SEARCH · Engineering Papers

Results for “target variability”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16

All sources NASA NTRS DOE OSTI

DOE OSTI2021

Data-assisted combustion simulations with dynamic submodel assignment using random forests

This investigation outlines a data-assisted approach that employs random forest classifiers for local and dynamic submodel assignment in turbulent-combustion simulations. This method is demonstrated in simulations of a single-element GOX/GCH4 rocket combustor; a priori as well as a posteriori assessments are conducted to (i) evaluate the accuracy and adjustability of the classifier for targeting different quantities of interest (QoIs), and (ii) assess improvements, resulting from the data-assisted combustion model assignment, in predicting target QoIs during simulation runtime. Results from the a priori study show that random forests, trained with local flow properties as input variables and combustion model errors as training labels, assign three different combustion models – finite-rate chemistry (FRC), flamelet progress variable (FPV) model, and inert mixing (IM) – with reasonable classification performance even when targeting multiple QoIs. Applications in a posteriori studies demonstrate improved predictions from data-assisted simulations, in temperature and CO mass fraction, when compared with monolithic FPV calculations. An additional a posteriori data-assisted simulation of a modified configuration demonstrates that the present approach can be successfully applied to different configurations, as long as thermophysical behavior can be represented by the training data. Furthermore, these results demonstrate that this data-driven framework holds promise for dynamic combustion submodel assignments in reacting flow simulations.

42 ENGINEERING↗

DOE OSTI2021

Ultra-high energy density relativistic plasmas from nanostructures: scaling to ultra-high intensities (Final Report)

This project investigated the ultra-high energy density (UHED) regime of matter found in the center of stars, using a compact PW-class laser. These extreme conditions are typically only obtained in the laboratory in the central hot-spot of spherically imploded capsules in inertial confinement fusion experiments driven by the world’s largest lasers. We have shown that near-solid density arrays of aligned nanostructures can be volumetrically heated to multi-keV temperatures by irradiation at relativistic intensity with ultrafast laser pulses of modest energy, opening a path for the generation of UHED plasmas with compact lasers. This new UHED plasma generation approach promises to create an environment with extreme energy densities and degrees of ionization, record conversion of optical laser light into ultrafast x-ray pulses, gigantic magnetic fields and pressures, and directed beams of high energy particles . In this project we achieved record degree of ionization in volumetric heating solid density and near-solid density plasmas. Gold plasmas which spectra is characterized by L shell transition emission from ions with charge up to the Ne-like state, Au+ 72 were generated using ultrafast laser pulses of less than 10 J of energy from a compact laser focused to an intensity of ~ 3x10 21 Wcm -2 . We also conducted measurements to determine the heat penetration depth in Ni nanowire arrays as compared to Ni foil targets by monitoring the line emission of a Co buried tracer underneath a variable amount of Ni. The measurements revealed that the nanowire plasmas are roughly six times larger in depth than the solid density target plasmas. A result of this increased plasma in nanowire arrays is a greatly increased conversion of optical laser light into > 1 KeV x-rays, a record conversion efficiency of 20 %. Critical to the realization of the proposed experiments was the generation of ultrafast laser pulses with ultra-high contrast that can deposit the energy deep into the nanowire arrays before the nanowires explode to create a continuous plasma. Supporting the proposed experiments was the recent demonstration at Colorado State University of a Petawatt-class laser that emits 30 fs pulses at high repetition rates. The experiments combined this unique laser tool with a variety of tailored nanowire arrays fabricated in house and with an extensive suite of diagnostics. The experiments were accompanied by 3-dimensional particle-in-cell simulations and detailed atomic physics simulations with transient kinetics and radiation transport. The proposed research allowed us to continue training Ph.D students and post-docs with broad experience in HEDP Science.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Nickase fidelity drives EvolvR-mediated diversification in mammalian cells

