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At least 1,189 records · Page 66

Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability

Filamentous fungi drive carbon and nutrient cycling across our global ecosystems, through its interactions with growing and decaying flora and their constituent microbiomes. The remarkable metabolic diversity, secretion ability, and fiber-like mycelial structure that have evolved in filamentous fungi have been increasingly exploited in commercial operations. The industrial potential of mycelial fermentation ranges from the discovery and bioproduction of enzymes and bioactive compounds, the decarbonization of food and material production, to environmental remediation and enhanced agricultural production. Despite its fundamental impact in ecology and biotechnology, molds and mushrooms have not, to-date, significantly intersected with synthetic biology in ways comparable to other industrial cell factories (e.g. Escherichia coli,Saccharomyces cerevisiae, and Komagataella phaffii). In this review, we summarize a suite of synthetic biology and computational tools for the mining, engineering and optimization of filamentous fungi as a bioproduction chassis. A combination of methods across genetic engineering, mutagenesis, experimental evolution, and computational modeling can be used to address strain development bottlenecks in established and emerging industries. These include slow mycelium growth rate, low production yields, non-optimal growth in alternative feedstocks, and difficulties in downstream purification. In the scope of biomanufacturing, we then detail previous efforts in improving key bottlenecks by targeting protein processing and secretion pathways, hyphae morphogenesis, and transcriptional control. Bringing synthetic biology practices into the hidden world of molds and mushrooms will serve to expand the limited panel of host organisms that allow for commercially-feasible and environmentally-sustainable bioproduction of enzymes, chemicals, therapeutics, foods, and materials of the future.

59 BASIC BIOLOGICAL SCIENCES↗

GDSA framework, a computational framework for complex modeling problems in radioactive waste management

This paper details a computational framework to produce automated, graphical workflows, and how this framework can be deployed to support complex modeling problems like those in nuclear engineering. Key benefits of the framework include: automating previously manual workflows; intuitive construction and communication of workflows through a graphical interface; and automated file transfer and handling for workflows deployed across heterogeneous computing resources. This paper demonstrates the framework's application to probabilistic post-closure performance assessment of systems for deep geologic disposal of nuclear waste. However, the framework is a general capability that can help users running a variety of computational studies.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Experimental and modeling study of water time histories during H 2 S-N 2 O combustion in a shock tube

Here, with the interest in directly burning sour gas in gas turbines, and the fact that even small amounts of H 2 S or its combustion products can alter combustion characteristics, many research studies have been performed to better understand the combustion chemistry of H 2 S. In the present study, the water formation was followed by laser absorption with N 2 O as an oxidant, instead of O 2 . Nitrous Oxide being essentially consumed via N 2 O (+M) ⇌ N 2 + O (+M), the water formation via the H 2 S + O route can then be probed to further validate the models. Three H 2 S/N 2 O mixtures diluted in 98% Ar were studied to cover the following range of equivalence ratios: 0.5, 1.0, and 2.0, over a wide range of temperatures (1580–1940 K) around atmospheric pressure. A chemical kinetic model was then developed first by validating the base N 2 O kinetics mechanism, then by investigating the experimental results presented herein. The N 2 O kinetics mechanism was updated with recent work on the low- and high-pressure limits for N 2 O decomposition (N 2 O (+M) ⇌ N 2 + O (+M)) as well as a review of rate coefficients for N 2 O + H ⇌ N 2 + OH from the literature. Good agreement is shown for H 2 /N 2 O mixtures. Updates were then made to the H 2 S kinetics mechanism, specifically, an update from the literature on SO 2 + H (+M) ⇌ SO + OH (+M) and an adjustment to SO + SH ⇌ S 2 + OH. Additionally, reactions between SH and N 2 O were determined using W1BD data and transition state theory which required the addition of an NNS sub-mechanism. With these updates, the mechanism provides good agreement with the H 2 S/N 2 O experiments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Insight into premixed diethoxymethane flames: Laminar burning velocities, temperatures, and emissions behaviour

