SEARCH · Engineering Papers

Results for “CoLocate”

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 55 records · Page 3

All sources NASA NTRS DOE OSTI

NASA NTRS1987

The Spring 1985 high precision baseline test of the JPL GPS-based geodetic system

The Spring 1985 High Precision Baseline Test (HPBT) was conducted. The HPBT was designed to meet a number of objectives. Foremost among these was the demonstration of a level of accuracy of 1 to 2:10 to the 7th power, or better, for baselines ranging in length up to several hundred kilometers. These objectives were all met with a high degree of success, with respect to the demonstration of system accuracy in particular. The results from six baselines ranging in length from 70 to 729 km were examined for repeatability and, in the case of three baselines, were compared to results from colocated VLBI systems. Repeatability was found to be 5:10 to the 8th power (RMS) for the north baseline coordinate, independent of baseline length, while for the east coordinate RMS repeatability was found to be larger than this by factors of 2 to 4. The GPS-based results were found to be in agreement with those from colocated VLBI measurements, when corrected for the physical separations of the VLBI and CPG antennas, at the level of 1 to 2:10 to the 7th power in all coordinates, independent of baseline length. The results for baseline repeatability are consistent with the current GPA error budget, but the GPS-VLBI intercomparisons disagree at a somewhat larger level than expected. It is hypothesized that these differences may result from errors in the local survey measurements used to correct for the separations of the GPS and VLBI antenna reference centers.

Davidson, John M.↗

NASA NTRS1989

Influence of time lag and noncolocation on integrated structural/control system designs

Recent research efforts have led to the development of simultaneous structural/control system design procedures. Absent in any of the work is the time delay present in the control system sensors and actuators and the computational time delay for synthesizing actuator commands from sensor measurements. Madden has shown that the time delay present in the control system can have profound effects on the resulting system performance and stability regardless of its source. In addition, many of the simultaneous structural/control system design procedures have used colocated sensors and actuators for implementation of the control system. In actual practice, colocation in not always possible. The issue of stability degradation when using noncolocated sensor and actuators was raised. The integrated structural/control system design procedure is extended to include the effects of time lag and noncolocation of sensors and actuators on the resulting optimum designs.

Manning, R. A.↗

NASA NTRS1993

A layered approach to structural control system design for the JPL phase B testbed

This paper describes our efforts in structural control experiments for a flexible precision structure using both passive and active control. Specifically, a layered structural control approach utilizing passive viscous dampers, colocated and noncolocated active control is used. The passive dampers and active colocated control loops are used to enhance stability and robustness and the noncolocated multivariable controller is designed with respect to a partially controlled structure to further improve the performance. Our approach to the multivariable design problem requires not only a state space model description of the plant, but also an accompanying uncertainty model. To support the multivariable robust control design development, a significant effort in system identification was undertaken. The process of identification and identified results are discussed. Noncolocated controllers are designed using the H(infinity)/mu-synthesis methodology. The order of the controller is typically large, hence, model reduction is performed for practical digital implementation on a real-time control system developed at JPL. Finally, experimental results are presented and some of lessons are discussed.

Chu, Cheng-Chih↗

NASA NTRS1996

Covisualization by computational optical-sectioning microscopy of integrin and associated proteins at the cell membrane of living onion protoplasts

Using higher-resolution wide-field computational optical-sectioning fluorescence microscopy, the distribution of antigens recognized by antibodies against animal beta 1 integrin, fibronectin, and vitronectin has been visualized at the outer surface of enzymatically protoplasted onion epidermis cells and in depectinated cell wall fragments. On the protoplast all three antigens are colocalized in an array of small spots, as seen in raw images, in Gaussian filtered images, and in images restored by two different algorithms. Fibronectin and vitronectin but not beta 1 integrin antigenicities colocalize as puncta in comparably prepared and processed images of the wall fragments. Several control visualizations suggest considerable specifity of antibody recognition. Affinity purification of onion cell extract with the same anti-integrin used for visualization has yielded protein that separates in SDS-PAGE into two bands of about 105-110 and 115-125 kDa. These bands are again recognized by the visualization antibody, which was raised against the extracellular domain of chicken beta 1 integrin, and are also recognized by an antibody against the intracellular domain of chicken beta 1 integrin. Because beta 1 integrin is a key protein in numerous animal adhesion sites, it appears that the punctate distribution of this protein in the cell membranes of onion epidermis represents the adhesion sites long known to occur in cells of this tissue. Because vitronectin and fibronection are matrix proteins that bind to integrin in animals, the punctate occurrence of antigenically similar proteins both in the wall (matrix) and on enzymatically prepared protoplasts reinforces the concept that onion cells have adhesion sites with some similarity to certain kinds of adhesion sites in animals.

