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At least 55 records · Page 3

Biomimetic Rebuilding of Multifunctional Red Blood Cells: Modular Design Using Functional Components

The design and synthesis of artificial materials that mimic the structures, mechanical properties, and ultimately functionalities of biological cells remains a current holy grail of materials science. Here based on a silica cell bio-replication approach, we report the design and construction of synthetic rebuilt red blood cells (RRBCs) that fully mimic the broad properties of native RBCs: size, biconcave shape, deformability, oxygen carrying capacity, long circulation time. Four successive nano-scale processing steps: RBC bioreplication, layer-by-layer polymer deposition, and precision silica etching, followed by RBC ghost membrane vesicles fusion are employed for RRBC construction. A panel of physicochemical analyses including zeta potential measurement, fluorescence microscopy, and antibody-mediated agglutination assay proved the recapitulation of RBC shape, size, and membrane structure. Flow-based deformation studies carried out in a microfluidic blood capillary model confirrned the ability of RRBCs to deform and pass through small slits and reconstitute themselves in a manner comparable to native RBCs. Circulation studies of RRBCs conducted ex-ovo in a chick embryo and in vivo in a mouse model demonstrated the requirement of both deformability and native cell membrane surface to achieve long-term circulation. To confer additional non-native functionalities to RRBCs, we developed modular procedures in which to load functional cargos such as hemoglobin, drugs, magnetic nanoparticles, and ATP biosensors within the RRBC interior to enable various functions, including oxygen delivery, therapeutic drug delivery, magnetic manipulation, and toxin biosensing and detection. Taken together, RRBCs represent a class of long circulating RBC-inspired artificial hybrid materials with a broad range of potential applications.

59 BASIC BIOLOGICAL SCIENCES↗

Lipid sponge droplets as programmable synthetic organelles

Living cells segregate molecules and reactions in various subcellular compartments known as organelles. Spatial organization is likely essential for expanding the biochemical functions of synthetic reaction systems, including artificial cells. Many studies have attempted to mimic organelle functions using lamellar membrane-bound vesicles. However, vesicles typically suffer from highly limited transport across the membranes and an inability to mimic the dense membrane networks typically found in organelles such as the endoplasmic reticulum. Here, we describe programmable synthetic organelles based on highly stable nonlamellar sponge phase droplets that spontaneously assemble from a single-chain galactolipid and nonionic detergents. Due to their nanoporous structure, lipid sponge droplets readily exchange materials with the surrounding environment. In addition, the sponge phase contains a dense network of lipid bilayers and nanometric aqueous channels, which allows different classes of molecules to partition based on their size, polarity, and specific binding motifs. The sequestration of biologically relevant macromolecules can be programmed by the addition of suitably functionalized amphiphiles to the droplets. We demonstrate that droplets can harbor functional soluble and transmembrane proteins, allowing for the colocalization and concentration of enzymes and substrates to enhance reaction rates. Droplets protect bound proteins from proteases, and these interactions can be engineered to be reversible and optically controlled. Our results show that lipid sponge droplets permit the facile integration of membrane-rich environments and self-assembling spatial organization with biochemical reaction systems.

59 BASIC BIOLOGICAL SCIENCES↗

A nonradial pulsation model for the rapidly rotating Delta Scuti star Kappa(2) Bootis

A sectorial nonradial pulsation model is used to construct theoretical line profiles which mimic the variations for Kappa(2) Boo. Synthetic spectra generated with the appropriate Teff and log g are used as input. It is found that the data can be reproduced by the combination of a high-degree l is approximately equal to 12 mode with P(osc) aproximately equal to 0.071 d, and a low-degree mode, l is approximately equal to 0-2 with P(osc) approximately equal to 0.071-0.079 d. The projected rotational velocity (v sin i - 115 +/-5 km/s) was determined by fitting synthetic line profiles to the observed spectra. The velocity amplitude of the high-degree oscillations is estimated to be about 3.5 km/s. It is found that the ratio of the horizontal and radial pulsation amplitudes is small (about 0.02) and consistent with p-mode oscillations. Comparisons are made with models invoking starspots, and it is impossible to fit the observations of Kappa(2) Boo by a starspot model without assuming unrealistic values of radius or equatorial velocity.