Diethoxymethane ((CH 3 CH 2 O) 2 CH 2 , DEM) is a promising carbon-neutral fuel. DEM is a diether or acetal with a molecular structure similar to oxymethylene ethers (CH 3 O–(CH 2 O)n–CH 3 , OME n ). Thus, DEM can be expected to have a similar combustion behavior to OMEs, reducing harmful emissions such as NO x and particulate matter (PM) in internal combustion engines. From both experimental and kinetic modeling, fundamental studies on DEM are scarce in the literature. More studies are required to gain a detailed insight into the oxidation kinetics of DEM. Laminar burning velocity (LBV) is a critical property that allows a detailed assessment of the potential application of DEM in combustion devices. Unfortunately, the literature on the LBV of DEM is limited. Therefore, in this study we have investigated the LBV of DEM using two reactors for the first time, namely a heat flux burner and a combustion chamber. The experimental data is reported for equivalence ratio between 0.7 and 1.7, initial temperatures of 368–423 K, and initial pressure of 1–5 bar. In addition, we developed a detailed kinetic model extending our recent work of Shrestha et al. (Combust. Flame. 246 (2022) 112,426) to characterize the combustion behavior of DEM utilizing the new experimental data from this work and the literature data. Our model performs remarkably well in capturing the newly measured LBV experimental data over various experimental conditions. We found that DEM and dimethoxy methane (DMM) have similar values of LBVs (within ±1.5 cm/s) for a given condition, which indicates that intermediate chemistry governs the flame chemistry. Despite DEM being a larger molecule that is expected to have slightly lower LBVs than DMM, its effect on the measured values of LBVs is negligible. Finally, we experimentally measured NO x formation in DEM flame for the first time. The stochiometric flame has the highest NO x formation. The proposed model predicted the equivalence ratio dependence of NO x nicely. However, it overestimates the NO x formation for stoichiometric DEM/air mixtures by ~30 %. The model suggests that the thermal NO formation route is favored at lean and stochiometric conditions. In contrast, the prompt NO formation route is enhanced for rich mixtures.

10 SYNTHETIC FUELS↗

The impact of autonomous vehicles on commute ridesharing with uncertain work end time

The uncertainty in work end time can prevent ridesharing between two commuters with identical home and work locations. This effect can be alleviated by autonomous vehicles (AV): when two commuters share a ride from home to work, if the realized work end times result in a long wait between the two, an additional AV can be easily repositioned from home to work, whereas with regular human-driven vehicles one has to either bear the long wait or request expensive taxi service. This observation implies that AVs have great potential for increasing commute ridesharing. To study this effect, we develop evening commute bottleneck models with uncertain work end time and establish mode choice equilibrium for the round-trip commute. We find that, with regular vehicles, because of the expected waiting cost caused by work end time uncertainty, commuters typically do not share rides even though they have the same home and work locations. With AVs, commuters always share rides for the morning commute, and they also share rides for the evening commute if their work end times turn out to be close; otherwise, they reposition an additional AV to pick one of them up. Finally, our numerical examples show that AVs can encourage commute ridesharing and significantly reduce the expected round-trip travel costs for commuters.

97 MATHEMATICS AND COMPUTING↗

Architecting the Third Dimension of Electrochemical Energy Storage

Three-dimensional (3D) architectural design has emerged as a powerful strategy to push electrochemical energy storage (EES) devices beyond the intrinsic limitations of conventional two-dimensional (2D) electrodes. While planar architectures enable high packing density and mature manufacturing, they suffer from limited ion transport and low active-material loading. In contrast, 3D architectures introduce low-tortuosity networks and high surface area that enhance charge and mass transport while supporting thick, high mass-loading electrodes. However, their practicality remains hindered by challenges in volumetric density, mechanical stability, and large-scale manufacturability. Here, this Perspective examines the key evaluation and design principles that govern 3D device performance. We discuss the fundamental trade-offs between porosity, volumetric density, and mechanical stability that shape 3D design and highlight emerging strategies for integrating materials engineering, structural optimization, device integration, computational modeling, and scalable manufacturing. By aligning structural functionality with manufacturability, 3D architectures can evolve from laboratory prototypes to commercially viable energy storage systems.

