multi-qubit devices

We have developed a modular interconnect platform for the control and readout of multiple solid-state qubits at cryogenic temperatures. The setup provides 74 filtered dc-bias connections, 32 control and readout connections with −3 dB frequency above 5 GHz, and 4 microwave feed lines that allow low loss (less than 3 dB) transmission 10 GHz. The incorporation of a radio-frequency interposer enables the platform to be separated into two printed circuit boards, decoupling the simple board that is bonded to the qubit chip from the multilayer board that incorporates expensive connectors and components. This modular approach lifts the burden of duplicating complex interconnect circuits for every prototype device. We report the performance of this platform at milli-Kelvin temperatures, including signal transmission and crosstalk measurements.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A modular ultra-high vacuum millikelvin scanning tunneling microscope

We describe the design, construction, and performance of an ultra-high vacuum (UHV) scanning tunneling microscope (STM) capable of imaging at dilution-refrigerator temperatures and equipped with a vector magnet. The primary objective of our design is to achieve a high level of modularity by partitioning the STM system into a set of easily separable, interchangeable components. This naturally segregates the UHV needs of STM instrumentation from the typically non-UHV construction of a dilution refrigerator, facilitating the usage of non-UHV materials while maintaining a fully bakeable UHV chamber that houses the STM. Here, the modular design also permits speedy removal of the microscope head from the rest of the system, allowing for repairs, modifications, and even replacement of the entire microscope head to be made at any time without warming the cryostat or compromising the vacuum. Without using cryogenic filters, we measured an electron temperature of 184 mK on a superconducting Al(100) single crystal.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Chiral algebra, localization, modularity, surface defects, and all that

We study the 2D vertex operator algebra (VOA) construction in 4D N = 2 superconformal field theories on S 3 × S 1 , focusing on both old puzzles and new observations. The VOA lives on a two-torus T 2 ⊂ S 3 × S 1 , it is 1 2 Z -graded, and this torus is equipped with the natural choice of spin structure (1,0) for the Z + 1 2 -graded operators, corresponding to the NS sector vacuum character. By analyzing the possible refinements of the Schur index that preserves the VOA, we find that it admits discrete deformations, which allows access to the remaining spin structures (1,1), (0,1), and (0,0), of which the latter two involve the inclusion of a particular surface defect. For Lagrangian theories, we perform the detailed analysis: we describe the natural supersymmetric background, perform localization, and derive the gauged symplectic boson action on a torus in any spin structure. In the absence of flavor fugacities, the 2D and 4D path integrals precisely match, including the Casimir factors. We further analyze the 2D theory: we identify its integration cycle and the two-point functions and interpret flavor holonomies as screening charges in the VOA. Next, we make some observations about modularity; the T-transformation acts on our four partition functions and lifts to a large diffeomorphism on S 3 × S 1 . More interestingly, we generalize the four partition functions on the torus to an infinite family labeled by both the spin structure and the integration cycle inside the complexified maximal torus of the gauge group. Members of this family transform into one another under the full modular group, and we confirm the recent observation that the S-transform of the Schur index in Lagrangian theories exhibits logarithmic behavior. Finally, we comment on how locally our background reproduces the Ω-background.

97 MATHEMATICS AND COMPUTING↗

An Application of Molecular Recognition for the Efficient Removal of Cesium from Hanford Nuclear Waste by Modular Solvent Extraction

In this work, experimental results leading to flowsheet design are presented showing how a calixarene-crown ether based solvent-extraction process can meet the challenge of cesium removal from nuclear tank wastes stored at the US Department of Energy Hanford site. Cleanup of legacy Cold War nuclear waste stored in underground tanks represents one of the greatest environmental challenges facing the US Department of Energy in terms of risk, cost, and effectiveness of applicable science and technology. Planning for the cleanup at the Hanford Site calls for the removal of the radioactive fission product 137Cs from its alkaline salt waste, including the use of modular processes that can be deployed near the tank farms. To meet the resulting need for extremely high selectivity, the Next-Generation Caustic-Side Solvent Extraction (NG-CSSX) process employing a calix[4]arene-crown ether in modified kerosene has been adapted to remove sub-millimolar cesium in competition with molar sodium and potassium in a high-nitrate alkaline matrix. Potassium loading in the solvent was determined in extraction, scrubbing, and stripping, leading to an empirical model closely approximating cesium distribution ratios for a variety of Hanford waste types. Process chemistry has been developed based on this molecular-recognition approach, focusing on the competitive effect of potassium loading and the mitigating process modifications needed, including extending the scrub section. The result is a modular flowsheet design that can achieve cesium decontamination factors well in excess of 15,000 even for the worst-case Hanford waste.

Williams, Neil [ORNL] (ORCID:000000023159226X)↗