Kennelly, E. J.↗

The Effect of Fatty Acids to Protect Forward Osmosis Membranes from Damage

NASA has conducted research and development on forward osmosis (FO) membranes for wastewater reclamation in space since 1993. The lessons learned during operation of the International Space Station and FO based technologies on the ground taught us that reliability is a key limitation. Membranes are susceptible to organic fouling, oxidation and calcium scaling, and these factors tend to damage the membrane reducing their operating life and performance. The development of a Synthetic Biological Membrane (SBM), a membrane that mimics naturally occurring biological processes, will mitigate membrane damage and improve reliability. The SBM is a lipid-based membrane with a protective fatty acid layer configured for use in a FO water purification system. In this configuration, the protective layer on the surface of the lipid membrane is composed of fatty acids (FA). The FA interact with the chemicals found in the wastewater feed, and protect the membrane from damage. In this study, we conducted preliminary experiments to determine the feasibility of using fatty acids to alleviate damage from calcium scaling, oxidation and organic fouling.

Romero Mangado, Jaione↗

The Kimberlina synthetic multiphysics dataset for CO 2 monitoring investigations

Abstract We present a synthetic multi‐scale, multi‐physics dataset constructed from the Kimberlina 1.2 CO 2 reservoir model based on a potential CO 2 storage site in the Southern San Joaquin Basin of California. Among 300 models, one selected reservoir‐simulation scenario produces hydrologic‐state models at the onset and after 20 years of CO 2 injection. Subsequently, these models were transformed into geophysical properties, including P‐ and S‐wave seismic velocities, saturated density where the saturating fluid can be a combination of brine and supercritical CO 2 , and electrical resistivity using established empirical petrophysical relationships. From these 3D distributions of geophysical properties, we have generated synthetic time‐lapse seismic, gravity and electromagnetic responses with acquisition geometries that mimic realistic monitoring surveys and are achievable in actual field situations. We have also created a series of synthetic well logs of CO 2 saturation, acoustic velocity, density and induction resistivity in the injection well and three monitoring wells. These were constructed by combining the low‐frequency trend of the geophysical models with the high‐frequency variations of actual well logs collected at the potential storage site. In addition, to better calibrate our datasets, measurements of permeability and pore connectivity have been made on cores of Vedder Sandstone, which forms the primary reservoir unit. These measurements provide the range of scales in the otherwise synthetic dataset to be as close to a real‐world situation as possible. This dataset consisting of the reservoir models, geophysical models, simulated time‐lapse geophysical responses and well logs forms a multi‐scale, multi‐physics testbed for designing and testing geophysical CO 2 monitoring systems as well as for imaging and characterization algorithms. The suite of numerical models and data have been made publicly available for downloading on the National Energy Technology Laboratory's (NETL) Energy Data Exchange (EDX) website.

58 GEOSCIENCES↗

SYNCA: A Synthetic Cyclotron Antenna for the Project 8 Collaboration

Cyclotron Radiation Emission Spectroscopy (CRES) is a technique for measuring the kinetic energy of charged particles through a precision measurement of the frequency of the cyclotron radiation generated by the particle's motion in a magnetic field. The Project 8 collaboration is developing a next-generation neutrino mass measurement experiment based on CRES. One approach is to use a phased antenna array, which surrounds a volume of tritium gas, to detect and measure the cyclotron radiation of the resulting β-decay electrons. To validate the feasibility of this method, Project 8 has designed a test stand to benchmark the performance of an antenna array at reconstructing signals that mimic those of genuine CRES events. To generate synthetic CRES events, a novel probe antenna has been developed, which emits radiation with characteristics similar to the cyclotron radiation produced by charged particles in magnetic fields. This paper outlines the design, construction, and characterization of this Synthetic Cyclotron Antenna (SYNCA). Furthermore, we perform a series of measurements that use the SYNCA to test the position reconstruction capabilities of the digital beamforming reconstruction technique. Finally, we find that the SYNCA produces radiation with characteristics closely matching those expected for cyclotron radiation and reproduces experimentally the phenomenology of digital beamforming simulations of true CRES signals.