25 ENERGY STORAGE↗

Anomalous temperature dependence of elastic limit in metallic glasses

Abstract Understanding the atomistic mechanisms of inelastic deformation in metallic glasses (MGs) remains challenging due to their amorphous structure, where local carriers of plasticity cannot be easily defined. Using molecular dynamics (MD) simulations, we analyzed the onset of inelastic deformation in CuZr MGs, specifically the temperature dependence of the elastic limit, in terms of localized shear transformation (ST) events. We find that although the ST events initiate at lower strain with increasing temperature, the elastic limit increases with temperature in certain temperature ranges. We explain this anomalous behavior through the framework of an energy-strain landscape (ESL) constructed from high-throughput strain-dependent energy barrier calculations for the ST events identified in the MD simulations. The ESL reveals that the anomalous behavior is caused by the transition of ST events from irreversible to reversible with increasing temperature. An analytical formulation is developed to predict this transition and the temperature dependence of the elastic limit.

36 MATERIALS SCIENCE↗

Nature of charge density wave in kagome metal ScV6Sn6

Abstract Recently, kagome lattice materials have emerged as a new model material platform for discovering and engineering novel quantum phases of matter. In this work, we elucidate the driving mechanism of the $$\sqrt{{{3}}}$$ 3 × $$\sqrt{{{3}}}$$ 3 charge order in a newly discovered kagome metal ScV 6 Sn 6 . Through multimodal investigations combining angle-resolved photoemission spectroscopy, phonon dispersion calculations, and phase diagram study, we identify the central role of unstable planar Sn and Sc phonon modes, while the electronic instability and van Hove singularities originating from the V kagome lattice have a marginal influence. Our results highlight that the $$\sqrt{{{3}}}$$ 3 × $$\sqrt{{{3}}}$$ 3 charge order in ScV 6 Sn 6 is fundamentally distinguished from the electronically driven 2 × 2 charge order in the canonical kagome system AV 3 Sb 5 , uncovering a new mechanism to induce symmetry-breaking phase transition in kagome lattice materials.

36 MATERIALS SCIENCE↗

An anti-PD-1–GITR-L bispecific agonist induces GITR clustering-mediated T cell activation for cancer immunotherapy

Costimulatory receptors such as glucocorticoid-induced tumor necrosis factor receptor–related protein (GITR) play key roles in regulating the effector functions of T cells. In human clinical trials, however, GITR agonist antibodies have shown limited therapeutic effect, which may be due to suboptimal receptor clustering-mediated signaling. To overcome this potential limitation, a rational protein engineering approach is needed to optimize GITR agonist-based immunotherapies. Here we show a bispecific molecule consisting of an anti-PD-1 antibody fused with a multimeric GITR ligand (GITR-L) that induces PD-1-dependent and FcγR-independent GITR clustering, resulting in enhanced activation, proliferation and memory differentiation of primed antigen-specific GITR + PD-1 + T cells. The anti-PD-1–GITR-L bispecific is a PD-1-directed GITR-L construct that demonstrated dose-dependent, immunologically driven tumor growth inhibition in syngeneic, genetically engineered and xenograft humanized mouse tumor models, with a dose-dependent correlation between target saturation and Ki67 and TIGIT upregulation on memory T cells. Anti-PD-1–GITR-L thus represents a bispecific approach to directing GITR agonism for cancer immunotherapy.

