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At least 1,243 records · Page 69

Structures of single-layer {beta}-sheet proteins evolved from {beta}-hairpin repeats

Free-standing single-layer beta-sheets are extremely rare in naturally occurring proteins, even though beta-sheet motifs are ubiquitous. Here we report the crystal structures of three homologous, single-layer, anti-parallel beta-sheet proteins, comprised of three or four twisted beta-hairpin repeats. The structures reveal that, in addition to the hydrogen bond network characteristic of beta-sheets, additional hydrophobic interactions mediated by small clusters of residues adjacent to the turns likely play a significant role in the structural stability and compensate for the lack of a compact hydrophobic core. These structures enabled identification of a family of secreted proteins that are broadly distributed in bacteria from the human gut microbiome and are putatively involved in the metabolism of complex carbohydrates. A conserved surface patch, rich in solvent-exposed tyrosine residues, was identified on the concave surface of the beta-sheet. These new modular single-layer beta-sheet proteins may serve as a new model system for studying folding and design of beta-rich proteins.

beta-hairpin repeats↗

Digital Twins for Nuclear Power Plants and Facilities

The nuclear digital twin (DT) is the virtual representation of a nuclear energy system across its lifecycle. The nuclear DT uses real-time information and other data sources to improve the process of design, licensing, construction, security, O&M, decommissioning, and waste disposal. By leveraging the knowledge base and experience from the past 40 years of LWR operation, the nuclear DT is helping to accelerate the development and deployment of advanced nuclear technology in areas of passive safety, new fuel forms, instrumentation, and reactor control. For the currently operating nuclear fleet, DTs are reducing the operational risks, increasing plant availability, increasing energy capability, and reducing electricity production costs. For advanced fission and fusion reactors, DTs are being used to design for passive safety and built-in security-by-design. Rapidly deployable small modular reactor (SMR) and microreactor designs compatible with modular construction techniques and advanced manufacturing will be the new normal, reducing the need for large capital expenditures and compressing construction schedules. In addition, lower operational and maintenance costs will be realized by reducing the complexity of operations, staffing needs, and maintenance-related activities.

Kropaczek, Dave↗

Sequencing BPS spectra

In this article, we provide both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (re fined) modular S-matrix. This leads to the identi fication of modular transformations in Chern-Simons theory and 3d N = 2 theory via the 3d/3d correspondence. In conclusion, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Holographic duality for Ising CFT with boundary

We extend the holographic duality between 3d pure gravity and 2d Ising CFT proposed in ref. [1] to CFTs with boundaries. Besides the usual asymptotic boundary, the dual bulk spacetime now has a real cutoff, on which live branes with finite tension, giving Neumann boundary condition on the metric tensor. The strongly coupled bulk theory requires that we dress the well-known semiclassical AdS/BCFT answer with boundary gravitons, turning the partition function into the form of Virasoro characters. Using this duality, we relate the brane tensions to the modular S-matrix elements of the dual BCFT and derive the transformation between gravitational solutions with different brane tensions under modular S action.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

The holographic shape of entanglement and Einstein’s equations

We study shape-deformations of the entanglement entropy and the modular Hamiltonian for an arbitrary subregion and state (with a smooth dual geometry) in a holographic conformal field theory. More precisely, we study a double-deformation comprising of a shape deformation together with a state deformation, where the latter corresponds to a small change in the bulk geometry. Using a purely gravitational identity from the Hollands-Iyer-Wald formalism together with the assumption of equality between bulk and boundary modular flows for the original, undeformed state and subregion, we rewrite a purely CFT expression for this double deformation of the entropy in terms of bulk gravitational variables and show that it precisely agrees with the Ryu-Takayanagi formula including quantum corrections. As a corollary, this gives a novel, CFT derivation of the JLMS formula for arbitrary subregions in the vacuum, without using the replica trick. Finally, we use our results to give an argument that if a general, asymptotically AdS spacetime satisfies the Ryu-Takayanagi formula for arbitrary subregions, then it must necessarily satisfy the non-linear Einstein equation.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Duality web on a 3D Euclidean lattice and manifestation of hidden symmetries

