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At least 55 records · Page 3

Fusion and fission of particle-like chiral nematic vortex knots

Vortex knots have been seen decaying in many physical systems. Here we describe topologically protected vortex knots, which remain stable and undergo fusion and fission and conserve a topological invariant. The host medium, a chiral nematic liquid crystal, exhibits intrinsic chirality of molecular alignment, whereas cores of the vortex lines are structurally achiral regions in which a molecular twist cannot be defined. We can reversibly switch between fusion and fission of these vortex knots by applying electric pulses. This reveals the physical embodiments of concepts in knot theory, such as connected sums of knots and band surgeries. Our findings demonstrate the interplay of chirality effects at hierarchical levels from constituent molecules to the host medium and the energetically stable chiral vortex knots. This emergent physical behaviour may enable applications in electro-optics and photonics in which such fusion and fission processes of vortex knots can be used for controlling light.

Applied mathematics

Retrobiosynthesis of unnatural lactams via reprogrammed polyketide synthase

Engineered polyketide synthases (PKSs) have great potential as biocatalysts. These unnatural enzymes are capable of synthesizing molecules that are either not amenable to biosynthesis or are extremely challenging to access chemically. PKSs can thus be a powerful platform to expand the chemical landscape beyond the limits of conventional metabolic engineering. Here we employ a retrobiosynthesis approach to design and construct PKSs to produce δ-valerolactam (VL) and three enantiopure α-substituted VL analogues that have no known biosynthetic route. We introduce the engineered PKSs and pathways for various malonyl-CoA derivatives into Pseudomonas putida and use proteomics, metabolomics and culture condition optimization to improve the production of our target compounds. These α-substituted VLs are polymerized into polyamides (nylon-5) or converted into their N-acryloyl derivatives. RAFT polymerization produces bio-derived polymers with potential biomedical applications. Overall, this interdisciplinary effort highlights the versatility and effectiveness of a PKS-based retrobiosynthesis approach in exploring and developing innovative biomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

Machine learning-led semi-automated medium optimization reveals salt as key for flaviolin production in Pseudomonas putida

Although synthetic biology can produce valuable chemicals in a renewable manner, its progress is still hindered by a lack of predictive capabilities. Media optimization is a critical, and often overlooked, process which is essential to obtain the titers, rates and yields needed for commercial viability. Here, we present a molecule- and host-agnostic active learning process for media optimization that is enabled by a fast and highly repeatable semi-automated pipeline. Its application yielded 60% and 70% increases in titer, and 350% increase in process yield in three different campaigns for flaviolin production in Pseudomonas putida KT2440. Explainable Artificial Intelligence techniques pinpointed that, surprisingly, common salt (NaCl) is the most important component influencing production. The optimal salt concentration is very high, comparable to seawater and close to the limits that P. putida can tolerate. The availability of fast Design-Build-Test-Learn (DBTL) cycles allowed us to show that performance improvements for active learning are rarely monotonous. This work illustrates how machine learning and automation can change the paradigm of current synthetic biology research to make it more effective and informative, and suggests a cost-effective and underexploited strategy to facilitate the high titers, rates and yields essential for commercial viability.

59 BASIC BIOLOGICAL SCIENCES

Biasing from galaxy trough and peak profiles with the DES Y3 redMaGiC galaxies and the weak lensing mass map