60 APPLIED LIFE SCIENCES↗

Recent progress in molecular engineering to tailor organic–inorganic interfaces in composite membranes

Organic-inorganic composite membranes are of great interest in modern water treatment processes because they offer potentially superior separation efficiency and advanced funtionality by integrating the properties of polymers and inorganics. The biggest challenge in the fabrication and applications of organic-inorganic composite membranes is the incompatibility of organic-inorganic interfaces. In this minireview, we summarize the most recent advances in molecular engineering to tailor the properties of interfaces in composite membranes. Three typical models (i.e. mixed matrix model, interface composite model, and dual-layer composite model) are presented to demonstrate how to regulate these interfaces via molecular engineering and how the interfacial properties ultimately affect the membrane performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Controllable growth of interpenetrating or random copolymer networks

Interpenetrating and random copolymer networks are vital in a number of industrial applications, including the fabrication of automotive parts, damping materials, and tissue engineering scaffolds. We develop a theoretical model for a process that enables the controlled growth of interpenetrating network (IPNs), or a random copolymer network (RCN) of specified size and mechanical properties. In this process, a primary gel “seed” is immersed into a solution containing the secondary monomer and crosslinkers. After the latter species are absorbed into the primary network, the absorbed monomers are polymerized to form the secondary polymer chains, which then can undergo further crosslinking to form an IPN, or undergo inter-chain exchange with the existing network to form a RCN. The swelling and elastic properties of the IPN and RCN networks can be tailored by modifying the monomer and crosslinker concentrations in the surrounding solution, or by tuning the enthalpic interactions between the primary polymer, secondary monomer and solvent through a proper choice of chemistry. This process can be used repeatedly to fabricate gels with a range of mechanical properties from stiff, rigid materials to soft, flexible networks, allowing the method to meet the materials requirements of a variety of applications.

36 MATERIALS SCIENCE↗

Dysfunctionality Hazard Curve: Risk-Based Tool to Support the Resilient Design of Systems Subjected to Multihazards

While resilience metrics have been proposed and studied given a functionality recovery curve, they have not emphasized enough on accounting for the uncertainties in the multihazard occurrences and intensities. Moreover, these resilience metrics are not risk-based (i.e., they do not express the system's resilience loss as a frequency of exceedance), leading to inconsistencies in system performance description when compared to performance-based engineering frameworks. A risk-based tool termed dysfunctionality hazard curve is proposed to assess the resilience of systems subjected to single hazards or multihazards with inter-event dependencies. Dysfunctionality hazard curve expresses system resilience performance as frequency of exceedance of time to full functionality. In doing so, it characterizes system recovery as a sequence of repair activities and also considers the uncertainties in the multihazard occurrences and intensities. Dysfunctionality hazard curve is demonstrated for a residential building susceptible to earthquake and hurricane hazards. Results indicate that Dysfunctionality hazard curve for earthquakes is greater than that for hurricane winds under single hazards. Under multihazards, considering inter-event dependencies during system recovery leads to larger dysfunctionality hazard curve than ignoring them. Finally, the concept of dysfunctionality hazard curve is also extended to a system-of-systems consisting of residential and commercial buildings.

42 ENGINEERING↗

Calibrating a finite-strain phase-field model of fracture for bonded granular materials with uncertainty quantification

To study the mechanical behavior of mock high explosives, an experimental and simulation program was developed to calibrate, with quantified uncertainty, a material model of the bonded granular material Idoxuridine and nitroplasticized Estane-5703. This paper reports on the efficacy of such a framework as a generalizable methodology for calibrating material models against experimental data with uncertainty quantification. Additionally, this paper studies the effect of two manufacturing temperatures and three initial granular configurations on the unconfined compressive behavior of the resulting bonded granular materials. In each of these cases, the same calibration framework was used; in that, hundreds of high-fidelity direct numerical simulations using a new, graphics processing unit-enabled, high-performance finite element method software, Ratel, were run to calibrate a finite-strain phase-field fracture model against experimental data. It was found that manufacturing temperature influenced the elastic response of the mock high explosives, with higher temperatures yielding a stiffer response. By contrast, it was found that the initial configuration of the grains had a negligible impact on the overall behavior of the mock high explosives though it remains possible that local damage accumulation within the specimens could be altered by the initial configurations. Overall, the calibration framework was successful at creating well-calibrated models, showing its usefulness as an engineering and scientific tool.