NASA Discipline Plant Biology↗

NASA NTRS2004

GEO Sounding Using Microwave Instruments

There are several microwave instruments in low Earth orbit (LEO) that are used for atmospheric temperature and humidity sounding in conjunction with companion IR sounders as well as by themselves. These instruments have achieved a certain degree of maturity and undergoing a redesign to minimize their size, mass, and power from the previous generation instruments. An example of these instruments is the AMSU-A series, now flying on POES and AQUA spacecraft with the IR sounders HIRS and AIRS. These older microwave instruments are going to be replaced by the ATMS instruments that will fly on NPP and NPOESS satellites with the CrIS sounder. A number of techniques learned from the ATMS project in instrument hardware design and data processing are directly applicable to a similar microwave sounder on a geosynchronous platform. These techniques can significantly simplify the design of a Geostationary orbit (GEO) microwave instrument, avoiding costly development and minimizing the risk of not being able to meet the scientific requirements. In fact, some of the 'enabling' technology, such as the use of MMIC microwave components (which is the basis for the ATMS' much reduced volume) can be directly applied to a GEO sounder. The benefits of microwave sounders are well known; for example, they penetrate non-precipitating cloud cover and allow for use of colocated IR observations in up to 80% cloud cover. The key advantages of a microwave instrument in GEO will be the ability to provide high temporal resolution as well as uniform spatial resolution and extend the utility of a colocated advanced IR sounder to cases in which partial cloud cover exists. A footprint of the order of 100 km by 100 km resolution with hemispherical coverage within one hour can be easily achieved for sounding channels in the 50 to 59 GHz range. A GEO microwave sounder will also allow mesoscale sampling of select regions.

Shiue, James↗

NASA NTRS2013

ALMA Observations of the Molecular Gas in the Debris Disk of the 30 Myr Old Star HD 21997

The 30 Myr old A3-type star HD 21997 is one of the two known debris dust disks having a measurable amount of cold molecular gas. With the goal of understanding the physical state, origin, and evolution of the gas in young debris disks, we obtained CO line observations with the Atacama Large Millimeter/submillimeter Array (ALMA). Here, we report on the detection of (12)CO and (13)CO in the J = 2-1 and J = 3-2 transitions and C(18)O in the J = 2-1 line. The gas exhibits a Keplerian velocity curve, one of the few direct measurements of Keplerian rotation in young debris disks. The measured CO brightness distribution could be reproduced by a simple star+disk system, whose parameters are r(sub in) < 26 AU, r(sub out) = 138 +/- 20 AU, Stellar M = 1.8 +0.5/−0.2 Solar M, and i = 32. Deg. 6 +/- 3 deg..1. The total CO mass, as calculated from the optically thin C(18)O line, is about (4-8) ×10(exp −2 ) Solar M, while the CO line ratios suggest a radiation temperature on the order of 6-9 K. Comparing our results with those obtained for the dust component of the HD 21997 disk from ALMA continuum observations by Moor et al., we conclude that comparable amounts of CO gas and dust are present in the disk. Interestingly, the gas and dust in the HD 21997 system are not colocated, indicating a dust-free inner gas disk within 55 AU of the star. We explore two possible scenarios for the origin of the gas. A secondary origin, which involves gas production from colliding or active planetesimals, would require unreasonably high gas production rates and would not explain why the gas and dust are not colocated. We propose that HD 21997 is a hybrid system where secondary debris dust and primordial gas coexist. HD 21997, whose age exceeds both the model predictions for disk clearing and the ages of the oldest T Tauri-like or transitional gas disks in the literature, may be a key object linking the primordial and the debris phases of disk evolution.

molecular gas↗

NASA NTRS2020

Inversion of multiangular polarimetric measurements from the ACEPOL campaign: an application of improving aerosol property and hyperspectral ocean color retrievals