47 OTHER INSTRUMENTATION↗

Water, Solute, and Ion Transport in De Novo-Designed Membrane Protein Channels

Biological organisms engineer peptide sequences to fold into membrane pore proteins capable of performing a wide variety of transport functions. Synthetic de novo-designed membrane pores can mimic this approach to achieve a potentially even larger set of functions. Here, in this work, we explore water, solute, and ion transport in three de novo designed β-barrel membrane channels in the 5–10 Å pore size range. We show that these proteins form passive membrane pores with high water transport efficiencies and size rejection characteristics consistent with the pore size encoded in the protein structure. Ion conductance and ion selectivity measurements also show trends consistent with the pore size, with the two larger pores showing weak cation selectivity. MD simulations of water and ion transport and solute size exclusion are consistent with the experimental trends and provide further insights into structure–function correlations in these membrane pores.

59 BASIC BIOLOGICAL SCIENCES↗

Probabilistic estimation of depth-resolved profiles of soil thermal diffusivity from temperature time series: Supporting Data

This dataset consists of soil temperature time series that were used to estimate soil thermal diffusivity and its uncertainty trough the probabilistic modelling approach developed and presented in the article named "Probabilistic estimation of depth-resolved profiles of soil thermal diffusivity from temperature time series" and published in Earth Surface Dynamics. There are two compressed (.zip) files that contains synthetic (Synthetic_soiltemp_Teller.zip) and field (Field_soiltemp_Teller.zip) data. There is one MATLAB file that requires MATLAB to execute but any text editor can open it. The Synthetic_soiltemp_Teller.zip file includes 5 comma-delimited data files (.csv) each of which contains soil temperature time series generated through forward modeling (i.e., heat-conduction process in a heterogeneous medium using an explicit finite difference method) to mimic various types of temperature gradients, trend and fluctuations. These synthetic soil temperatures were used to investigate the impact of different environmental conditions on the uncertainty of thermal diffusivity estimates. The Field_soiltemp_Teller.zip file contains 28 comma-delimited data files (.csv) out of which (a) 27 files includes soil temperature time series recorded from 27 temperature probes located in a site along Teller Road about 40 km northwest of Nome, Alaska (64.72°N, 165.94°W), (b) one includes the name and coordinates of the 27 probes. These field soil temperatures were used to infer soil thermal diffusivity at numerous locations and depths in a discontinuous permafrost environment, and to evaluate the links between the estimated soil thermal diffusivity values and soil physical properties. The comma-delimited data files (.csv) of the synthetic and field soil temperature time series includes date and time (UTC) in the first column and soil temperature from 5 cm below the ground surface to 1.05 m depth (with 5 or 10 cm spacing between sensors) in the other columns. The measurements were acquired every 15 minutes. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Sample Analysis at Mars Instrument Simulator