We generalize our previous lattice construction of the abelian bosonization duality in 2 + 1 dimensions to the entire web of dualities as well as the N f = 2 self-duality, via the lattice implementation of a set of modular transformations in the theory space. The microscopic construction provides explicit operator mappings, and allows the manifestation of some hidden symmetries. It also exposes certain caveats and implicit assumptions beneath the usual application of the modular transformations to generate the web of dualities. Lastly, we make brief comments on the non-relativistic limit of the dualities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Orientation reversal and the Chern-Simons natural boundary

We show that the fundamental property of preservation of relations, underlying resurgent analysis, provides a new perspective on crossing a natural boundary, an important general problem in theoretical and mathematical physics. This reveals a deeper rigidity aspect of resurgence in a quantum field theory path integral. The physical context here is the non-perturbative completion of complex Chern-Simons theory that associates to a 3-manifold a collection of q-series invariants labeled by Spinc structures, for which crossing the natural boundary corresponds to orientation reversal of the 3-manifold. Our new resurgent perspective leads to a practical numerical algorithm that generates q-series which are dual to unary q-series composed of false theta functions. Until recently, these duals were only known in a limited number of cases, essentially based on Ramanujan’s mock theta functions, and the common belief was that the duals might not even exist in the general case. Resurgence analysis identifies as primary objects Mordell integrals: up to changes of variables, they are Laplace transforms of resurgent functions. Their unique Borel summed transseries decomposition on either side of the Stokes line is simply the unique decomposition into real and imaginary parts. In turn, the latter are combinations of unary q-series in terms of q and its modular counterpart $\overset{\sim }{q}$ , and are resurgent by construction. The Mordell integral is analytic across the natural boundary of the q and $\overset{\sim }{q}$ series, and uniqueness of a similar decomposition which preserves algebraic relations on the other side of the boundary defines the unique boundary crossing of the q series. We demonstrate that this continuation can be efficiently implemented numerically. In the cases where unique mock modular identities are known, they are found by this numerical procedure, but the procedure can go well beyond the known list of identities. A particularly interesting feature of the resurgent approach is that it reveals new aspects, and is very different from other known approaches based on indefinite theta series, Appell-Lerch sums, and representation theory of logarithmic vertex operator algebras.

Chern-Simons theories↗

Bootstrapping the spectral function: on the uniqueness of Liouville and the universality of BTZ

Here, we introduce spectral functions that capture the distribution of OPE coefficients and density of states in two-dimensional conformal field theories, and show that nontrivial upper and lower bounds on the spectral function can be obtained from semidefinite programming. We find substantial numerical evidence indicating that OPEs involving only scalar Virasoro primaries in a c > 1 CFT are necessarily governed by the structure constants of Liouville theory. Combining this with analytic results in modular bootstrap, we conjecture that Liouville theory is the unique unitary c > 1 CFT whose primaries have bounded spins. We also use the spectral function method to study modular constraints on CFT spectra, and discuss some implications of our results on CFTs of large c and large gap, in particular, to what extent the BTZ spectral density is universal.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Recovering the QNEC from the ANEC

We study the relative entropy in QFT comparing the vacuum state to a special family of purifications determined by an input state and constructed using relative modular flow. We use this to prove a conjecture by Wall that relates the shape derivative of relative entropy to a variational expression over the averaged null energy (ANE) of possible purifications. Furthermore, this variational expression can be used to easily prove the quantum null energy condition (QNEC). We formulate Wall’s conjecture as a theorem pertaining to operator algebras satisfying the properties of a half-sided modular inclusion, with the additional assumption that the input state has finite averaged null energy. We also give a new derivation of the strong superadditivity property of relative entropy in this con- text. We speculate about possible connections to the recent methods used to strengthen monotonicity of relative entropy with recovery maps.