36 MATERIALS SCIENCE↗

Artificial neural network potentials for mechanics and fracture dynamics of two-dimensional crystals **

Understanding the mechanics and failure of materials at the nanoscale is critical for their engineering and applications. The accurate atomistic modeling of brittle failure with crack propagation in covalent crystals requires a quantum mechanics-based description of individual bond-breaking events. Artificial neural network potentials (NNPs) have emerged to overcome the traditional, physics-based modeling tradeoff between accuracy and accessible time and length scales. Previous studies have shown successful applications of NNPs for describing the structure and dynamics of molecular systems and amorphous or liquid phases of materials. However, their application to deformation and failure processes in materials is still uncommon. In this study, we discuss the apparent limitations of NNPs for the description of deformation and fracture under loadings and propose a way to generate and select training data for their employment in simulations of deformation and fracture simulations of crystals. We applied the proposed approach to 2D crystalline graphene, utilizing the density-functional tight-binding method for more efficient and extensive data generation in place of density functional theory. Then, we explored how the data selection affects the accuracy of the developed artificial NNPs. It revealed that NNP’s reliability should not only be measured based on the total energy and atomic force comparisons for reference structures but also utilize comparisons for physical properties, e.g. stress–strain curves and geometric deformation. In sharp contrast to popular reactive bond order potentials, our optimized NNP predicts straight crack propagation in graphene along both armchair and zigzag (ZZ) lattice directions, as well as higher fracture toughness of ZZ edge direction. Our study provides significant insight into crack propagation mechanisms on atomic scales and highlights strategies for NNP developments of broader materials.

2D materials↗

Pattern formation in odd viscoelastic fluids

Nonreciprocal interactions fueled by local energy consumption can be found in biological and synthetic active matter at scales where viscoelastic forces are important. Such systems can be described by “odd” viscoelasticity, which assumes fewer material symmetries than traditional theories. Here we study odd viscoelasticity analytically and using lattice Boltzmann simulations. We identify a pattern-forming instability which produces an oscillating array of fluid vortices, and we elucidate which features govern the growth rate, wavelength, and saturation of the vortices. Our observation of pattern formation through odd mechanical response can inform models of biological patterning and guide engineering of odd dynamics in soft active matter systems. Published by the American Physical Society 2024

Floyd, Carlos (ORCID:0000000262707250)↗

Predicting the Cetane Number, Sooting Tendency, and Energy Density of Terpene Fuel Additives

Abstract Discovering renewable fuels and fuel additives is paramount in reducing carbon emissions from internal combustion engines. Terpenes, a group of compounds that can be synthesized from plant matter and microorganisms, have gained significant interest in recent years as promising candidates for fuels/additives. Terpenes are a diverse class of compounds that contain rings and methyl branches, resulting in high energy densities and optimal cold weather behavior. Their variation in bond order, carbon chains, and functional groups lead to varying degrees of soot formation and performance in existing engines. The present work leverages predictive models, namely artificial neural networks, to predict the cetane number (CN), sooting tendency (quantified with yield sooting index, YSI), and energy density (quantified with lower heating value, LHV) of terpenes and hydrogenated terpenes whose sooting propensities were previously determined through experimental means. Predicted sooting propensities of these terpenes are compared with experimental values, and predicted cetane numbers and energy densities are used to comment on the compounds’ ability to act as fuels/additives. Expected prediction errors for CN, YSI, and LHV, defined by blind test set median absolute error, are within 5.56 cetane units, 3.63 yield sooting index units, and 0.77 MJ/kg respectively. Additionally, the present work investigates a variety of correlation/dependence metrics for property-property relationships, furthering our understanding of how combustion-relevant properties are related.

09 BIOMASS FUELS↗