The Sample Analysis at Mars Instrument Simulator (SAMSIM) is a numerical model dedicated to plan and validate operations of the Sample Analysis at Mars (SAM) instrument on the surface of Mars. The SAM instrument suite, currently operating on the Mars Science Laboratory (MSL), is an analytical laboratory designed to investigate the chemical and isotopic composition of the atmosphere and volatiles extracted from solid samples. SAMSIM was developed using Matlab and Simulink libraries of MathWorks Inc. to provide MSL mission planners with accurate predictions of the instrument electrical, thermal, mechanical, and fluid responses to scripted commands. This tool is a first example of a multi-purpose, full-scale numerical modeling of a flight instrument with the purpose of supplementing or even eliminating entirely the need for a hardware engineer model during instrument development and operation. SAMSIM simulates the complex interactions that occur between the instrument Command and Data Handling unit (C&DH) and all subsystems during the execution of experiment sequences. A typical SAM experiment takes many hours to complete and involves hundreds of components. During the simulation, the electrical, mechanical, thermal, and gas dynamics states of each hardware component are accurately modeled and propagated within the simulation environment at faster than real time. This allows the simulation, in just a few minutes, of experiment sequences that takes many hours to execute on the real instrument. The SAMSIM model is divided into five distinct but interacting modules: software, mechanical, thermal, gas flow, and electrical modules. The software module simulates the instrument C&DH by executing a customized version of the instrument flight software in a Matlab environment. The inputs and outputs to this synthetic C&DH are mapped to virtual sensors and command lines that mimic in their structure and connectivity the layout of the instrument harnesses. This module executes, and thus validates, complex command scripts prior to their up-linking to the SAM instrument. As an output, this module generates synthetic data and message logs at a rate that is similar to the actual instrument.

Benna, Mehdi↗

Histidine methyltransferase SETD3 methylates structurally diverse histidine mimics in actin

Actin histidine N τ -methylation by histidine methyltransferase SETD3 plays an important role in human biology and diseases. Here, we report integrated synthetic, biocatalytic, biostructural, and computational analyses on human SETD3-catalyzed methylation of actin peptides possessing histidine and its structurally and chemically diverse mimics. Our enzyme assays supported by biostructural analyses demonstrate that SETD3 has a broader substrate scope beyond histidine, including N-nucleophiles on the aromatic and aliphatic side chains. Quantum mechanical/molecular mechanical molecular dynamics and free-energy simulations provide insight into binding geometries and the free energy barrier for the enzymatic methyl transfer to histidine mimics, further supporting experimental data that histidine is the superior SETD3 substrate over its analogs. This work demonstrates that human SETD3 has a potential to catalyze efficient methylation of several histidine mimics, overall providing mechanistic, biocatalytic, and functional insight into actin histidine methylation by SETD3.

59 BASIC BIOLOGICAL SCIENCES↗

Propulsion of synthetic protocells and coacervates driven by biochemical catalysis

An important area in the design of biomolecular materials is the mimicry of cellular function through the assembly of molecular components into synthetic cells, or protocells. Through compartmentalization and subsequent evolution, biological cells have achieved the goals of specificity, amplification, and response. By assembling cell-like structures that mimic the organization and size of a natural cell but that incorporate novel components and respond to synthetic triggers, we can extend their capabilities beyond what is currently achievable in biology. For applications in energy, these include the ability to convert chemical to mechanical energy, and to enable the response of sensors and responders once a threshold has been reached. This technical report summarizes progress made on this project as of Dec 31, 2023.

36 MATERIALS SCIENCE↗

Random heteropolymers as enzyme mimics

Despite successes in replicating the primary–secondary–tertiary structure hierarchy of protein, it remains elusive to synthetically materialize protein functions that are deeply rooted in their chemical, structural and dynamic heterogeneities. We propose that for polymers with backbone chemistries different from that of proteins, programming spatial and temporal projections of sidechains at the segmental level can be effective in replicating protein behaviours; and leveraging the rotational freedom of polymer can mitigate deficiencies in monomeric sequence specificity and achieve behaviour uniformity at the ensemble level. Here, guided by the active site analysis of about 1,300 metalloproteins, we design random heteropolymers (RHPs) as enzyme mimics based on one-pot synthesis. We introduce key monomers as the equivalents of the functional residues of protein and statistically modulate the chemical characteristics of key monomer-containing segments, such as segmental hydrophobicity. The resultant RHPs form pseudo-active sites that provide key monomers with protein-like microenvironments, co-localize substrates with catalytic or cofactor-binding sidechains and catalyse reactions such as oxidation and cyclization of citronellal with isopulegol/menthoglycol selectivity. This RHP design led to enzyme-like materials that can retain catalytic activity under non-biological conditions, are compatible with scalable processing and have expanded substrate scope, including environmentally long-lasting antibiotic tetracycline.