Abstract In vivo genetic diversifiers have previously enabled efficient searches of genetic variant fitness landscapes for continuous directed evolution. However, existing genomic diversification modalities for mammalian genomic loci exclusively rely on deaminases to generate transition mutations within target loci, forfeiting access to most missense mutations. Here, we engineer CRISPR-guided error-prone DNA polymerases (EvolvR) to diversify all four nucleotides within genomic loci in mammalian cells. We demonstrate that EvolvR generates both transition and transversion mutations throughout a mutation window of at least 40 bp and implement EvolvR to evolve previously unreported drug-resistantMAP2K1variants via substitutions not achievable with deaminases. Moreover, we discover that the nickase’s mismatch tolerance limits EvolvR’s mutation window and substitution biases in a gRNA-specific fashion. To compensate for gRNA-to-gRNA variability in mutagenesis, we maximize the number of gRNA target sequences by incorporating a PAM-flexible nickase into EvolvR. Finally, we find a strong correlation between predicted free energy changes underlying R-loop formation and EvolvR’s performance using a given gRNA. The EvolvR system diversifies all four nucleotides to enable the evolution of mammalian cells, while nuclease and gRNA-specific properties underlying nickase fidelity can be engineered to further enhance EvolvR’s mutation rates.

Science & Technology - Other Topics↗

NASA NTRS1980

Radar target for remotely sensing hydrological phenomena

An apparatus for remotely measuring and accessing water status relative to snow and glacial melt, surface runoff, rainfall, evaporation, flow rate, and soil moisture is described. A radar target located at a selected location on the surface of the Earth is designed to collect water and render its cross sectional area variable as a function of the height of the water level within the target. The target is remotely monitored by an orbiting or airborne synthetic aperature radar. The target appears as a bright spot embedded within the radar image. The target brightness is indicative of the height of the water level within the ground located target.

Sivertson, W. E., Jr.↗

DOE OSTI2016

Prospects for detection of target-dependent annual modulation in direct dark matter searches

Earth's rotation about the Sun produces an annual modulation in the expected scattering rate at direct dark matter detection experiments. The annual modulation as a function of the recoil energy E R imparted by the dark matter particle to a target nucleus is expected to vary depending on the detector material. However, for most interactions a change of variables from E R to v min , the minimum speed a dark matter particle must have to impart a fixed E R to a target nucleus, produces an annual modulation independent of the target element. We recently showed that if the dark matter-nucleus cross section contains a non-factorizable target and dark matter velocity dependence, the annual modulation as a function of v min can be target dependent. Here we examine more extensively the necessary conditions for target-dependent modulation, its observability in present-day experiments, and the extent to which putative signals could identify a dark matter-nucleus differential cross section with a non-factorizable dependence on the dark matter velocity.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1977

Prediction of pilot reserve attention capacity during air-to-air target tracking

Reserve attention capacity of a pilot was calculated using a pilot model that allocates exclusive model attention according to the ranking of task urgency functions whose variables are tracking error and error rate. The modeled task consisted of tracking a maneuvering target aircraft both vertically and horizontally, and when possible, performing a diverting side task which was simulated by the precise positioning of an electrical stylus and modeled as a task of constant urgency in the attention allocation algorithm. The urgency of the single loop vertical task is simply the magnitude of the vertical tracking error, while the multiloop horizontal task requires a nonlinear urgency measure of error and error rate terms. Comparison of model results with flight simulation data verified the computed model statistics of tracking error of both axes, lateral and longitudinal stick amplitude and rate, and side task episodes. Full data for the simulation tracking statistics as well as the explicit equations and structure of the urgency function multiaxis pilot model are presented.

Onstott, E. D.↗

DOE OSTI2021

Universal Compiling and (No-)Free-Lunch Theorems for Continuous-Variable Quantum Learning

Quantum compiling, where a parameterized quantum circuit is trained to learn a target unitary, is an important primitive for quantum computing that can be used as a subroutine to obtain optimal circuits or as a tomographic tool to study the dynamics of an experimental system. While much attention has been paid to quantum compiling on discrete-variable hardware, less has been paid to compiling in the continuous-variable paradigm. Here we motivate several, closely related, short-depth continuous-variable algorithms for quantum compilation. We analyze the trainability of our proposed cost functions and numerically demonstrate our algorithms by learning arbitrary Gaussian operations and Kerr nonlinearities. We further make connections between this framework and quantum learning theory in the continuous-variable setting by deriving no-free-lunch theorems. These generalization bounds demonstrate a linear resource reduction for learning Gaussian unitaries using entangled coherent-Fock states and an exponential resource reduction for learning arbitrary unitaries using two-mode-squeezed states.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2002

Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses

The effects of single-base-pair near-terminal and terminal mismatches on the dissociation temperature (T(d)) and signal intensity of short DNA duplexes were determined by using oligonucleotide microarrays and neural network (NN) analyses. Two perfect-match probes and 29 probes having a single-base-pair mismatch at positions 1 to 5 from the 5' terminus of the probe were designed to target one of two short sequences representing 16S rRNA. Nonequilibrium dissociation rates (i.e., melting profiles) of all probe-target duplexes were determined simultaneously. Analysis of variance revealed that position of the mismatch, type of mismatch, and formamide concentration significantly affected the T(d) and signal intensity. Increasing the concentration of formamide in the washing buffer decreased the T(d) and signal intensity, and it decreased the variability of the signal. Although T(d)s of probe-target duplexes with mismatches in the first or second position were not significantly different from one another, duplexes with mismatches in the third to fifth positions had significantly lower T(d)s than those with mismatches in the first or second position. The trained NNs predicted the T(d) with high accuracies (R(2) = 0.93). However, the NNs predicted the signal intensity only moderately accurately (R(2) = 0.67), presumably due to increased noise in the signal intensity at low formamide concentrations. Sensitivity analysis revealed that the concentration of formamide explained most (75%) of the variability in T(d)s, followed by position of the mismatch (19%) and type of mismatch (6%). The results suggest that position of the mismatch at or near the 5' terminus plays a greater role in determining the T(d) and signal intensity of duplexes than the type of mismatch.

Non-NASA Center↗

DOE OSTI2024

Target mass corrections in lepton–nucleus DIS: Theory and applications to nuclear PDFs

Motivated by the wide range of kinematics covered by current and planned deep-inelastic scattering (DIS) facilities, we revisit the formalism, practical implementation, and numerical impact of target mass corrections (TMCs) for DIS on unpolarized nuclear targets. An important aspect is that we only use nuclear and later partonic degrees of freedom, carefully avoiding a picture of the nucleus in terms of nucleons. After establishing that formulae used for individual nucleon targets (p,n), derived in the Operator Product Expansion (OPE) formalism, are indeed applicable to nuclear targets, here we rewrite expressions for nuclear TMCs in terms of re-scaled (or averaged) kinematic variables. As a consequence, we find a representation for nuclear TMCs that is approximately independent of the nuclear target. We go on to construct a single-parameter fit for all nuclear targets that is in good numerical agreement with full computations of TMCs. We discuss in detail qualitative and quantitative differences between nuclear TMCs built in the OPE and the parton model formalisms, as well as give numerical predictions for current and future facilities.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2016

Effective Cytotoxic T Lymphocyte Targeting of Persistent HIV-1 during Antiretroviral Therapy Requires Priming of Naive CD8 + T Cells

Curing HIV-1 infection will require elimination of persistent cellular reservoirs that harbor latent virus in the face of combination antiretroviral therapy (cART). Proposed immunotherapeutic strategies to cure HIV-1 infection include enhancing lysis of these infected cells by cytotoxic T lymphocytes (CTL). A major challenge in this strategy is overcoming viral immune escape variants that have evaded host immune control. Here we report that naive CD8 + T cells from chronic HIV-1-infected participants on long-term cART can be primed by dendritic cells (DC). These DC must be mature, produce high levels of interleukin 12p70 (IL-12p70), be responsive to CD40 ligand (CD40L), and be loaded with inactivated, autologous HIV-1. These DC-primed CD8 + T cell responders produced high levels of gamma interferon (IFN-γ) in response to a broad range of both conserved and variable regions of Gag and effectively killed CD4 + T cell targets that were either infected with the autologous latent reservoir-associated virus or loaded with autologous Gag peptides. In contrast, HIV-1-specific memory CD8 + T cells stimulated with autologous HIV-1-loaded DC produced IFN-γ in response to a narrow range of conserved and variable Gag peptides compared to the primed T cells and most notably, displayed significantly lower cytolytic function. Our findings highlight the need to selectively induce new HIV-1-specific CTL from naive precursors while avoiding activation of existing, dysfunctional memory T cells in potential curative immunotherapeutic strategies for HIV-1 infection.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Mini-99 Experiment Design and Target Assembly

