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At least 163 records · Page 9

The bright frontiers of microbial metabolic optogenetics

In recent years, light-responsive systems from the field of optogenetics have been applied to several areas of metabolic engineering with remarkable success. By taking advantage of light's high tunability, reversibility, and orthogonality to host endogenous processes, optogenetic systems have enabled unprecedented dynamical controls of microbial fermentations for chemical production, metabolic flux analysis, and population compositions in co-cultures. In this article, we share our opinions on the current state of this new field of metabolic optogenetics. Furthermore, we make the case that it will continue to impact metabolic engineering in increasingly new directions, with the potential to challenge existing paradigms for metabolic pathway and strain optimization as well as bioreactor operation.

59 BASIC BIOLOGICAL SCIENCES↗

“Quantum Geometric Nesting” and Solvable Model Flat-Band Systems

We introduce the concept of “quantum geometric nesting” (QGN) to characterize the idealized ordering tendencies of certain flat-band systems implicit in the geometric structure of the flat-band subspace. Perfect QGN implies the existence of an infinite class of local interactions that can be explicitly constructed and give rise to solvable ground states with various forms of possible fermion bilinear order, including flavor ferromagnetism, density waves, and superconductivity. For the ideal Hamiltonians constructed in this way, we show that certain aspects of the low-energy spectrum can also be exactly computed including, in the superconducting case, the phase stiffness. Examples of perfect QGN include flat bands with certain symmetries (e.g., chiral or time reversal) and non-symmetry-related cases exemplified with an engineered model for pair-density wave. Extending this approach, we obtain exact superconducting ground states with nontrivial pairing symmetry. Published by the American Physical Society 2024

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Pyrophosphate-free glycolysis in Clostridium thermocellum increases both thermodynamic driving force and ethanol titers

Background: Clostridium thermocellum is a promising candidate for production of cellulosic biofuels, however, its final product titer is too low for commercial application, and this may be due to thermodynamic limitations in glycolysis. Previous studies in this organism have revealed a metabolic bottleneck at the phosphofructokinase (PFK) reaction in glycolysis. In the wild-type organism, this reaction uses pyrophosphate (PP i ) as an energy cofactor, which is thermodynamically less favorable compared to reactions that use ATP as a cofactor. Previously we showed that replacing the PP i -linked PFK reaction with an ATP-linked reaction increased the thermodynamic driving force of glycolysis, but only had a local effect on intracellular metabolite concentrations, and did not affect final ethanol titer. Results: In this study, we substituted PP i -pfk with ATP-pfk, deleted the other PPi-requiring glycolytic gene pyruvate:phosphate dikinase (ppdk), and expressed a soluble pyrophosphatase (PPase) and pyruvate kinase (pyk) genes to engineer PP i -free glycolysis in C. thermocellum. We demonstrated a decrease in the reversibility of the PFK reaction, higher levels of lower glycolysis metabolites, and an increase in ethanol titer by an average of 38% (from 15.1 to 21.0 g/L) by using PP i -free glycolysis. Conclusions: By engineering PP i -free glycolysis in C. thermocellum, we achieved an increase in ethanol production. These results demonstrate that optimizing the thermodynamic landscape through metabolic engineering can enhance product titers. While further increases in ethanol titers are necessary for commercial application, this work represents a significant step toward engineering glycolysis in C. thermocellum to increase ethanol titers.

09 BIOMASS FUELS↗

Time-reversal symmetry breaking superconductivity between twisted cuprate superconductors

Twisted interfaces between stacked van der Waals (vdW) cuprate crystals present a platform for engineering superconducting order parameters by adjusting stacking angles. Using a cryogenic assembly technique, we construct twisted vdW Josephson junctions (JJs) at atomically sharp interfaces between Bi 2 Sr 2 CaCu 2 O 8+x crystals, with quality approaching the limit set by intrinsic JJs. Near 45° twist angle, we observe fractional Shapiro steps and Fraunhofer patterns, consistent with the existence of two degenerate Josephson ground states related by time-reversal symmetry (TRS). By programming the JJ current bias sequence, we controllably break TRS to place the JJ into either of the two ground states, realizing reversible Josephson diodes without external magnetic fields. Furthermore, our results open a path to engineering topological devices at higher temperatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Macrovoid resolved simulations of transport through HPRO relevant membrane geometries

