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At least 217 records · Page 12

Engineering activatable promoters for scalable and multi-input CRISPRa/i circuits

Dynamic, multi-input gene regulatory networks (GRNs) are ubiquitous in nature. Multilayer CRISPR-based genetic circuits hold great promise for building GRNs akin to those found in naturally occurring biological systems. We develop an approach for creating high-performing activatable promoters that can be assembled into deep, wide, and multi-input CRISPR-activation and -interference (CRISPRa/i) GRNs. By integrating sequence-based design and in vivo screening, we engineer activatable promoters that achieve up to 1,000-fold dynamic range in an Escherichia coli-based cell-free system. These components enable CRISPRa GRNs that are six layers deep and four branches wide. We show the generalizability of the promoter engineering workflow by improving the dynamic range of the light-dependent EL222 optogenetic system from 6-fold to 34-fold. Additionally, high dynamic range promoters enable CRISPRa systems mediated by small molecules and protein–protein interactions. We apply these tools to build input-responsive CRISPRa/i GRNs, including feedback loops, logic gates, multilayer cascades, and dynamic pulse modulators. Our work provides a generalizable approach for the design of high dynamic range activatable promoters and enables classes of gene regulatory functions in cell-free systems.

42 ENGINEERING↗

Impacts of the morphology of new neighborhoods on microclimate and building energy

In anticipation of emerging global urbanization and consequent increases in energy use and carbon dioxide emissions, better understanding and quantification of climate effects on energy use in cities are needed, requiring coordinated research into large-scale, regional, and microclimate impacts to and from the city structure. The methodology described here addresses this need by (1) demonstrating a process for creating and testing example morphologies for new neighborhoods for their impact on local and regional meteorology within a two-way-coupled four-domain nested mesoscale weather model (6 km horizontal resolution outer domain, 90 m horizontal innermost domain) and (2) allocating resulting building-level meteorological profiles to each building in a neighborhood for parallel computation of building-by-building energy use. Our Chicago Loop test case shows that the morphology of even a small new added development to a neighborhood affects not only its own microclimate, but also the microclimate of the original neighborhood to which the development was added, and that these changes in microclimate affect both neighborhoods’ building energy use. Furthermore, this method represents an important step toward quantifying and analyzing the relationships among climatic conditions, urban morphology, and energy use and using these relationships to inform energy-efficient urban development and planning.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

EPICS for small-scale laboratories with Python soft IOCs

While the Experimental Physics and Industrial Control System (EPICS) is widely used at large laboratories for slow controls and instrumentation, the deployment of a full EPICS installation can be difficult, with a steep learning curve to new users. Taking advantage of the pythonSoftIOC module, we developed an EPICS slow controls implementation for Jefferson Lab's Hall B cryotarget written entirely in Python and based on software IOCs that communicate with instruments over Ethernet. Here, this system ran successfully, interfacing with Jefferson Lab's full EPICS network, and we offer it as an example of the capabilities of pythonSoftIOC to build lightweight, yet robust and flexible instrumentation platforms that would be easily adapted for use at a small-scale laboratory. University groups can use these examples to build complete slow controls systems, from device communication to data archiving and display, using open-source, mature EPICS tools and student-friendly Python as an alternative to expensive and proprietary systems such as LabVIEW.

Computing↗

Security-by-Design: Light Water Small Modular Reactor

The growing demand for nuclear power is increasing pressure to find solutions to cost prohibitive requirements of both construction and security. Offsite response has been proposed as an option to reduce costs associated with training and maintaining an onsite response force. A previous report explored this option and revealed that security could be provided at the required level, but cost savings was not a result of this methodology. An offsite response strategy required costly active and passive delay barriers to provide sufficient time for responders to muster and deploy to a site in time to interrupt a determined and well-equipped adversary. Also, contrary to the hypothesis, the number of responders required for this strategy exceeded that needed for an onsite response force, as the adversaries could avail themselves of advantageous positions within the facility to repel arriving responders. This report builds upon the previous evaluation by using the same hypothetical light water small modular reactor (LWSMR) facility model, but this time an onsite response strategy was assessed. The goal of this analysis was to show that an onsite response strategy could be implemented effectively at a cost point that removes barriers within the industry at this critical time of growth and development. The assessment of the facility design and response strategy was completed through modeling using Scribe3D© and subsequent scenario analysis over the course of a two-day tabletop exercise. Subject matter experts in nuclear security, nuclear facility design, and response strategy and tactics contributed to the effort to ensure accurate representation of hypothetical scenarios. Several adaptations were made to the layout of the LWSMR based on lessons learned during the first day of scenario analysis. The subsequent design evaluated on the second day proved to provide a robust response posture against a large and well-trained adversary force. This report details the process of the analysis and compares the cost of the final facility design with that of the LWSMR model used for evaluation of offsite response. Ultimately, the results of this effort indicate that, when implemented correctly, an onsite response strategy is the best option from a security and cost perspective.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Building-Integrated Microscale Sensors for CO 2 -Level Monitoring