Qualification of nuclear fuels requires an understanding of a myriad of fuel performance variables, which requires time-consuming irradiations in test reactors. Accelerating burnup accumulation to reduce the irradiation time has historically been accomplished by increasing the 235 U enrichment in integral fuel tests, which inherently couples the fuel’s temperature and fission heat generation. Separate effects irradiation testing of nuclear fuel, using the MiniFuel target in the Oak Ridge National Laboratory’s (ORNL’s) High Flux Isotope Reactor (HFIR), offers an approach for decoupling fuel temperature and fission rate by reducing the quantity of the fuel and relying primarily on gamma heating in the surrounding components to drive fuel temperatures. However, if the fission rate is high enough, the fuel temperature will still vary over time as the fission heating changes, primarily due to poor heat conduction between the fuel and the surrounding components. This work details the design, analysis, and fabrication of a MiniFuel target which utilizes sodium bonding to improve the heat rejection from the fuel specimen, enabling the testing of higher 235 U enrichments (~8wt.%) to further accelerate burnup accumulation without prohibitively large temperature variations throughout the course of the irradiation.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

Dynamic Building Load Control to Facilitate High Penetration of Solar Photovoltaic Generation (Final Technical Report)

Solar photovoltaic (PV) resources are the most common form of distributed generation in residential and commercial customer premises within electric distribution networks. A higher penetration of PV generation in distribution circuits will impose challenges on maintaining service voltages within the range of industry standards, power quality, and power flow. Buildings consume 74% of the electricity produced in the United States, and a significant portion of the building load is dispatchable, making them responsive to electrical grid needs. Oak Ridge National Laboratory—in collaboration with Southern Company; the University of Tennessee, Knoxville; and the Georgia Institute of Technology—is examining the PV integration issues in distribution-level electrical grids and developing integrated demand-side control and communication systems to enable responsive loads. The proposed responsive loads mechanism performs renewable generation following to increase the penetration of solar PV within each feeder. The specific objectives of this project are to (1) examine distribution-level PV integration scenarios to understand requirements, (2) undertake an end-to-end simulation-based design of a distributed control strategy of loads geographically near the PV generation asset to minimize the effect on the distribution feeder, (3) deploy and demonstrate the control technology developed in partnership with utilities, and (4) perform a scalability analysis at the utility scale. This 3-year integrated project aims to develop, demonstrate, and validate demand-side control technology to enable increased the penetration of renewables while mitigating challenges that arise due to their intermittency. Activities in Budget Period (BP) 1 focused on a literature review and the formal design of a control system for integrating local distribution with generation and loads. The team used modeling and simulation to evaluate the impact of varying buildings loads, variable PV generation, and power flow dynamics on the distribution circuit. The dynamic models developed in BP 1 were used in BP 2 to develop a model-based control design and a test bed. The test bed has enabled the simulation-based testing and comparison of different control designs and formulations applied to different configurations of the distribution grid, PVs, and building loads. The control approaches developed in BP 2 were implemented in BP 3 in the form of hardware deployed at the Central Baptist Church (CBC) in Knoxville, Tennessee, for testing and evaluation. The outcome of this project was the development and demonstration of open-source, low-cost, low-touch sensing and control retrofits to distributed PV generation and building loads that, in a coordinated fashion, provide the load-shaping response needed to integrate high levels of renewable penetration. This research addresses the target metrics by dynamically controlling a load with solar generation variability to minimize the extent of two-way power flow, enhance reliability, facilitate high PV penetration (>100% of peak load in a line segment), and generate scalable software and hardware solutions adaptable to any penetration levels. The research and development activities are focused and designed to be impactful within the relevant 2020 targets time frame.An accurate open-source integration simulation framework for end-to-end control design was developed and deployed at the CBC facility for testing and evaluation. This final report provides a detailed review of the technical results achieved during this 3-year integrated project. A novel spectral analysis of PV data is demonstrated to derive the requirements of the control design. A detailed simulation-based analysis of PV integration at increasing penetration levels is presented using 1 year of PV data to demonstrate the impact on the distribution circuits. Two different control strategies were developed and demonstrated via simulation to track variable PV generation with adaptive load dispatch. The report concludes with a summary of accomplishments and recommendations for a path forward.