We measure the correspondence between the distribution of galaxies and matter around troughs and peaks in the projected galaxy density, by comparing redMaGiC galaxies (0.15 < z < 0.65) to weak lensing mass maps from the Dark Energy Survey (DES) Y3 data release. We obtain stacked profiles, as a function of angle θ, of the galaxy density contrast δ g and the weak lensing convergence κ, in the vicinity of these identified troughs and peaks, referred to as ‘void’ and ‘cluster’ superstructures. The ratio of the profiles depend mildly on θ, indicating good consistency between the profile shapes. We model the amplitude of this ratio using a function $F(\boldsymbol{\eta }, \theta )$ that depends on cosmological parameters $\boldsymbol{\eta }$, scaled by the galaxy bias. We construct templates of $F(\boldsymbol{\eta }, \theta )$ using a suite of N-body (‘Gower Street’) simulations forward-modelled with DES Y3-like noise and systematics. We discuss and quantify the caveats of using a linear bias model to create galaxy maps from the simulation dark matter shells. We measure the galaxy bias in three lens tomographic bins (near to far): $2.32^{+0.86}_{-0.27}, 2.18^{+0.86}_{-0.23}, 1.86^{+0.82}_{-0.23}$ for voids, and $2.46^{+0.73}_{-0.27}, 3.55^{+0.96}_{-0.55}, 4.27^{+0.36}_{-1.14}$ for clusters, assuming the best-fit Planck cosmology. Similar values with ∼0.1σ shifts are obtained assuming the mean DES Y3 cosmology. The biases from troughs and peaks are broadly consistent, although a larger bias is derived for peaks, which is also larger than those measured from the DES Y3 3 × 2-point analysis. This method shows an interesting avenue for measuring field-level bias that can be applied to future lensing surveys.

cosmology: observations

First Look at Quartic-in-Spin Binary Dynamics at Third Post-Minkowskian Order

We compute the conservative and radiation-reaction contributions to classical observables in the gravitational scattering between a spinning and a spinless black hole to the fourth order in spin and third order in the gravitational constant. The conservative results are obtained from two-loop amplitudes for the scattering process of a massive scalar with a massive spin-𝑠 field (𝑠=0, 1, 2) minimally coupled to gravity, employing the recently introduced spin interpolation method to resolve all spin-Casimir terms. The two-loop amplitude exhibits a spin-shift symmetry in both probe limits, which we conjecture to be a sign of yet unknown integrability of Kerr orbits through the quartic order in spin and to all orders in the gravitational constant. We obtain the radial action from the finite part of the amplitude and use it to compute classical observables, including the impulse and spin kick. This is done using the recently introduced covariant Dirac brackets, which allow for the computation of classical scattering observables for general (nonaligned) spin configurations. Finally, employing the radiation-reaction amplitude proposed by Alessio and Di Vecchia, together with the Dirac brackets, we obtain radiation-reaction contributions to observables at all orders in spin and beyond the aligned-spin limit. We find agreement with known results up to the quadratic order in spin for both conservative and radiation-reaction contributions. Our results advance the state of the art in the understanding of spinning binary dynamics in general relativity and demonstrate the power and simplicity of the Dirac bracket formalism for relating scattering amplitudes to classical observables.

general relativity

Interacting dark sector within ETHOS: Cosmological constraints from SPT cluster abundance with DES and HST weak lensing data

We use galaxy cluster abundance measurements from the South Pole Telescope enhanced by multicomponent matched filter confirmation and complemented with mass information obtained using weak-lensing data from Dark Energy Survey Year 3 (DES Y3) and targeted Hubble Space Telescope observations for probing deviations from the cold dark matter paradigm. Concretely, we consider a class of dark sector models featuring interactions between dark matter (DM) and a dark radiation (DR) component within the framework of the effective theory of structure formation (ETHOS). We focus on scenarios that lead to power suppression over a wide range of scales, and thus can be tested with data sensitive to large scales, as realized, for example, for DM–DR interactions following from an unbroken non-Abelian 𝑆⁢𝑈⁡(𝑁) gauge theory (interaction rate with power-law index 𝑛 = 0 within the ETHOS parametrization). Cluster abundance measurements are mostly sensitive to the amount of DR interacting with DM, parametrized by the ratio of DR temperature to the cosmic microwave background (CMB) temperature, 𝜉 DR = 𝑇 DR /𝑇 CMB . We find an upper limit 𝜉 DR < 17% at 95% credibility. When the cluster data are combined with Planck 2018 CMB data along with baryon acoustic oscillation (BAO) measurements we find 𝜉 DR < 10%, corresponding to a limit on the abundance of interacting DR that is around 3 times tighter than that from CMB + BAO data alone. We also discuss the complementarity of weak lensing informed cluster abundance studies with probes sensitive to smaller scales, explore the impact on our analysis of massive neutrinos, and comment on a slight preference for the presence of a nonzero interacting DR abundance, which enables a physical solution to the 𝑆 8 tension.