97 MATHEMATICS AND COMPUTING↗

Structure and enzymatic characterization of CelD endoglucanase from the anaerobic fungus Piromyces finnis

Anaerobic fungi found in the guts of large herbivores are prolific biomass degraders whose genomes harbor a wealth of carbohydrate-active enzymes (CAZymes), of which only a handful are structurally or biochemically characterized. Here, we report the structure and kinetic rate parameters for a glycoside hydrolase (GH) family 5 subfamily 4 enzyme (CelD) from Piromyces finnis, a modular, cellulosome-incorporated endoglucanase that possesses three GH5 domains followed by two C-terminal fungal dockerin domains (double dockerin). We present the crystal structures of an apo wild-type CelD GH5 catalytic domain and its inactive E154A mutant in complex with cellotriose at 2.5 and 1.8 Å resolution, respectively, finding the CelD GH5 catalytic domain adopts the (β/α) 8 -barrel fold common to many GH5 enzymes. Structural superimposition of the apo wild-type structure with the E154A mutant-cellotriose complex supports a catalytic mechanism in which the E154 carboxylate side chain acts as an acid/base and E278 acts as a complementary nucleophile. Further analysis of the cellotriose binding pocket highlights a binding groove lined with conserved aromatic amino acids that when docked with larger cellulose oligomers is capable of binding seven glucose units and accommodating branched glucan substrates. Activity analyses confirm P. finnis CelD can hydrolyze mixed linkage glucan and xyloglucan, as well as carboxymethylcellulose (CMC). Measured kinetic parameters show the P. finnis CelD GH5 catalytic domain has CMC endoglucanase activity comparable to other fungal endoglucanases with k cat = 6.0 ± 0.6 s –1 and K m = 7.6 ± 2.1 g/L CMC. Enzyme kinetics were unperturbed by the addition or removal of the native C-terminal dockerin domains as well as the addition of a non-native N-terminal dockerin, suggesting strict modularity among the domains of CelD.

59 BASIC BIOLOGICAL SCIENCES↗

Omics-driven onboarding of the carotenoid producing red yeast Xanthophyllomyces dendrorhous CBS 6938

Transcriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Here, we derive constitutive and light-regulated promoters directly from transcriptomics data of the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938 (anamorph Phaffia rhodozyma) and use these promoters with other genetic elements to create a modular synthetic biology parts collection for this organism. X. dendrorhous is currently the sole biotechnologically relevant yeast in the Tremellomycete class-it produces large amounts of astaxanthin, especially under oxidative stress and exposure to light. Thus, we performed transcriptomics on X. dendrorhous under different wavelengths of light (red, green, blue, and ultraviolet) and oxidative stress. Differential gene expression analysis (DGE) revealed that terpenoid biosynthesis was primarily upregulated by light through crtI, while oxidative stress upregulated several genes in the pathway. Further gene ontology (GO) analysis revealed a complex survival response to ultraviolet (UV) where X. dendrorhous upregulates aromatic amino acid and tetraterpenoid biosynthesis and downregulates central carbon metabolism and respiration. The DGE data was also used to identify 26 constitutive and regulated genes, and then, putative promoters for each of the 26 genes were derived from the genome. Simultaneously, a modular cloning system for X. dendrorhous was developed, including integration sites, terminators, selection markers, and reporters. Each of the 26 putative promoters were integrated into the genome and characterized by luciferase assay in the dark and under UV light. The putative constitutive promoters were constitutive in the synthetic genetic context, but so were many of the putative regulated promoters. Notably, one putative promoter, derived from a hypothetical gene, showed ninefold activation upon UV exposure. Thus, this study reveals metabolic pathway regulation and develops a genetic parts collection for X. dendrorhous from transcriptomic data. Therefore, this study demonstrates that combining systems biology and synthetic biology into an omics-to-parts workflow can simultaneously provide useful biological insight and genetic tools for nonconventional microbes, particularly those without a related model organism. This approach can enhance current efforts to engineer diverse microbes.