Modeling the transport properties such as diffusivity and permeability of high pressure reverse osmosis (HPRO) membranes is critical for the selection and manufacture of membranes suitable for operation under high pressure. These properties can be significantly affected by the changes in heterogeneous pore structures due to compaction. Here, the modeling platform presented in this work resolves the two scale porosity in HPRO relevant membranes. A synthetic membrane geometry is constructed based on available experimental visualizations of pore structures. The simulations directly capture the flow channeling that results from a combination of material properties and geometric features of the macrovoids. A parametric study is presented to account for the transition of flow characteristics from a material governed regime to a macrovoid governed regime. Permeability of the membrane is evaluated using the simulation data and compared with an existing model that scales with the square of tortuosity over a range of material properties. The model is found to perform well under a narrow range of tortuosity while deviating from the calculated permeabilities at extreme conditions. The effective permeability of the membrane is found to vary by at least two orders of magnitude between the two flow regimes. It is also observed that tortuosity is a bounded property with its upper limit determined by the macrovoid geometry. Consequently, the tortuosity based correlations fail near a flow regime that is mainly governed by the macrovoids. The modeled permeability can be more than an order of magnitude smaller than the simulation result. A new model based on flux-weighted porosity of a membrane is introduced and its correlation with tortuosity is studied. The model agrees with the simulated data as, in addition to tortuosity, it also accounts for the flux partition within and outside the flow channels. Such correlations enable extending the existing understanding of flow characteristics to enhance predictability of porous media models.

42 ENGINEERING↗

Engineering and evaluation of FXa bypassing agents that restore hemostasis following Apixaban associated bleeding

Direct oral anticoagulants (DOACs) targeting activated factor Xa (FXa) are used to prevent or treat thromboembolic disorders. DOACs reversibly bind to FXa and inhibit its enzymatic activity. However, DOAC treatment carries the risk of anticoagulant-associated bleeding. Currently, only one specific agent, andexanet alfa, is approved to reverse the anticoagulant effects of FXa-targeting DOACs (FXaDOACs) and control life-threatening bleeding. However, because of its mechanism of action, andexanet alfa requires a cumbersome dosing schedule, and its use is associated with the risk of thrombosis. Here, we present the computational design, engineering, and evaluation of FXa-variants that exhibit anticoagulation reversal activity in the presence of FXaDOACs. Our designs demonstrate low DOAC binding affinity, retain FXa-enzymatic activity and reduce the DOAC-associated bleeding by restoring hemostasis in mice treated with apixaban. Importantly, the FXaDOACs reversal agents we designed, unlike andexanet alfa, do not inhibit TFPI, and consequently, may have a safer thrombogenic profile.

59 BASIC BIOLOGICAL SCIENCES↗

An Organic Carboxylate Host for Stable Sodium Metal Batteries

Sodium metal batteries (SMBs) hold great promise for the development of high-energy, sustainable energy storage solutions, but their practical deployment is hampered by unstable solid electrolyte interphases, uncontrollable sodium dendrite growth, and low Coulombic efficiency (CE) during repeated Na plating/stripping cycles. To address these challenges, we introduce an organic interlayer, containing perylenetetracarboxylic dianhydride sodium salt (Na4PT), on the surface of Cu current collector. This interlayer forms a sodiophilic organic interphase that lowers the nucleation barriers for sodium deposition and guides the formation of the interphase through polar carbonyl/carboxylate sites and a π-conjugated organic framework. A dendrite-free sodium metal anode is achieved using Na4PT coated Cu current collector. Under capacity-limited Na plating/stripping, Na||Na4PT@Cu half-cells deliver reversible capacities of 500 and 1,000 mAh g−1 at 0.1 and 1 A g−1 for 500 cycles with average CE above 99%. Post-cycling scanning electron microscopy and X-ray photoelectron spectroscopy measurements confirm that Na4PT@Cu promotes compact and uniform Na deposits and supports the formation of a stable interphase with reduced parasitic decomposition, directly correlating interfacial chemistry/morphology with high plating/stripping reversibility. These results highlight organic carboxylate coating as a practical interface engineering strategy for dendrite-free SMBs.

Chen, Chengxiang [University of Miami]↗

Resolving Charge Distribution for Compositionally Heterogeneous Battery Cathode Materials

The isostructural nature of Li-layered cathodes allows for accommodating multiple transition metals (TMs). However, little is known about how the local TM stoichiometry influences the charging behavior of battery particles thus impacting battery performance. In this work, we develop heterogeneous compositional distributions in polycrystalline LiNi 1–x–y Mn x Co y O 2 (NMC) particles to investigate the interplay between local stoichiometry and charge distribution. These NMC particles exhibit a broad, continuous distribution of local Ni/Mn/Co stoichiometry, which does not compromise the global layeredness. The local Mn and Ni concentrations in individual NMC particles are positively and negatively correlated with the electrochemically induced Ni oxidation, respectively, whereas the Co concentration does not impose a clear effect on the Ni oxidation. The resulting material delivers excellent reversible capacity, rate capability, and cycle life at high operating voltages. Engineering Ni/Mn/Co distribution in NMC particles may provide a path toward controlling the charge distribution and thus chemomechanical properties of polycrystalline battery particles.