79 ASTRONOMY AND ASTROPHYSICS

Review of Particle Physics

The Review summarizes much of particle physics and cosmology. Using data from previous editions, plus 3,200 new measurements from 903 papers, we list, evaluate, and average measured properties of gauge bosons and the recently discovered Higgs boson, leptons, quarks, mesons, and baryons. We summarize searches for hypothetical particles such as supersymmetric particles, heavy bosons, axions, dark photons, etc. Particle properties and search limits are listed in Summary Tables. We give numerous tables, figures, formulae, and reviews of topics such as Higgs Boson Physics, Supersymmetry, Grand Unified Theories, Neutrino Mixing, Dark Energy, Dark Matter, Cosmology, Particle Detectors, Colliders, Probability and Statistics. Most of the 118 reviews are updated, including many that are heavily revised.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

A More La Niña–Like Response to Radiative Forcing after Flux Adjustment in CESM2

Abstract In response to greenhouse gas forcing, most coupled global climate models project the tropical Pacific SST trend toward an “El Niño–like” state, with a reduced zonal SST gradient and a weakened Walker circulation. However, observations over the last five decades reveal a trend toward a more “La Niña–like” state with a strengthening zonal SST gradient. Recent research indicates that the identified trend differences are unlikely to be entirely due to internal variability and probably result, at least in part, from systematic model biases. In this study, Community Earth System Model, version 2 (CESM2), is used to explore how mean-state biases within the model may influence its forced response to radiative forcing in the tropical Pacific. The results show that using flux adjustment to reduce the mean-state bias in CESM2 over the tropical regions results in a more La Niña–like trend pattern in the tropical Pacific, with a strengthening of the tropical Pacific zonal SST gradient and a relatively enhanced Walker circulation, as hypothesized to occur if the ocean thermostat mechanism is stronger than the atmospheric mechanisms which by themselves would weaken the Walker circulation. We also find that the historical strengthening of the tropical Pacific zonal gradient is transient but persists into the near term in a high-emissions future warming scenario. These results suggest the potential of flux adjustment as a method for developing alternative projections that represent a wider range of possible future tropical Pacific warming scenarios, especially for a better understanding of regional patterns of climate risk in the near term.

Zhuo, Jing-Yi [Lamont-Doherty Earth Observatory, C

From Modular ADMS to Plug-and-Play Ops: Distribution Grid Operations with Platform-Level Orchestration to Enable Ambitious App Hosting

The core function of the distribution grid is to provide electricity to consumers affordably, reliably, and securely. In pursuing these core objectives, distribution utilities are accountable to customers, regulators, and in some cases, shareholders. Other third parties such as aggregators and microgrids can also have a stake in the smooth operation of the grid. Each of these stakeholders has economic, business, and/or governance objectives that inform their expectations of the distribution grid. This multi-objective, multi-stakeholder environment creates tension that must be reconciled to successfully design and operate the distribution grid. Innovative companies are competing to bring high-tech solutions to electric utilities and their customers that address each of these objectives. Many developers of advanced distribution management systems (ADMS) and distributed energy resource management systems (DERMS) have adopted a modular architecture that allows grid operators to select functions and features according to their individual system needs. A modular platform also allows the solution provider to develop and integrate specific new product modules; however, the need to pursue multiple objectives with a fixed set of controllable devices makes integration expensive whether it is done at the product development stage or the deployment stage. This cost creates a significant barrier to adoption and can lengthen the product to market time of new solutions. To fundamentally address the complexity of system integration for distribution grid operations, the U.S. Department of Energy Office of Electricity has funded the GridAPPS-D project at PNNL, which streamlines integration by contributing to standards development, defining system architecture, applying advanced mathematics, and developing open-source software to demonstrate the concept of an open data-integration platform for distribution operations. The open data-integration platform concept enables system operators and solution providers to deploy ambitious, best-of-breed applications (or apps) without continually reengineering for integration. Ambitious apps developed by different solution providers will inevitably attempt to achieve different control objectives with the same set of controllable devices. If the open platform itself can resolve these conflicts in a way that achieves the best available outcomes for all apps, doesn’t restrict the ambitious design of apps, and ensures safe and secure operations, apps will be able to plug-and-play with the platform at the same time as other ambitious apps. In this paper, we describe a framework called App Deconfliction that empowers a platform to assign setpoints to controllable devices based on the values preferred by different apps (and even external stakeholder entities like customers or aggregators). The App Deconfliction framework is compatible with several methods for determining setpoint values. We present two methods based on game theory that provide a subtle built-in incentive structure for developers to adapt their apps to the fact that they will be operating in a moderated multi-app environment and to favor device setpoints that have the most effect on their objectives over those that have the least effect. Our simulation-based demonstrations have shown that game-theory-based deconfliction can lead to a 7% improvement in control space utilization compared to design-based methods.