14 SOLAR ENERGY↗

DOE OSTI2022

A Variable Pressure Multi-Pressure Rail System Design for Agricultural Applications

This paper presents a solution for reducing energy loss in the hydraulic control system of agricultural tractors and their implements. The solution is referred to as a multi-pressure rail (MPR) and provides power to the hydraulic functions following a pressure control logic, as opposed to the traditional flow control logic typical of hydraulic systems used in off-road vehicles. The proposed hydraulic control system allows for elimination of redundant flow control valves in the state-of-the-art system, which cause excessive throttling losses leading to poor overall energy efficiency. Related work on MPR technology targets construction vehicles, where the MPR solution can allow energy recovery during overrunning loads and better engine management. This paper alternatively addresses the case of agricultural applications where functions mostly operate under resistive load conditions with slow dynamics, which offers an opportunity to target throttle losses. For this purpose, the paper introduces a variable pressure control strategy to handle the instantaneous pressure at each rail. To develop both the controller and the hydraulic system architecture, a stationary test rig is conceived and used to validate a numerical simulation model of the MPR system and its control strategy. Particular focus is given to the dynamic behavior of the system during the switches of a function between different pressure rails, which needs to ensure reduced oscillations of the flow provided to each hydraulic function. Once validated, the simulation model is used to predict the energy savings of the MPR solution in an actual application: a 435 hp hydraulic tractor powering a 16-row planter, for which operating features during typical drive cycles were available to the authors. The results show up to 59% total power reduction at the pump shaft, corresponding to 89.8% system efficiency gain.

36 MATERIALS SCIENCE↗

DOE OSTI2023

EUI Benchmarks for Net-Zero Energy Buildings in India

In our study we present EUI benchmarks for NZEBs for six building types across residential and non-residential typologies and for India's five climate zones. This approach is similar to the simulation-based benchmarks used by the B3 program in Minnesota, the Cal-Arch methodology in California, and the US Solar Decathlon approach, which combine simulations with actual building data. Of the six building types we explore one in detail with a range of operation scenarios, specifically narrowing down the EUI benchmarks for mixed-mode building operation and for variable temperature set-points as prescribed in the National Building Code of India.The contribution of this work is to provide rigorous end-use level EUI benchmarks for six building types, and to describe a method for simulation-based EUI benchmarks for mixed-mode operation with variable setpoints to highlight the difference between the standard approach used for the five building types and the On-Site Construction Worker Housing which additionally has the mixed-mode variable setpoint approach.On-Site Construction Worker Housings are typically poorly constructed temporary structures, without adequate thermal comfort, It is critical to provide adequate thermal comfort to protect people from the warming effects of climate change, and to discover super efficient and cost-effective ways to do so.The methodology used for the On-Site Construction Worker Housing (CWH) results in an 80% acceptability according to the India Model for Adaptive Comfort in the National Building Code of India. EUIs of all six buildings are 60% lower than the minimum compliance with India's Energy Conservation Building Codes, providing benchmarks for efficiency levels. The end-use level EUI benchmarks are now provided to over 1800 Solar Decathlon India participants so that they can compare the performance of their NZEB designs.In particular, the CWH results provide an insight into the importance of the mixed-mode operation with variable temperature set-points. The results from the simulation study show that for an NZEB target, the EUI with standard thermal comfort model and without mixed operation is 58.26 kWh/m2*year, while that with the variable set-points of the adaptive model with mixed mode operation is 24.23 kWh/m2*year. This is a 58% reduction in EUI. Given that many building types including residential, and non-residential operate in mixed mode, it is important to take this work further to develop mixed-mode operation NZEB benchmarks so that the carbon intensity of these buildings could be lower than the standard thermal comfort model approach.

benchmarking↗

DOE OSTI2022

A Hierarchy of Global Ocean Models Coupled to CESM1

Abstract We develop a hierarchy of simplified ocean models for coupled ocean, atmosphere, and sea ice climate simulations using the Community Earth System Model version 1 (CESM1). The hierarchy has four members: a slab ocean model, a mixed‐layer model (MLM) with entrainment and detrainment, an Ekman MLM, and an ocean general circulation model (OGCM). Flux corrections of heat and salt are applied to the simplified models ensuring that all hierarchy members have the same climatology. We diagnose the needed flux corrections from auxiliary simulations in which we restore the temperature and salinity to the daily climatology obtained from a target CESM1 simulation. The resulting three‐dimensional corrections contain the interannual variability fluxes that maintain the correct vertical gradients of temperature and salinity in the tropics. We find that the inclusion of mixed‐layer entrainment and Ekman flow produces sea surface temperature and surface air temperature fields whose means and variances are progressively more similar to those produced by the target CESM1 simulation. We illustrate the application of the hierarchy to the problem of understanding the response of the climate system to the loss of Arctic sea ice. We find that the shifts in the positions of the mid‐latitude westerly jet and of the Inter‐tropical Convergence Zone (ITCZ) in response to sea‐ice loss depend critically on upper ocean processes. Specifically, heat uptake associated with the mixed‐layer entrainment influences the shift in the westerly jet and ITCZ. Moreover, the shift of ITCZ is sensitive to the form of Ekman flow parameterization.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Assessing the Key Requirements for 450 GW of Renewable Capacity in India by 2030