25 ENERGY STORAGE↗

Quantitative phase retrieval and characterization of magnetic nanostructures via Lorentz (scanning) transmission electron microscopy

Magnetic materials phase reconstruction using Lorentz transmission electron microscopy (LTEM) measurements have traditionally been achieved using longstanding methods such as off-axis holography (OAH) fast-Fourier transform technique and the transport-of-intensity equation (TIE). The increase in access to processing power alongside the development of advanced algorithms have allowed for phase retrieval of nanoscale magnetic materials with greater efficacy and resolution. Specifically, reverse-mode automatic differentiation (RMAD) and the extended electron ptychography iterative engine (ePIE) are two recent developments of phase retrieval that can be applied to analyzing micro-to-nano- scale magnetic materials. This work evaluates phase retrieval using TIE, RMAD, and ePIE in simulations of Permalloy (Ni 80 Fe 20 ) nanoscale islands, or nanomagnets. Extending beyond simulations, we demonstrate total phase retrieval and image reconstructions of a NiFe nanowire using OAH and RMAD in LTEM and ePIE in Lorentz-mode-4D scanning transmission electron microscopy experiments and determine the saturation magnetization through corroborations with micromagnetic modeling. Finally, we demonstrate the efficacy of these methods in retrieving the total phase and highlight its use in characterizing and analyzing the proximity effect of the magnetic nanostructures.

Lorentz transmission electron microscopy↗

Simulation of Reverse Osmosis Membrane Compaction Using Material Point Method (MPM)

Access to fresh drinking water in the future requires effective management of industrial wastewater and water purification from available resources. In this study, we present the simulation methodology and the analysis of a Reverse Osmosis (RO) membrane under various pressure conditions using the Material Point Method (MPM). In contrast to other numerical methods, MPM solves the continuum governing equations on material points in a Lagrangian framework. The method does not require a grid connecting the material points hence making it suitable to simulate large deformations during membrane compaction. The time integration is carried out using the explicit Euler method, while the spatial discretization is performed using linear or cubic-spline shape functions. A series of planar images containing detailed pore structures obtained from X-ray tomography experiments is converted to a three-dimensional collection of material points to simulate the membrane. Compressive loads are applied to the top layer of the membrane to simulate the experiments. The membrane deformation and pore size distribution before and after load application are reported and compared with the experimental measurements. The presentation discusses the numerical methods used, the performance of the solver on high-performance computing machines, and the results of membrane compaction in detail.

ENGINEERING,MATHEMATICS AND COMPUTING↗

Using time reversal with long duration broadband noise signals to achieve high amplitude and a desired spectrum at a target location

Time Reversal (TR) is a signal processing technique that can be used to focus acoustic waves to a specific location in space, with most applications aiming to create an impulsive focus. Here, this study instead aims to focus long-duration noise signals using TR. This paper seeks to generate higher amplitude noise at a desired location over an existing method of broadcasting equalized noise. Additionally, this paper explores various characteristics associated with focusing long duration noise using TR. The dependence of the focal amplitude on the duration of the focused signal is explored as well as the implications of using multiple sources when focusing noise. The focal amplitude decreases with longer duration and then levels off when the duration exceeds a few seconds. Coherent addition of focused noise is observed if all loudspeakers have coherent noise signals convolved with their reversed impulse responses. Lastly, focusing noise with a desired spectrum is explored.

42 ENGINEERING↗

A tunable autonomous RNA-fueled micro-engine

Autonomous molecular machines capable of converting chemical energy into mechanical motion are foundational components for synthetic nanoscale systems. Inspired by biological motors, we report the construction of a tunable, RNA-fueled DNA origami engine that drives the cyclic movement of a 500 nm-diameter particle at the microscale. The engine operates via sequential RNA–DNA hybridization and enzymatic cleavage by RNase H, enabling reversible switching between folded and unfolded conformations without external intervention. By modulating RNA and enzyme concentrations and controlling temperature, we achieve tunable switching kinetics, with transition periods as short as ~10 s. Kinetic modeling reveals that the folding pathway is governed by both productive RNA binding and the enzymatic clearance of misfolded intermediates, while unfolding is primarily controlled by RNase H activity. Since the RNA fuel binds specifically to the DNA strands, each engine is addressable simply by changing the sequences. This work demonstrates a programmable, self-resetting molecular actuator and offers a blueprint for building more complex nanomechanical systems with forces and energies comparable to molecular motors.