24 POWER TRANSMISSION AND DISTRIBUTION

Transforming Energy Through Computational Excellence: NREL's Computational Science Center

Computational methods underpin advancing the science and engineering of energy efficiency, sustainable transportation, renewable power technologies, and developing a knowledge base to optimize energy systems. NREL's Computational Science Center (CSC) proudly focuses on providing the service of computing, advancing the science of computing, and enabling NREL's clean energy mission.

applied mathematics

Experimental observation of nonlinear relation between pressure and water flux is consistent with the solution-diffusion model

In several recent studies, it has been proposed that the fundamental understanding of penetrant transport in dense polymer membranes occurring via the solution-diffusion model, which has been the generally accepted theoretical framework for describing penetrant transport in such materials for the past several decades, is flawed. An alternate mechanistic framework based on the idea of two-phase flow in a porous medium (i.e., pore-flow) has been broadly advanced instead, with proponents of this approach claiming that the pore-flow theoretical framework provides the necessary mechanistic insight to design novel polymeric membrane materials for emerging applications. In this study, we show experimental results for hydraulic permeation of water that are entirely consistent with the solution-diffusion theory, without modification, for three dense polymeric membranes: crosslinked poly(ethylene glycol diacrylate) (XLPEGDA), Nafion 117 ionomer in the sodium counterion form (Nafion 117-Na), and cellulose acetate (CA). By measuring water flux at transmembrane pressures up to 240 bar, we observe a nonlinear relationship between the transmembrane pressure (TMP) and water flux, J w , for XLPEGDA and Nafion 117-Na, while this relationship is linear for CA. We demonstrate that the behavior of these three materials is described via the solution-diffusion model. According to the solution-diffusion model, flux is, to a good approximation, proportional to the transmembrane concentration difference induced by the pressure difference across the membrane, rather than to TMP itself. Water sorption isotherms are reported for all three materials. They further justify the nonlinear relationship between TMP and J w observed in XLPEGDA and Nafion 117-Na, emphasizing that the nonlinearity in the flux/TMP relationship stems from nonlinearities in the sorption isotherm with pressure. Additionally, the relationship between water flux and TMP can be predicted, a priori, with no adjustable parameters when a predictive model for the diffusion coefficient of water is employed in conjunction with the experimental water sorption isotherms in the solution-diffusion model. Furthermore, our results demonstrate the validity of the solution-diffusion model to describe transport of penetrants in dense polymer membranes, while highlighting the sensitivity of the solution-diffusion model to the many physical and mathematical simplifications commonly applied to the theory in literature.

materials

Information and Statistics in Nuclear Experiment and Theory (ISNET)

As with all empirical sciences, nuclear physics operates in the virtuous cycle of the scientific method: observations inspire theoretical models; models lead to new predictions; predictions are tested in experiments; experiments lead to new observations; and so on. Evaluating what we are inferring, and how certain we are of it, is key to this process. These requirements, and a general interest in applying novel statistical, mathematical, and computational techniques, led to the formation of a dedicated research community entitled “Information and Statistics in Nuclear Experiment and Theory (ISNET)” (https://isnet-series.github.io/), which now includes more than 300 members. While the community’s interests lean toward nuclear theory, the unifying theme for this group is the inference of knowledge from data.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