NASA's Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission, scheduled for launch in the time frame of late 2022 to early 2023, will carry the Ocean Color Instrument (OCI), a hyperspectral scanning radiometer, and two multiangle polarimeters (MAPs), the UMBC Hyper-Angular Rainbow Polarimeter 2 (HARP2) and the SRON Spectro-Polarimeter for Planetary EXploration one (SPEXone). One purpose of the PACE MAPs is to better characterize aerosol properties, which can then be used to improve atmospheric correction for the retrieval of ocean color in coastal waters. Though this is theoretically promising, the use of MAP data in the atmospheric correction of colocated hyperspectral ocean color measurements have not yet been well demonstrated. In this work, we performed aerosol retrievals using the MAP measurements from the Research Scanning Polarimeter (RSP) and demonstrate its application to the atmospheric correction of hyperspectral radiometric measurements from SPEX airborne. Both measurements were collected on the same aircraft from the Aerosol Characterization from Polarimeter and Lidar (ACEPOL) field campaign in 2017. Two cases over ocean with small aerosol loading (aerosol optical depth ∼0.04) are identified including colocated RSP and SPEX airborne measurements and Aerosol Robotic Network (AERONET) ground-based observations. The aerosol retrievals are performed and compared with two options: one uses reflectance measurement only and the other uses both reflectance and polarization. It is demonstrated that polarization information helps reduce the uncertainties of aerosol microphysical and optical properties. The retrieved aerosol properties are then used to compute the contribution of atmosphere and ocean surface for atmospheric correction over the discrete bands from RSP measurements and the hyperspectral SPEX airborne measurements. The water-leaving signals determined this way are compared with both AERONET and Moderate Resolution Imaging Spectroradiometer (MODIS) ocean color products for performance analysis. The results and lessons learned from this work will provide a basis to fully exploit the information from the unique combination of sensors on PACE for aerosol characterization and ocean ecosystem research.

Meng Gao↗

NASA NTRS2020

The Prevalence of Precipitation from Polar Supercooled Clouds

Supercooled clouds substantially impact polar surface energy budgets but large-scale models often underestimate their occurrence, which motivates accurately establishing metrics of basic processes. An analysis of long-term measurements at Utqiaġvik, Alaska, and McMurdo Station, Antarctica, combines lidar-validated use of soundings to identify supercooled cloud layers and colocated ground-based profiling radar measurements to quantify cloud base precipitation. We find that more than 85 % (75 %) of sampled supercooled layers are precipitating over the Arctic (Antarctic) site, with more than 75 % (50 %) precipitating continuously to the surface. Such high frequencies can be reconciled with substantially lesser spaceborne estimates by considering differences in radar hydrometeor detection sensitivity. While ice precipitation into supercooled clouds from aloft is common, we also find that the great majority of supercooled cloud layers without ice falling into them are themselves continuously generating precipitation. Such sustained primary ice formation is consistent with continuous activation of immersion-mode ice nucleating particles (INPs), suggesting that supercooled cloud formation is a principal gateway to ice formation at temperatures greater than ~ −38 °C over polar regions. The prevalence of weak precipitation fluxes is also consistent with supercooled cloud longevity, and with well-observed and widely simulated case studies. An analysis of colocated microwave radiometer retrievals suggests that weak precipitation fluxes can be nonetheless consequential to moisture budgets for supercooled clouds owing to small liquid water paths. Finally, we suggest that these ground-based precipitation rate statistics offer valuable guidance for improving the representation of polar cloud processes in large-scale models.

Polar clouds↗

NASA NTRS2021

The Prevalence of Precipitation From Polar Supercooled Clouds

Supercooled clouds substantially impact polar surface energy budgets, but large-scale models often underestimate their occurrence, which motivates accurately establishing metrics of basic processes. An analysis of long-term measurements at Utqiaġvik, Alaska, and McMurdo Station, Antarctica, combines lidar-validated use of soundings to identify supercooled cloud layers and colocated ground-based profiling radar measurements to quantify cloud base precipitation. We find that more than 85 % (75 %) of sampled supercooled layers are precipitating over the Arctic (Antarctic) site, with more than 75 % (50 %) precipitating continuously to the surface. Such high frequencies can be reconciled with substantially lesser spaceborne estimates by considering differences in radar hydrometeor detection sensitivity. While ice precipitation into supercooled clouds from aloft is common, we also find that the great majority of supercooled cloud layers without ice falling into them are themselves continuously generating precipitation. Such sustained primary ice formation is consistent with continuous activation of immersion-mode ice-nucleating particles (INPs), suggesting that supercooled cloud formation is a principal gateway to ice formation at temperatures greater than ∼−38 ∘C over polar regions. The prevalence of weak precipitation fluxes is also consistent with supercooled cloud longevity and with well-observed and widely simulated case studies. An analysis of colocated microwave radiometer retrievals suggests that weak precipitation fluxes can be nonetheless consequential to moisture budgets for supercooled clouds owing to small liquid water paths. The results here also demonstrate that the observed abundance of mixed-phase clouds can vary substantially with instrument sensitivity and methodology. Finally, we suggest that these ground-based precipitation rate statistics offer valuable guidance for improving the representation of polar cloud processes in large-scale models.