36 MATERIALS SCIENCE↗

Abbr. Final report: Self-assembled molecular containers as artificial water channels: towards biomimetic desalination membranes

Global water scarcity demands advances in desalination technologies that can deliver more fresh water with less energy. Current reverse osmosis membranes are fundamentally limited by a trade-off between how much water they can pass and how well they block salts. To address this challenge, we developed a bottom-up strategy to design and test artificial water channels that mimic the efficiency of biological proteins but are built from robust synthetic molecules. Over two years, we synthesized and evaluated more than twenty molecular channel candidates, including supramolecular macrocycles and nanographene pores with atomically precise structures. We showed that small chemical modifications allow direct control over pore size and chemistry, which in turn govern water permeability and salt rejection. In collaboration with university partners, we reported the first experimental demonstration of water transport through a nanographene pore, bridging a long-standing gap between simulation and experiment. Several of the artificial channels we developed achieved water–salt selectivity beyond conventional polymer membranes, highlighting their potential for next-generation desalination and precision separations.

36 MATERIALS SCIENCE↗

A Case Study on Pathogen Transport, Deposition, Evaporation and Transmission: Linking High-Fidelity Computational Fluid Dynamics Simulations to Probability of Infection

A high-fidelity, low-Mach computational fluid dynamics simulation tool that includes evaporating droplets and variable-density turbulent flow coupling is well-suited to ascertain transmission probability and supports risk mitigation methods development for airborne infectious diseases such as COVID-19. A multi-physics large-eddy simulation-based paradigm is used to explore droplet and aerosol pathogen transport from a synthetic cough emanating from a kneeling humanoid. For an outdoor configuration that mimics the recent open-space social distance strategy of San Francisco, maximum primary droplet deposition distances are shown to approach 8.1 m in a moderate wind configuration with the aerosol plume transported in excess of 15 m. In quiescent conditions, the aerosol plume extends to approximately 4 m before the emanating pulsed jet becomes neutrally buoyant. A dose–response model, which is based on previous SARS coronavirus (SARS-CoV) data, is exercised on the high-fidelity aerosol transport database to establish relative risk at eighteen virtual receptor probe locations.

59 BASIC BIOLOGICAL SCIENCES↗

Synthetic Soil Aggregates: Bioprinted Habitats for High-Throughput Microbial Metaphenomics

The dynamics of microbial processes are difficult to study in natural soil, owing to the small spatial scales on which microorganisms operate and to the opacity and chemical complexity of the soil habitat. To circumvent these challenges, we have created a 3D-bioprinted habitat that mimics aspects of natural soil aggregates while providing a chemically defined and translucent alternative culturing method for soil microorganisms. Our Synthetic Soil Aggregates (SSAs) retain the porosity, permeability, and patchy resource distribution of natural soil aggregates—parameters that are expected to influence emergent microbial community interactions. We demonstrate the printability and viability of several different microorganisms within SSAs and show how the SSAs can be integrated into a multi-omics workflow for single SSA resolution genomics, metabolomics, proteomics, lipidomics, and biogeochemical assays. We study the impact of the structured habitat on the distribution of a model co-culture microbial community and find that it is significantly different from the spatial organization of the same community in liquid culture, indicating a potential for SSAs to reproduce naturally occurring emergent community phenotypes. The SSAs have the potential as a tool to help researchers quantify microbial scale processes in situ and achieve high-resolution data from the interplay between environmental properties and microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗

An improved synthetic signal injection routine for the Haloscope At Yale Sensitive To Axion Cold dark matter (HAYSTAC)