This research effort enabled the development of new classes of small-scale sensing systems that use mass and/or electrochemical sensors to detect the presence of carbon dioxide (CO 2 ). The concentration of this gas within the indoor environment is an important metric, as it can help enable the use of variable speed ventilation fans in commercial and governmental buildings, thus saving a significant amount of energy. Furthermore, there is a pressing need for enhanced CO 2 sensing to improve the comfort and productivity of people in commercial and government buildings, including academic spaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ghost imaging second harmonic generation microscopy

Second harmonic generation (SHG) microscopy is useful for visualizing interfaces and sub-structures within a wide range of materials due to the propensity for SHG to occur in non-centrosymmetric environments. However, since SHG is a nonlinear process generally necessitating small focal sizes for higher peak powers, a raster scanning approach is usually needed to build an SHG image over a significant sample size. While raster scanning is effective, there is a cost in terms of the time needed to acquire the image and, also, some materials cannot withstand the higher optical intensities within the small focal volume. As such, we describe a SHG microscopy approach based on ghost imaging (GI), which enables imaging data to be collected in parallel rather than sequentially as in raster scanning techniques. We experimentally demonstrate the approach and combine GI-SHG with compressive sensing to make further substantial gains in reducing the amount of sampling required for image reconstruction. Furthermore, GI-SHG is shown to have significant advantages for imaging in highly scattering environments, partly because GI is a background-free approach requiring spatial correlations between photons that travel two paths, with one path entirely devoid of sample interaction. This basic property of GI means that only the photons that travel unimpeded through the sample preserve the spatial correlations needed to reconstruct the image, while more scattered photons do not contribute to the overall GI signal. Finally, we compare the image quality and sampling properties of three different reconstruction algorithms used for compressive sensing.

47 OTHER INSTRUMENTATION↗

Precipitation hardening of laser powder bed fusion Ti-6Al-4V

Here, the laser powder bed fusion (PBF-L) additive manufacturing (AM) community has dedicated significant efforts into process optimization and control for defect-free Ti-6Al-4V. As defects become less of an issue for PBF-L Ti-6Al-4V, the processing-structure-properties (PSP) relationships between AM microstructures can now be explored to optimize mechanical properties. Lower temperature aging treatments around 550 °C in wrought Ti-6A-4V have been historically understood to precipitation harden the α phase with an ordered, hexagonal close packed (HCP) α 2 phase. The α 2 phase existed as nanoscale Ti 3 Al precipitates coherent with the parent α phase. The goal of the present investigation was to implement a vacuum heat treatment of 545 °C for 100 hours on PBF-L Ti-6Al-4V. This vacuum heat treatment took place after an initial hot isostatic pressure (HIP) treatment that decomposed the as-built, martensitic microstructure. The vacuum aging successfully produced nanoscale precipitates of α 2 phase within α-laths, confirmed via atom probe tomography (APT). Microstructural-length scale and quasi-static mechanical properties were investigated by nanoindentation and uniaxial tensile tests of miniaturized test specimens. Given the sensitivity of Ti-6Al-4V mechanical properties to small changes in chemistry, all test specimens originated from the same build. The α 2 precipitation resulted in significantly harder α-laths (≈ 2 GPa) as measured via nanoindentation, as well as a relative yield and ultimate tensile strength increase of 60 MPa and 38 MPa, respectively. Analysis of Variance (ANOVA) of the datasets revealed no statistical differences in total elongation between the HIPed and HIPed + aged specimens, indicative of the aging treatment producing a net benefit of strength with no loss in ductility.