Supercooled clouds↗

NASA NTRS2024

Low-Cost Sensor Performance Intercomparison, Correction Factor Development, and 2+ Years of Ambient PM2.5 Monitoring in Accra, Ghana

Particulate matter air pollution is a leading cause of global mortality, particularly in Asia and Africa. Addressing the high and wide-ranging air pollution levels requires ambient monitoring, but many low- and middle-income countries (LMICs) remain scarcely monitored. To address these data gaps, recent studies have utilized low-cost sensors. These sensors have varied performance, and little literature exists about sensor intercomparison in Africa. By colocating 2 QuantAQ Modulair-PM, 2 PurpleAir PA-II SD, and 16 Clarity Node-S Generation II monitors with a reference-grade Teledyne monitor in Accra, Ghana, we present the first intercomparisons of different brands of low-cost sensors in Africa, demonstrating that each type of low-cost sensor PM2.5 is strongly correlated with reference PM2.5, but biased high for ambient mixture of sources found in Accra. When compared to a reference monitor, the QuantAQ Modulair-PM has the lowest mean absolute error at 3.04 μg/m3, followed by PurpleAir PA-II (4.54 μg/m3) and Clarity Node-S (13.68 μg/m3). We also compare the usage of 4 statistical or machine learning models (Multiple Linear Regression, Random Forest, Gaussian Mixture Regression, and XGBoost) to correct low-cost sensors data, and find that XGBoost performs the best in testing (R2: 0.97, 0.94, 0.96; mean absolute error: 0.56, 0.80, and 0.68 μg/m3 for PurpleAir PA-II, Clarity Node-S, and Modulair-PM, respectively), but tree-based models do not perform well when correcting data outside the range of the colocation training. Therefore, we used Gaussian Mixture Regression to correct data from the network of 17 Clarity Node-S monitors deployed around Accra, Ghana, from 2018 to 2021. We find that the network daily average PM2.5 concentration in Accra is 23.4 μg/m3, which is 1.6 times the World Health Organization Daily PM2.5 guideline of 15 μg/m3. While this level is lower than those seen in some larger African cities (such as Kinshasa, Democratic Republic of the Congo), mitigation strategies should be developed soon to prevent further impairment to air quality as Accra, and Ghana as a whole, rapidly grow.

Humidity↗

DOE OSTI2024

Review of Hazards and Accidentology of an Integrated Energy Systems to Nuclear Power Plant Safety

With the interconnectivity of industrial processes in a nuclear integrated energy system (IES) the primary issue becomes the safety of the nuclear power plant (NPP). The industrial processes being supported are assumed to have been in colocation prior to the addition of an NPP. Do the hazards from each process reach beyond the perimeter of the plant to affect the NPP? This paper reviews hazards and accident statistics from processes in an IES as a first step to answer this question. Hazards and accidentology discussed cover hydrogen, ammonia, syngas, methanol, synthetic fuels, and oil refineries. They include mainly fire, explosion, and toxicity in varying degrees. Historical accident statistics are given whenever available, and accident causes are evaluated and ranked based on their frequencies. Lessons learned from previous accidents are presented. Future work will focus on utilizing the data collected for accidentology of the industrial processes to perform Failure Modes and Effects Analysis and analyze the impacts of additional hazards on the colocated existing nuclear power plant or newly built advanced nuclear reactor. The analysis will provide the frequency and consequence of external events that can affect the NPP.