In this policy brief, we assess the prerequisites for India to achieve 450 GW of solar and wind cumulative installed capacity by 2030. We examine requirements such as availability of land, new transmission buildout, financing and pace of deployment, as well as the impact on grid reliability and cost of generation. We also examine the impact of policies promoting domestic manufacturing. Deploying 307 GW of solar and 142 GW of wind capacity would use only about 1.25% of land that is categorized as barren or waste, which is equivalent to about 0.22% of the total land area in India. Because of the good solar resource across large swaths of India, the solar energy buildout—and thus the land use—potentially can be spread out. India would need about 280 GW of new interstate transmission capacity by 2030, a little over double the transmission expansion that has already been planned through 2025. However, most of the new transmission buildout is driven by the near doubling of electricity demand between 2020 and 2030. The total investment needed (in generation and storage resources) to realize this target is around USD 26.5 billion annually, which is 20% lower than the annual investment in India’s power sector across all generation resources between 2015 and 2019. We estimate that using domestically manufactured panels instead of imported panels may increase solar PPA prices by about 10%–15% in the medium term, but solar power would still be a cost-effective way to meet growing demand instead of building new fossil fuel-based power plants, because the price of electricity from solar plants has fallen below the variable cost of most existing coal units. To reach this target, India would need to build about 35–40 GW of solar and wind capacity every year in this decade. India’s power sector achieved a pace of capacity addition of 22 GW per year in the previous decade (including thermal and renewable). Policy and regulatory measures would be needed to increase the pace of deployment.

14 SOLAR ENERGY↗

DOE OSTI2021

Soil organic carbon is not just for soil scientists: measurement recommendations for diverse practitioners

Soil organic carbon (SOC) regulates terrestrial ecosystem functioning, provides diverse energy sources for soil microorganisms, governs soil structure, and regulates the availability of organically bound nutrients. Investigators in increasingly diverse disciplines recognize how quantifying SOC attributes can provide insight about ecological states and processes. Today, multiple research networks collect and provide SOC data, and robust, new technologies are available for managing, sharing, and analyzing large data sets. Here, we advocate that the scientific community capitalize on these developments to augment SOC data sets via standardized protocols. We describe why such efforts are important and the breadth of disciplines for which it will be helpful, and outline a tiered approach for standardized sampling of SOC and ancillary variables that ranges from simple to more complex. We target scientists ranging from those with little to no background in soil science to those with more soil-related expertise, and offer examples of the ways in which the resulting data can be organized, shared, and discoverable.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2017

Hydrogel Tethering Enhances Interdomain Stabilization of Single-Chain Antibodies

Self-assembly of recombinant proteins within the biosilica of living diatoms represents a means to construct functional materials in a reproducible and scalable manner that enable applications that harness the inherent specificities of proteins to sense and respond to environmental cues. Here we describe the use of a silaffin-derived lysine-rich 39 amino-acid targeting sequence (Sil3T8) to direct a single chain fragment variable (scFv) antibody or an enhanced green fluorescent protein (EGFP) to assemble within the biosilica frustule, resulting in abundances in excess of 200,000 proteins per frustule. The fluorescence of either a derivative of trinitrotoluene (TNT) bound to the scFv or the endogenous fluorescence of EGFP was used to monitor pro-tein conformational dynamics, accessibility to external quenchers, binding affinity, and conformational stability. We find that proteins within isolated frustules undergo isotropic rotational motions with two-fold increases in rotational correlation times, which are indicative of weak macromolecular associations within the biosilica. Solvent accessibilities and high-affinity (pM) binding are comparable to those in solution. In contrast to solution conditions, scFv antibod-ies within the biosilica matrix retain their binding affinity in the presence of chaotropic agents (i.e., 8 M urea). These results argue that dramatic increases in protein conforma-tional stability within the biosilica frustule matrices arise through molecular crowding, acting to retain native protein folds and associated functionality to allow the utility of engineered proteins under a range of harsh environmental conditions associated with environmental sensing and industrial catalytic transformations.

Biosilica↗