36 MATERIALS SCIENCE↗

The DESI One-Percent Survey: A Concise Model for the Galactic Conformity of Emission-line Galaxies

Galactic conformity is the phenomenon whereby a galaxy of a certain physical property is correlated with its neighbors of the same property, implying a possible causal relationship. Here, the observed auto correlations of emission-line galaxies (ELGs) from the highly complete DESI One-Percent Survey exhibit a strong clustering signal on small scales, providing clear evidence for the conformity effect of ELGs. Building upon the original subhalo abundance-matching (SHAM) method developed by Gao et al., we propose a concise conformity model to improve the ELG–halo connection. In this model, the number of satellite ELGs is boosted by a factor of ~5 in the halos whose central galaxies are ELGs. We show that the mean ELG satellite number in such central halos is still smaller than 1 and that the model does not significantly increase the overall satellite fraction. With this model, we can well recover the ELG auto correlations to the smallest scales explored with the current data (i.e., r p > 0.03 Mpc h –1 in real space and at s > 0.3 Mpc h –1 in redshift space), while the cross correlations between luminous red galaxies and ELGs are nearly unchanged. Although our SHAM model has only eight parameters, we further verify that it can accurately describe the ELG clustering in the entire redshift range from z = 0.8 to 1.6. We therefore expect that this method can be used to generate high-quality ELG lightcone mocks for DESI.

79 ASTRONOMY AND ASTROPHYSICS↗

Understanding Uncertainty in Microstructure Evolution and Constitutive Properties in Additive Process Modeling

Coupled process–microstructure–property modeling, and understanding the sources of uncertainty and their propagation toward error in part property prediction, are key steps toward full utilization of additive manufacturing (AM) for predictable quality part development. The OpenFOAM model for process conditions, the ExaCA model for as-solidified grain structure, and the ExaConstit model for constitutive mechanical properties are used as part of the ExaAM modeling framework to examine a few of the various sources of uncertainty in the modeling workflow. In addition to “random” uncertainty (due to random number generation in the orientations and locations of grains present), the heterogeneous nucleation density N 0 and the mean substrate grain spacing S 0 are varied to examine their impact of grain area development as a function of build height in the simulated microstructure. While mean grain area after 1 mm of build is found to be sensitive to N 0 and S 0 , particularly at small N 0 and large S 0 (despite some convergence toward similar values), the resulting grain shapes and overall textures develop in a reasonably similar manner. As a result of these similar textures, ExaConstit simulation using ExaCA representative volume elements (RVEs) from various permutations of N 0 , S 0 , and location within the build resulted in similar yield stress, stress–strain curve shape, and stress triaxiality distributions. It is concluded that for this particular material and scan pattern, 15 layers is sufficient for ExaCA texture and ExaConstit predicted properties to become relatively independent of additional layer simulation, provided that reasonable estimates for N 0 and S 0 are used. However, additional layers of ExaCA will need to be run to obtain mean grain areas independent of build height and baseplate structure.

36 MATERIALS SCIENCE↗

Shedding light on U.S. small and midsize data centers: Exploring insights from the CBECS survey

As demand for digital services accelerates, the energy and environmental footprint of data centers faces increasing scrutiny. While hyperscale cloud facilities have driven efficiency gains, small and midsize U.S. data centers remain a critical yet underexamined segment with significant untapped potential for energy savings. This study leverages data from the Commercial Buildings Energy Consumption Survey (CBECS) to analyze trends in server stocks, computing customers, cooling system adoption and efficiency, and geospatial distribution from 2012 to 2018. Findings reveal a sharp decline in small and midsize data centers, from 1.764 million to 1.398 million, with server counts dropping from 5.177 million to 4.262 million—aligning with the broader shift toward cloud computing. More than 40 % of servers in small data centers and 55 % in midsize data centers are housed in office buildings, and over half of all servers are concentrated in climate zones 5A (cold), 3A (mixed-humid), and 4A (mixed-humid), with the highest densities in metropolitan hubs. While direct expansion units remain the dominant cooling system, a clear transition toward more energy-efficient solutions, particularly air economizers, is evident. By integrating server and cooling system distributions, we estimate Power Usage Effectiveness (PUE) and Water Usage Effectiveness (WUE) for U.S. data centers by size and year. Results show that midsize data centers are more energy-efficient but more water-intensive due to the widespread use of water-cooled chillers. These findings highlight the trade-offs in cooling system selection and provide a critical foundation for policies aimed at enhancing efficiency in an evolving data center landscape.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

A GPC2 antibody-drug conjugate is efficacious against neuroblastoma and small-cell lung cancer via binding a conformational epitope