08 - HYDROGEN↗

DOE OSTI2024

The crystal structure of methanogen McrD , a methyl‐coenzyme M reductase‐associated protein

Methyl‐coenzyme M reductase (MCR) is a multi‐subunit (α 2 β 2 γ 2 ) enzyme responsible for methane formation via its unique F 430 cofactor. The genes responsible for producing MCR ( mcrA , mcrB and mcrG ) are typically colocated with two other highly conserved genes mcrC and mcrD . We present here the high‐resolution crystal structure for McrD from a human gut methanogen Methanomassiliicoccus luminyensis strain B10. The structure reveals that McrD comprises a ferredoxin‐like domain assembled into an α + β barrel‐like dimer with conformational flexibility exhibited by a functional loop. The description of the M. luminyensis McrD crystal structure contributes to our understanding of this key conserved methanogen protein typically responsible for promoting MCR activity and the production of methane, a greenhouse gas.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Visualization of a Limonene Synthesis Metabolon Inside Living Bacteria by Hyperspectral SRS Microscopy

Abstract Monitoring biosynthesis activity at single‐cell level is key to metabolic engineering but is still difficult to achieve in a label‐free manner. Using hyperspectral stimulated Raman scattering imaging in the 670–900 cm −1 region, localized limonene synthesis are visualized inside engineered Escherichia coli . The colocalization of limonene and GFP‐fused limonene synthase is confirmed by co‐registered stimulated Raman scattering and two‐photon fluorescence images. The finding suggests a limonene synthesis metabolon with a polar distribution inside the cells. This finding expands the knowledge of de novo limonene biosynthesis in engineered bacteria and highlights the potential of SRS chemical imaging in metabolic engineering research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Unveiling Highly Sensitive Active Site in Atomically Dispersed Gold Catalysts for Enhanced Ethanol Dehydrogenation

Developing a desirable ethanol dehydrogenation process necessitates a highly efficient and selective catalyst with low cost. Herein, we show that the “complex active site” consisting of atomically dispersed Au atoms with the neighboring oxygen vacancies (Vo) and undercoordinated cation on oxide supports can be prepared and display unique catalytic properties for ethanol dehydrogenation. The “complex active site” Au–Vo–Zr 3+ on Au 1 /ZrO 2 exhibits the highest H 2 production rate, with above 37,964 mol H 2 per mol Au per hour (385 g H 2 $\text{g}^{-1}_{\text{Au}} \text{h}^{–1}$) at 350 °C, which is 3.32, 2.94 and 15.0 times higher than Au 1 /CeO 2 , Au 1 /TiO 2 , and Au 1 /Al 2 O 3 , respectively. Combining experimental and theoretical studies, we demonstrate the structural sensitivity of these complex sites by assessing their selectivity and activity in ethanol dehydrogenation. Our study sheds new light on the design and development of cost-effective and highly efficient catalysts for ethanol dehydrogenation. Fundamentally, atomic-level catalyst design by colocalizing catalytically active metal atoms forming a structure-sensitive “complex site”, is a crucial way to advance from heterogeneous catalysis to molecular catalysis. Finally, our study advanced the understanding of the structure sensitivity of the active site in atomically dispersed catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Unveiling Highly Sensitive Active Site in Atomically Dispersed Gold Catalysts for Enhanced Ethanol Dehydrogenation

Developing a desirable ethanol dehydrogenation process necessitates a highly efficient and selective catalyst with low cost. Herein, we show that the “complex active site” consisting of atomically dispersed Au atoms with the neighboring oxygen vacancies (Vo) and undercoordinated cation on oxide supports can be prepared and display unique catalytic properties for ethanol dehydrogenation. The “complex active site” Au-Vo-Zr 3+ on Au 1 /ZrO 2 exhibits the highest H 2 production rate, with above 37,964 mol H 2 per mol Au per hour (385 g H 2 $g^{-1}_{Au}$ h -1 ) at 350 °C, which is 3.32, 2.94 and 15.0 times higher than Au 1 /CeO 2 , Au 1 /TiO 2 , and Au 1 /Al 2 O 3 , respectively. Combining experimental and theoretical studies, we demonstrate the structural sensitivity of these complex sites by assessing their selectivity and activity in ethanol dehydrogenation. Our study sheds new light on the design and development of cost-effective and highly efficient catalysts for ethanol dehydrogenation. Fundamentally, atomic-level catalyst design by colocalizing catalytically active metal atoms forming a structure-sensitive “complex site”, is a crucial way to advance from heterogeneous catalysis to molecular catalysis. In conclusion, our study advanced the understanding of the structure sensitivity of the active site in atomically dispersed catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Root phenotypes for improved nitrogen capture