60 APPLIED LIFE SCIENCES↗

Performance evaluations of signed and unsigned noisy approximate quantum Fourier arithmetic

The Quantum Fourier Transform (QFT) grants competitive advantages, especially in resource usage and circuit approximation, for performing arithmetic operations on quantum computers, and offers a potential route toward a numerical quantum-computational paradigm. In this paper, we utilize efficient techniques to implement QFT-based integer addition and multiplications. These operations are fundamental to various quantum applications including Shor’s algorithm, weighted-sum optimization problems in data processing and machine learning, and quantum algorithms requiring inner products. We carry out performance evaluations of these implementations based on IBM’s superconducting-qubit architecture using different compatible noise models. We isolate the sensitivity of the component quantum circuits on both one-/two-qubit gate error rates, and the number of the arithmetic operands’ superposed integer states. We analyze performance and identify the most effective approximation depths for unsigned quantum addition and quantum multiplication within the given context. We then perform a similar analysis of signed addition and compare to the unsigned results. We observe significant dependency of the optimal approximation depth on the degree of machine noise and the number of superposed states in certain performance regimes. Finally, we elaborate on the algorithmic challenges—relevant to signed, unsigned, modular and non-modular versions—that could also be applied to current implementations of QFT-based subtraction, division, exponentiation, and their potential tensor extensions. Here, we analyze the performance trends in our results and speculate on possible future developments within this computational paradigm.

Computational models↗

Mocking the u-plane integral

Abstract The u -plane integral is the contribution of the Coulomb branch to correlation functions of $${\mathcal {N}}=2$$ N = 2 gauge theory on a compact four-manifold. We consider the u -plane integral for correlators of point and surface observables of topologically twisted theories with gauge group $$\mathrm{SU}(2)$$ SU ( 2 ) , for an arbitrary four-manifold with $$(b_1,b_2^+)=(0,1)$$ ( b 1 , b 2 + ) = ( 0 , 1 ) . The u -plane contribution equals the full correlator in the absence of Seiberg–Witten contributions at strong coupling, and coincides with the mathematically defined Donaldson invariants in such cases. We demonstrate that the u -plane correlators are efficiently determined using mock modular forms for point observables, and Appell–Lerch sums for surface observables. We use these results to discuss the asymptotic behavior of correlators as function of the number of observables. Our findings suggest that the vev of exponentiated point and surface observables is an entire function of the fugacities.

Mathematics↗

Large Format Composite Additive Manufacturing for Low-Head Hydropower

Hydropower with a small elevation change from inlet to outlet, known as “low-head” hydropower, is a relatively untapped resource for reliable green power generation. One major barrier to entry is the cost of the components needed to generate the power. Each installation site is unique, with various head levels, flow rates, and other unique site characteristics that drive up the cost of development and installation. As a result, custom-made components are necessary because the sites are intrinsically inefficient. However, customized parts are generally more expensive to manufacture than ready-made parts. Often times, the cost of custom-made components is so high that the low-head hydropower installation becomes non-viable. Additive manufacturing offers the ability to make custom components, ideal for one-off applications, at low costs that are well suited for the needs of low-head hydropower. Indirect additive manufacturing, such as making tools or dies rather than end use components, can also be used to make low-cost composite tooling as needed for these custom applications. This paper explores the use of additive manufacturing, both directly and indirectly, to produce the components of a turbine system for a low-head hydropower site. The parts were designed to form a unique modular system, which saves time for future designs and iterations. The system has operated for more than three years without failure at a test site in Wisconsin, USA. This work serves as a basis for future application of AM to low-head systems, in which the modular components can be customized for each unique hydropower installation.