Glypican 2 (GPC2) is a MYCN-regulated, differentially expressed cell-surface oncoprotein and target for immune-based therapies in neuroblastoma. Here, we build on GPC2’s immunotherapeutic attributes by finding that it is also a highly expressed, MYCN-driven oncoprotein on small-cell lung cancers (SCLCs), with significantly enriched expression in both the SCLC and neuroblastoma stem cell compartment.By solving the crystal structure of the D3-GPC2-Fab/GPC2 complex at 3.3 Å resolution, we further illustrate that the GPC2-directed antibody-drug conjugate (ADC; D3-GPC2-PBD), that links a human GPC2 antibody (D3) to DNA-damaging pyrrolobenzodiazepine (PBD) dimers, binds a tumor-specific, conformation-dependent epitope of the core GPC2 extracellular domain. We then show that this ADC induces durable neuroblastoma and SCLC tumor regression via induction of DNA damage, apoptosis, and bystander cell killing, notably with no signs of ADC-induced in vivo toxicity. Furthermore, these studies provide preclinical data to support the clinical translation of ADCs targeting GPC2.

60 APPLIED LIFE SCIENCES↗

Substrate Partitioning into Protein Macromolecular Frameworks for Enhanced Catalytic Turnover

Spatial partitioning of chemical processes is an important attribute of many biological systems, the effect of which is reflected in the high efficiency of enzymes found within otherwise chaotic cellular environments. Barriers, often provided through the formation of compartments or phase segregation, gate the access of macromolecules and small molecules within the cell and provide an added level of metabolic control. Taking inspiration from nature, we have designed virus-like particles (VLPs) as nanoreactor compartments that sequester enzyme catalysts and have used these as building blocks to construct 3D protein macromolecular framework (PMF) materials, which are structurally characterized using small-angle X-ray scattering (SAXS). Additionally, the highly charged PMFs form a separate phase in suspension, and by tuning the ionic strength, we show positively charged molecules preferentially partition into the PMF, while negatively charged molecules are excluded. This molecular partitioning was exploited to tune the catalytic activity of enzymes enclosed within the individual particles in the PMF, the results of which showed that positively charged substrates had turnover rates that were 8500× faster than their negatively charged counterparts. Moreover, the catalytic PMF led to cooperative behavior resulting in charge dependent trends opposite to those observed with individual P22 nanoreactor particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Skewering the silos: using Brick to enable portable analytics, modeling and controls in buildings

Nearly all large commercial buildings have heating, ventilation and air conditioning (HVAC) systems, lighting systems, safety and other systems controlled by a computer—a dedicated server with a building energy management system (BMS). However, these BMSs are proprietary with each building’s assets (that is, fans, valves, pumps, and their setpoints) named and coded uniquely by the BMS vendor or engineer; building analytics and control algorithms are written specific to the assets and the building. Thus, any control updates or analytics to improve building performance—especially critical to reduce greenhouse emissions or improve load flexibility—are labor intensive and costly. The Brick schema was developed so the same analysis or control algorithms can work on a variety of buildings if each is digitally represented in a Brick data model. The goal of this project was to further the development of Brick to extend it beyond an academic project with demonstrated success in a small field study, to a practical choice for industrial and commercial stakeholders seeking to realize value from building data. To do this, we executed four objectives: (1) expand the Brick schema including its modeling capabilities and vocabulary, (2) develop tools for integrating Brick with existing digital technologies and representations in buildings, (3) develop an open-source analytics platform to facilitate use of Brick in delivering data value, and (4) demonstrate Brick-driven analytics and controls in real settings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Design Basis Model for Hosting Small Modular Reactors

An aggressive transition from fossil fuels to other types of energy implies the need to construct a large number of nuclear power plants in the near future. However, the real and perceived risks of nuclear energy remain a significant impediment to this transition. This paper describes a comprehensive work process that combines the rigor of model-based systems engineering (MBSE) with 1) the Idaho National Laboratory's (INL) decades of experience with small reactors and with 2) modern project delivery processes. The objective is to reduce the risk of building new facilities or converting existing facilities to nuclear power generation.

42 ENGINEERING↗

The FEWSION for Community Resilience (F4R) Process: Building Local Technical and Social Capacity for Critical Supply Chain Resilience