Abstract Background Suboptimal nitrogen availability is a primary constraint for crop production in low-input agroecosystems, while nitrogen fertilization is a primary contributor to the energy, economic, and environmental costs of crop production in high-input agroecosystems. In this article we consider avenues to develop crops with improved nitrogen capture and reduced requirement for nitrogen fertilizer. Scope Intraspecific variation for an array of root phenotypes has been associated with improved nitrogen capture in cereal crops, including architectural phenotypes that colocalize root foraging with nitrogen availability in the soil; anatomical phenotypes that reduce the metabolic costs of soil exploration, improve penetration of hard soil, and exploit the rhizosphere; subcellular phenotypes that reduce the nitrogen requirement of plant tissue; molecular phenotypes exhibiting optimized nitrate uptake kinetics; and rhizosphere phenotypes that optimize associations with the rhizosphere microbiome. For each of these topics we provide examples of root phenotypes which merit attention as potential selection targets for crop improvement. Several cross-cutting issues are addressed including the importance of soil hydrology and impedance, phenotypic plasticity, integrated phenotypes, in silico modeling, and breeding strategies using high throughput phenotyping for co-optimization of multiple phenes. Conclusions Substantial phenotypic variation exists in crop germplasm for an array of root phenotypes that improve nitrogen capture. Although this topic merits greater research attention than it currently receives, we have adequate understanding and tools to develop crops with improved nitrogen capture. Root phenotypes are underutilized yet attractive breeding targets for the development of the nitrogen efficient crops urgently needed in global agriculture.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Marine algae growth and carbon capture augmentation by antioxidant nanozymes

Large scale commercial cultivation of microalgae year-round is limited by seasonal stress conditions. The rapid growth and high CO 2 capture of the marine microalga Picochlorum celeri is largely inhibited under winter stress conditions of low temperature and high light. Herein, we demonstrated a nanotechnology approach to enhance the biomass productivity and CO 2 capture of P. celeri under abiotic stress by interfacing with antioxidant cerium oxide nanozymes (nanoceria). Antioxidant nanoceria catalytically scavenged reactive oxygen species (ROS) generated under stress conditions, reducing damage to the microalgae photosynthetic machinery in chloroplasts. Negatively charged poly-acrylic acid-coated nanoceria (PNC, 10 μM) were biocompatible in microalgae cells and colocalized with chloroplasts. In contrast, positively charged aminated nanoceria (ANC) resulted in microalgae aggregation (>50 μM) and were toxic at all concentrations tested (≥10 μM). PNC reduction of ROS levels in microalgae (78%) and superoxide levels (26%), enhanced microalgae growth (65%), photosynthetic performance (130%), and CO 2 uptake rate (380%) under low-temperature stress (15 °C) and high light (500 μmol/m 2 /s PAR) stress relative to controls without nanoceria. Nanoceria augmentation of microalgae provides a rapid and facile technology to increase algae CO 2 capture and biomass under stress conditions.

09 BIOMASS FUELS↗

DOE OSTI2025

Dynamics and lipid membrane coupling of the RAS-RAF complex revealed via multiscale simulations

To gain molecular and mechanistic insights into initiation of the RAS-RAF signaling cascade, we developed and used a combination of multiscale simulation and experimental approaches. The influence and impact of the membrane on RAS and RAF proteins is a factor we are just beginning to understand and appreciate in more detail. Molecular simulation is an ideal methodology to further study this complicated relationship between the membrane and associated proteins. Our previous work using Multiscale Machine-learned Modeling Infrastructure investigated different lipid compositions solely around the KRAS4b protein and the interplay between protein behavior and these membrane environments. Multiscale Machine-learned Modeling Infrastructure uses machine learning to couple adjacent simulation scales and has been efficiently scaled across some of the world’s largest high-performance computers. Recently, we have expanded this multiresolution framework to include the all-atom simulation scale and to incorporate the RAF RBDCRD domains. Here, we present the overall analysis results from this new simulation campaign comprising a mixture of RAS and RAF RBDCRD proteins. Approximately 35,000 coarse-grained and 10,000 all-atom molecular dynamics simulations were completed, sampled from a variety of protein/lipid composition configurations that were generated from a micron-scale continuum simulation containing hundreds of copies of the proteins. Our studies suggest that orientations of the RAS-RBDCRD complex on the membrane occupy distinct configurational states, and the spatial patterns of lipid arrangements around these different protein states are unique to each state. The extent and size of lipid “fingerprints” imposed on the membrane by the RAS-RBDCRD protein complex are significantly larger than observed for just the RAS protein on its own. These protein complexes strongly associate, but we do not observe statistically significant preferred protein-protein orientations. These observations indicate that spatial colocalization of RAS-RBDCRD proteins in the same vicinity may be assisted by specific membrane environments, acting to increase the probability of signaling complex formation.

Carpenter, Timothy S. [Lawrence Livermore National↗