36 MATERIALS SCIENCE↗

Automated compatibility checking of prefabricated components using 3D as-built models and BIM

There have been recent efforts to use reality capture technologies to perform remote quality control in construction. However, there is a lack of research efforts in detecting construction incompatibilities in modular construction using reality capture technologies. The construction incompatibilities in modular construction often cause reworks and delays in the project schedule. To address this issue, this paper presents a general compatibility analysis method that propose scanning the modules in manufacturing plant and construction site, and check module-to-module compatibility remotely, prior to the shipment and installation. This study provides three sample module-to-module compatibility scenarios to validate the proposed compatibility analysis. The case study results show that the compatibility analysis method was able to identify the compatibility issues with high accuracy. Lastly, the compatibility analysis method was validated in terms of accuracy and time performance in six scenarios that was defined on the modules.

42 ENGINEERING↗

Reinforced double-threaded slide-ring networks for accelerated hydrogel discovery and 3D printing

Traditionally, slide-ring gels are stretchable but soft as a result of an elasticity-stretchability trade-off. Herein, we introduce a new approach to breaking this trade-off and creating reinforced slide-ring networks with mobile crosslinkers. Our approach involves the construction of a polyethylene glycol double-threaded γ-cyclodextrin-based pro-slide-ring crosslinker that serves as a modular component for 3D printing and copolymerization. The resulting crystalline-domain-reinforced slide-ring hydrogels, or CrysDoS-gels, exhibit both high elasticity and high stretchability. The modular synthesis allows for high-throughput synthesis of CrysDoS-gels, generating a large amount of data for structure-property analysis. Here, by employing data science techniques, such as machine learning and linear regression, not only were we able to identify which chemical components influence the mechanical properties of CrysDoS-gels, but this analysis also aided in the discovery of better-performing CrysDoS-gels. Finally, we demonstrate the potential application of the newly discovered CrysDoS-gels as sensing devices by 3D printing them as stress sensors with high sensitivity and a broad detection range.

3D-printing↗

Phenomena-based graph representations and applications to chemical process simulation

Rapid and robust simulation of chemical processes is critical to conduct process design, optimization, techno-economic analysis, and sustainability analysis. Yet, efficiently solving simulation models remains a challenge due to the highly coupled and nonlinear nature of the underlying algebraic equations that capture the physical phenomena taking place in the process (e.g., material and energy conservation, phase equilibrium, reactions). In this work, we show that graph-theoretic representations of the physical phenomena within unit operations can help navigate and decompose equations to systematically identify alternative approaches for fast and robust numerical solutions. Specifically, we present a graph-theoretic abstraction that captures the connectivity between the model variables/equations and use this abstraction to group variables/equations into fundamental phenomena. We show that phenomena-based decomposition of the underlying equations can help decouple nonlinearities and enforce material/energy conservation at the process level to accelerate convergence. The proposed decomposition approach differs from the more traditional sequential modular simulation approach, in which equations are grouped and decomposed by unit operations. We implemented the phenomena-based decomposition in BioSTEAM—an open-source process simulation platform in Python—and demonstrated that this approach can converge a variety of separation process models. Compared to sequential modular simulation, the phenomena-based approach can converge idealized systems faster, but it can be slower for (or even fail to converge) highly coupled and nonideal process systems.

Convergence↗

Water desalination through the dewpoint evaporative system

This paper presents the first numerical analysis of a novel Dew Point Desalination unit (DPD), which utilizes the phenomenon of the evaporative cooling process to minimize energy consumption. The proposed solution is based on a modular structure, which allows it to obtain any required water production capacity. The analyses for various operational parameters and various climatic conditions are based on the numerical simulations conducted using a validated mathematical model. The system performance was described with different factors, including specific energy consumption (SEC) and daily water production rate respected to 1 m^3*s^-1 of passing air stream (DWP). It is shown that the DPD system can operate in almost every climate zone, and the desalinated water production consumes less than 1.5 kWh*m^-3 of electric energy It is noted the best performance of the DPD system is achieved in the semi-arid, desert and subtropical climate zones. In these climate zones, the 2-stage DPD system allows the production of desalinated water with an electric energy consumption SEC lower than 0.5 kWh*m^-3. The additional benefit of the DPD system is its modularity. The presented DPD system stands as a module, that can be multiplied as needed to achieve the desired size of the desalination plant.

Desalination↗