Microwave cavity haloscopes are among the most sensitive direct detection experiments searching for dark matter axions via their coupling to photons. When the power of the expected microwave signal due to axion–photon conversion is on the order of 10 −24 W, having the ability to validate the detector response and analysis procedure by injecting realistic synthetic axion signals becomes helpful. Here, we present a method based on frequency hopping spread spectrum for synthesizing axion signals in a microwave cavity haloscope experiment. It allows us to generate a narrow and asymmetric shape in frequency space that mimics an axion’s spectral distribution, which is derived from a Maxwell–Boltzmann distribution. In addition, we show that the synthetic axion’s power can be calibrated with reference to the system noise. Further, compared to the synthetic axion injection in the Haloscope At Yale Sensitive to Axion Cold dark matter (HAYSTAC) Phase I, we demonstrated synthetic signal injection with a more realistic line shape and calibrated power.

47 OTHER INSTRUMENTATION↗

An improved synthetic signal injection routine for HAYSTAC

Microwave cavity haloscopes are among the most sensitive direct detection experiments searching for dark matter axions via their coupling to photons. When the power of the expected microwave signal due to axion-photon conversion is on the order of 10-24 W, having the ability to validate the detector response and analysis procedure by injecting realistic synthetic axion signals becomes helpful. Here we present a method based on frequency hopping spread spectrum for synthesizing axion signals in a microwave cavity haloscope experiment. It allows us to generate a narrow and asymmetric shape in frequency space that mimics an axion's spectral distribution, which is derived from a Maxwell-Boltzmann distribution. In addition, we show that the synthetic axion's power can be calibrated with reference to the system noise. Compared to the synthetic axion injection in HAYSTAC phase I, we demonstrated synthetic signal injection with a more realistic lineshape and calibrated power.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Experimental Investigation of Polymer Induced Fouling of Heater Tubes in the First-ever Polymer Flood Pilot on Alaska North Slope

Polymer flooding has been validated in the lab and by successful applications in other countries, such as Canada and China, to be an effective EOR technique for heavy oil reservoirs. Currently, polymer flooding is being pilot tested for the first time in the Schrader Bluff viscous oil reservoir at Milne Point field on Alaska North Slope (ANS). One of the major concerns of the operator is the impact of polymer on the oil production system after polymer breakthrough, especially the polymer induced fouling issues in the heat exchanger. This study investigates the propensity of polymer fouling on the heater tubes as a function of different variables, with the ultimate goal of determining safe and efficient operating conditions. A unique experimental set-up was indigenously designed and developed to simulate the fouling process on the heating tube. The influence of heating tube skin temperature, tube material, and polymer concentration on fouling tendency was investigated. Under each test condition, the test was run five times with the same tube, and in each run, the freshly prepared synthetic brine and polymer solution were heated from 77°F to 122°F to mimic field operating conditions. The heating time and fouling amount were recorded for each run. The morphology and composition of the deposit samples were analyzed by environmental scanning electron microscopy (ESEM) and X-ray diffraction (XRD), respectively. It has been found that, in general, the presence of polymer in produced fluids would aggravate the fouling issues on both carbon steel and stainless steel surfaces at all tested skin temperatures (165°F, 250 °F and 350°F), but only higher skin temperatures of 250°F and 350°F could cause polymer induced fouling issues on the copper tube surface and the fouling tendency increased with polymer concentration. At the lower skin temperatures of 165°F, no polymer-induced fouling was identified on the copper tube. A critical temperature that is related to the cloud point of the polymer solution was believed to exist, below which polymer induced fouling would not occur and only mineral scale deposited, but above which the polymer would obviously aggravate the fouling issue. The heating efficiency of the tube would be reduced gradually as more fouling material accumulates on its surface. The ESEM results indicate that if polymer precipitated and deposited on the surface, it would bond to the mineral crystals to form a stronger three- dimensional network structure, and that is why the polymer induced fouling was tougher and more difficult to be removed from the tube surface. The XRD analysis results confirm that the presence of polymer in the fluids can enhance the mineral scale propensity. Overall, the study results have provided practical guidance to the field operator for the ongoing polymer flooding pilot test on ANS. This study may also prove to be valuable for other chemical EOR projects around the world.

Alaska North Slope↗