DNA nanomachines↗

A machine learning pipeline for identifying infiltration managed aquifer recharge locations from satellite imagery in the San Joaquin Valley, California

This study focuses on an agricultural region in California’s Central Valley, USA, where Managed Aquifer Recharge (MAR) is widely implemented to mitigate groundwater depletion under increasing water demand and climate variability. A deep learning and machine learning framework was developed to identify infiltration-MAR locations using satellite imagery and environmental data. The framework integrates surface water detection from Sentinel-2 imagery, geospatial delineation of water bodies, spatiotemporal tracking of water body dynamics, and supervised classification using meteorological, environmental, and topographic variables. The framework was applied to a 2379 km² study area southwest of Fresno, where 765 water bodies were detected, including 139 identified MAR sites based on publicly available datasets and expert knowledge. The classification model achieved an accuracy of 0.94 and an F1 score of 0.85. Feature importance analysis indicates that cropland, normalized difference vegetation index (NDVI), and evaporation are among the most influential predictors for infiltration-MAR. Notably, the framework suggests that engineered water management in infiltration-MAR systems can disrupt or even reverse the expected positive correlation between surface water extent and precipitation. These findings provide physically interpretable insights into the characteristics of existing infiltration-MAR facilities and demonstrate the potential of the proposed framework as a reproducible, interpretable, and potentially transferable tool for data-driven infiltration-MAR identification and inventory development under growing climatic and hydrological uncertainty.

Classification↗

Inadequacy of current approaches for characterizing membrane transport properties at high salinities

Cost optimal design of osmotic membrane processes requires an accurate estimate of membrane transport parameters across their full operational range. However, standard approaches for estimating these parameters rely on empirical methods, the accuracy of which remains unquantified as a function of temperature, salinity, and measurement error. Herein, we present a systematic accuracy analysis of previously developed methods for estimation of membrane transport properties in reverse osmosis, high-pressure reverse osmosis, forward osmosis, pressure retarded reverse osmosis, and osmotically assisted reverse osmosis. We use a Monte Carlo approach to sample the full range of feasible membrane water permeabilities, salt permeabilities, structural parameters, and operating conditions for these processes. These material and process parameters are then incorporated into a physical transport model for each process. Our analysis shows that the statistical uncertainty of current empirical methods for estimating membrane parameters increases by 5 times from low-salinity to high-salinity conditions. Here, the result of this work demonstrates that empirical methods are inadequate for precisely estimating membrane transport properties at high salinity and highlight a critical need for the development of statistically validated higher accuracy methods.

42 ENGINEERING↗

Exploiting ultra-large linear elasticity over a wide temperature range in nanocrystalline NiTi alloy

Many shape memory alloys can support large recoverable strains of a few percent by reversible stress-induced martensite transformation, yet they behave non-linear within a narrow operating temperature range. Developing the bulk metallic materials with ultra-large linear elasticity over a wide temperature range has proven to be difficult. In this work, a material design concept was proposed, that is true elastic deformation and reversible twinning-detwinning deformation run in parallel to overcome this challenge. By engineering the residual internal stress to realize the concurrency of true elastic deformation and twinning-detwinning deformation, a bulk nanocrystalline NiTi that possesses an ultra-large linear elastic strain up to 5.1 % and a high yield stress of 2.16 GPa over a wide temperature range of 270 °C was developed. This study offers a new avenue for developing the metallic materials with ultra-large linear elasticity over a wide temperature range of 270 °C (from 70 °C to -197 °C).

36 MATERIALS SCIENCE↗

An Active and Resilient Bilayer Oxygen Electrode for Intermediate Temperature Reversible Solid Oxide Cells

High temperature solid oxide cells (SOCs) have intrinsic advantage in efficiency over conventional internal combustion engines for power generation and low-temperature electrolysis cells for H2 production. This efficiency advantage could potentially lead to cost saving and emission reduction. However, commercialization of the current SOCs technology is hindered by its poor durability. One major component with the durability issue is oxygen electrode (OE). For example, the durability of OEs can be negatively affected by the gaseous Cr-species originated from the air oxidation of high-temperature alloy interconnect. For electrolysis operation, on the other hand, delamination of OE from electrolyte, particularly at high current densities, has been identified as a major cause for the performance degradation. Therefore, developing robust and active OEs is of critical importance to SOC technology. WE have previously demonstrated a new bilayer OE with strong activity and stability. Here in this presentation, we present recent results of electrochemical characterization on bilayer OE operating under both fuel cell and electrolysis modes. We will first show the optimization of bilayer OE in terms of thickness, morphology, and calcination temperature and their impacts on cell area specific resistance (ASR). With three-electrode symmetric cell configuration, we also show the results of charge transfer ASR of bilayer OE as a function of current density, temperature, and time in different atmospheres. The results are further compared with the baseline OE (LSCF+GDC) to demonstrate the advantage of bilayer OE.

Huang, Kevin↗