Local business leaders, policy makers, elected officials, city planners, emergency managers, and private citizens are responsible for, and deeply affected by, the performance of critical supply chains and related infrastructures. At the center of critical supply chains is the food-energy-water nexus (FEW); a nexus that is key to a community’s wellbeing, resilience, and sustainability. In the 21st century, managing a local FEW nexus requires accurate data describing the function and structure of a community’s supply chains. However, data is not enough; we need data-informed conversation and technical and social capacity building among local stakeholders to utilize the data effectively. There are some resources available at the mesoscale and for food, energy, or water, but many communities lack the data and tools needed to understand connections and bridge the gaps between these scales and systems. As a result, we currently lack the capacity to manage these systems in small and medium sized communities where the vast majority of people, decisions, and problems reside. This study develops and validates a participatory citizen science process for FEW nexus capacity building and data-driven problem solving in small communities at the grassroots level. The FEWSION for Community Resilience (F4R) process applies a Public Participation in Scientific Research (PPSR) framework to map supply chain data for a community’s FEW nexus, to identify the social network that manages the nexus, and then to generate a data-informed conversation among stakeholders. F4R was piloted and co-developed with participants over a 2-year study, using a design-based research process to make evidence-based adjustments as needed. Results show that the F4R model was successful at improving volunteers’ awareness about nexus and supply chain issues, at creating a network of connections and communication with stakeholders across state, regional, and local organizations, and in facilitating data-informed discussion about improvements to the system. In this paper we describe the design and implementation of F4R and discuss four recommendations for the successful application of the F4R model in other communities: 1) embed opportunities for co-created PPSR, 2) build social capital, 3) integrate active learning strategies with user-friendly digital tools, and 4) adopt existing materials and structure.

54 ENVIRONMENTAL SCIENCES↗

Decentralized and mobile biomass torrefaction to upgrade the biomass supply chain

As part of the Cyclotron Road program, Takachar seeks to investigate the scaling laws and behaviors of a small-scale biomass torrefaction reactor design and its technoeconomic feasibility in various potential applications. Traditionally, biomass is logistically expensive and complicated to utilize in various energy and chemical industries, because it is often loose, wet, bulky, and present in small pockets in dispersed regions. Biomass torrefaction is an approach whereby raw biomass is subject to moderate heat, releasing low-energy molecules. The resultant torrefied biomass becomes energy and volume dense, which reduces the relative transportation cost, and in many cases can even support a local value chain that would otherwise not be possible. However, conventional biomass torrefaction systems are often large-scale, centralized in design, rending them difficult to deploy in many biomass applications in rural/decentralized regions. By building upon prior research at Massachusetts Institute of Technology (MIT), the concept of small-scale, low-cost, and portable biomass torrefaction units was explored further. This investigation has led to the advancement and scale-up of the MIT technology which can be deployed to a much wider spectrum of the biomass market than the conventional technologies.

09 BIOMASS FUELS↗

Mind the gap: the power of combining photometric surveys with intensity mapping

The long wavelength modes lost to bright foregrounds in the interferometric 21-cm surveys can partially be recovered using a forward modeling approach that exploits the non-linear coupling between small and large scales induced by gravitational evolution. In this work, we build upon this approach by considering how adding external galaxy distribution data can help to fill in these modes. We consider supplementing the 21-cm data at two different redshifts with a spectroscopic sample (good radial resolution but low number density) loosely modeled on DESI-ELG at z=1 and a photometric sample (high number density but poor radial resolution) similar to LSST sample at z=1 and z=4 respectively. We find that both the galaxy samples are able to reconstruct the largest modes better than only using 21-cm data, with the spectroscopic sample performing significantly better than the photometric sample despite much lower number density. Here, we demonstrate the synergies between surveys by showing that the primordial initial density field is reconstructed better with the combination of surveys than using either of them individually. Methodologically, we also explore the importance of smoothing the density field when using bias models to forward model these tracers for reconstruction.

79 ASTRONOMY AND ASTROPHYSICS↗

Atomic-resolution lithography with an on-chip scanning tunneling microscope

In this work, atomic-resolution lithography with a Microelectromechanical-System (MEMS) based Scanning Tunneling Microscope (STM) is demonstrated for the first time. The microscope consists of a commercial UltraHigh-Vacuum (UHV) STM whose regular tip is replaced with a 1-Degree-of-Freedom (1-DOF) MEMS nanopositioner. This results in a hybrid STM system where XY-plane motions are provided by the piezotube of the original system and Z-axis motion by the MEMS with a higher bandwidth. Sharp tips made of Pt or W are added to the MEMS devices with postfabrication techniques. With this hybrid system, STM-based lithography is demonstrated on an H-passivated Si (100)-2×1 sample under UHV condition. Results prove the capability of the hybrid STM system for atomic-scale lithography. This capability, paired with the small footprint of the MEMS device, makes this approach a candidate for building a high-throughput parallel STM lithography platform by incorporating an array of 1-DOF MEMS devices that perform lithography in parallel.

Alipour, Afshin (ORCID:0000000263252067)↗