A mathematical framework for thermodynamic computing with applications to chemical reaction networks

The widespread adoption of energy-intensive computing applications has led to a growing need for energy-efficient computing approaches. Thermodynamic computing offers a promising approach for low-energy computation by leveraging the intrinsic computational capabilities of physical, chemical, or biological systems. However, the mathematical foundations of thermodynamic computing require further development to fully realize the potential energy efficiencies, as well as to assess factors like noise and operational speed. In this paper, we establish a mathematical framework for utilizing thermodynamic processes to perform fundamental operations, including addition, subtraction, multiplication, and division. We highlight the use of chemical reactions as potential computational units and explore synthetic chemical and biochemical systems as practical implementations. Additionally, we demonstrate how these principles can be applied to solving complex mathematical problems, such as ordinary differential equations (ODEs) and suggest the necessary components to implement the thermodynamic computing framework using chemical reactions based in a microfluidic device. This work enhances our understanding of thermodynamic processes for natural computing as a basis for scalable, energy-efficient computation in paradigm disruptive next-generation systems.

Cannon, William R. [Pacific Northwest National Lab

Bigpicc: a graph-based approach to identifying carcinogenic gene combinations from mutation data

Abstract Genome data from cancer patients represents relationships between the presence of a gene mutation and cancer occurrence in a patient. Different types of cancer in human are thought to be caused by combinations of two to nine gene mutations. Identifying these combinations through traditional exhaustive search requires the amount of computation that scales exponentially with the combination size and in most cases is intractable even for cutting-edge supercomputers. We propose a parameter-free heuristic approach that leverages the intrinsic topology of gene-patient mutations to identify carcinogenic combinations. The biological relevance of the identified combinations is measured by using them to predict the presence of tumor in previously unseen samples. The resulting classifiers for 16 cancer types perform on par with exhaustive search results, and score the average of 80.1% sensitivity and 91.6% specificity for the best choice of hit range per cancer type. Our approach is able to find higher-hit carcinogenic combinations targeting which would take years of computations using exhaustive search.

Biochemistry & Molecular Biology

Baryon–antibaryon photoproduction cross sections off the proton

The GlueX experiment at Jefferson Lab has observed 𝑝⁢$\overline{p}$ and, for the first time, Λ$\overlineΛ$ and 𝑝$\overlineΛ$ photoproduction from a proton target at photon energies up to 11.6 GeV. The angular distributions are forward peaked for all produced pairs, consistent with Regge-like 𝑡-channel exchange. Asymmetric wide-angle antibaryon distributions show the presence of additional processes. In a phenomenological model, we find consistency with a double-𝑡-channel exchange process where antibaryons are created only at the middle vertex. The model matches all observed distributions with a small number of free parameters. In the hyperon channels, we observe a clear distinction between photoproduction of the Λ$\overlineΛ$ and 𝑝$\overlineΛ$ systems but general similarity to the 𝑝$\overline{p}$ system. We report both total cross sections and cross sections differential with respect to momentum transfer and the invariant masses of the created particle pairs. No narrow resonant structures were found in these reaction channels. The suppression of 𝑠$\overline{s}$ quark pairs relative to 𝑑$\overline{d}$ quark pairs is similar to what has been seen in other reactions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Ergodic Lagrangian dynamics in a superhero universe

We present a fictional scenario that, while undeniably whimsical, provides the foundation for a unique exercise in extended problem solving, physics analysis, and quantitative model development. Starting with the foundational premise of the Wild Cards shared-world superhero universe, we demonstrate how a variety of concepts appropriate to the advanced undergraduate level—ergodicity, functional analysis, Lagrangian mechanics, and the ever-important simplifying approximation—can be combined into a rich, coherent mathematical model. The goal of this case study is to develop a useful pedagogical exercise in exploring an open-ended research question that presents, at first glance, no clear path forward. Being both eclectic and lengthy, this exercise offers a unique way for students to apply their core physics and mathematics education. It is perhaps best used within a senior honors seminar or within a brief (e.g., January term) elective class.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC