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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.

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At least 1,585 records · Page 88
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

High-throughput screening of environmental polysaccharide-degrading bacteria using biomass containment and complex insoluble substrates

Abstract Carbohydrate degradation by microbes plays an important role in global nutrient cycling, human nutrition, and biotechnological applications. Studies that focus on the degradation of complex recalcitrant polysaccharides are challenging because of the insolubility of these substrates as found in their natural contexts. Specifically, current methods to examine carbohydrate-based biomass degradation using bacterial strains or purified enzymes are not compatible with high-throughput screening using complex insoluble materials. In this report, we developed a small 3D printed filter device that fits inside a microplate well that allows for the free movement of bacterial cells, media, and enzymes while containing insoluble biomass. These devices do not interfere with standard microplate readers and can be used for both short- (24–48 h) and long-duration (> 100 h) experiments using complex insoluble substrates. These devices were used to quantitatively screen in a high-throughput manner environmental isolates for their ability to grow using lignocellulose or rice grains as a sole nutrient source. Additionally, we determined that the microplate-based containment devices are compatible with existing enzymatic assays to measure activity against insoluble biomass. Overall, these microplate containment devices provide a platform to study the degradation of complex insoluble materials in a high-throughput manner and have the potential to help uncover ecologically important aspects of bacterial metabolism as well as to accelerate biotechnological innovation.

3D printing↗
DOE OSTI2014

Soil carbon sensitivity to temperature and carbon use efficiency compared across microbial-ecosystem models of varying complexity

Global ecosystem models may require microbial components to accurately predict feedbacks between climate warming and soil decomposition, but it is unclear what parameters and levels of complexity are ideal for scaling up to the globe. Here we conducted a model comparison using a conventional model with first-order decay and three microbial models of increasing complexity that simulate short- to long-term soil carbon dynamics. We focused on soil carbon responses to microbial carbon use efficiency (CUE) and temperature. Three scenarios were implemented in all models: constant CUE (held at 0.31), varied CUE ( 0.016 C 1), and 50 % acclimated CUE ( 0.008 C 1). Whereas the conventional model always showed soil carbon losses with increasing temperature, the microbial models each predicted a temperature threshold above which warming led to soil carbon gain. The location of this threshold depended on CUE scenario, with higher temperature thresholds under the acclimated and constant scenarios. This result suggests that the temperature sensitivity of CUE and the structure of the soil carbon model together regulate the long-term soil carbon response to warming. Equilibrium soil carbon stocks predicted by the microbial models were much less sensitive to changing inputs compared to the conventional model. Although many soil carbon dynamics were similar across microbial models, the most complex model showed less pronounced oscillations. Thus, adding model complexity (i.e. including enzyme pools) could improve the mechanistic representation of soil carbon dynamics during the transient phase in certain ecosystems. This study suggests that model structure and CUE parameterization should be carefully evaluated when scaling up microbial models to ecosystems and the globe.

Li, Jianwei↗
DOE OSTI2012

Complexation of N4-Tetradentate Ligands with Nd(III) and Am(III)

To improve understanding of aza-complexants in trivalent actinide–lanthanide separations, a series of tetradentate N-donor ligands have been synthesized and their complexation of americium(III) and neodymium(III) investigated by UV–visible spectrophotometry in methanolic solutions. The six pyridine/alkyl amine/imine ligands are N,N0-bis(2-methylpyridyl)-1,2-diaminoethane, N,N0-bis(2-methylpyridyl)-1,3-diaminopropane, trans-N,N-bis(2-pyridylmethyl)-1,2-diaminocyclohexane (BPMDAC), N,N’-bis(2-pyridylmethyl)piperazine, N,N’-bis-[pyridin-2-ylmethylene]ethane-1,2-diamine, and trans-N,Nbis-([pyridin-2-ylmethylene]-cyclohexane-1,2-diamine. Each ligand has two pyridine groups and two aliphatic amine/imine N-donor atoms arranged with different degrees of preorganization and structural backbone rigidity. Conditional stability constants for the complexes of Am(III) and Nd(III) by these ligands establish the selectivity patterns. The overall selectivity of Am(III) over Nd(III) is similar to that reported for the terdentate bis(dialkyltriazinyl)pyridine molecules. The cyclohexane amine derivative (BPMDAC) is the strongest complexant and shows the highest selectivity for Am(III) over Nd(III) while the imines appear to prefer a bridging arrangement between two cations. These results suggest that this series of ligands could be employed to develop an enhanced actinide(III)– lanthanide(III) separation system.

actinide separation↗
DOE OSTI2017

Paramagnetic Cu{sup II} complexes with 1-(hetarylmethyl)silatranes

The structures of paramagnetic complexes CuCl{sub 2}•L with L = HetCH{sub 2}Si(OCH{sub 2}CH{sub 2}){sub 3}N [Het = pyrrol-1-yl (1), indol-1-yl (2), carbazol-9-yl (3), imidazole-1-yl (4), 3,5-dimethylpyrazol-1-yl (5), 1,2,4-triazol-1-yl (6), benzimidazol-1-yl (7), and 1,2,3-benzotriazol-1-yl (8)] were studied by the ESR and quantum chemical methods in terms of the density functional theory (DFT) approximation. The difference in structures of complexes CuCl{sub 2}•1—CuCl{sub 2}•8 is mainly determined by the nature of the five-membered heterocycle. The ESR spectra at room temperature are typical of the mononuclear complexes of Cu{sup II} of axial symmetry with various types of distortions. In complexes CuCl{sub 2}•1—CuCl{sub 2}•3, narrow symmetric signals of zero-valent copper are recorded. These signals remain in the spectra for at least six months, which can characterize them as efficient stabilizing matrices of nanoparticles.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2018

Synthesis and structures of Cu{sup I,II} complexes with a 2,2´-bipyridine derivative bearing a (+)-3-carene moiety

The complex salt {[CuL_2][Cu_4I_6]•MeCN}{sub n} (1) and the compound [Cu{sub 4}L{sub 3}I{sub 4}]•3 MeCN (2) (L is a chiral ligand bearing a natural monoterpene (+)-3-carene moiety) were synthesized. The crystal structures of compounds 1 and 2 were determined by X-ray diffraction. The structure of compound 1 consists of complex cations [CuL{sub 2}]{sup 2+} (N{sub 3}O{sub 2} polyhedron is a trigonal bipyramid) and Cu{sup I} coordination polymers (CuI{sub 4} polyhedron is a tetrahedron) as anions. The experimental magnetic moment μ{sub eff} at 300 K is 1.90 μ{sub B}, which is consistent with the X-ray diffraction data and the assumption that compound 1 is mixed-valence. The structure of compound 2 comprises a tetranuclear Cu{sup I} complex, in which three Cu atoms are coordinated by two N atoms of the ligand L and two I atoms, and the fourth Cu atom is coordinated by four I atoms (coordination polyhedra are distorted tetrahedra). Compounds L and 2 were found to influence the viability of human laryngeal carcinoma cells (Hep2). The IC{sub 50} value for complex 2 (13.0±1.7 μM) is substantially smaller than IC{sub 50} for compound L (30.5±0.5 μM).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Molecular complexes and solvation interactions in the reaction of quinone imines with thiols

This study aims to investigate the role of complexation between reagents and the role of solvation of reagents by solvents in the kinetics of chain reactions of quinone imines with thiols. The thermodynamic characteristics of the complexation of quinone imines with thiophenol in CCl{sub 4}, chlorobenzene, and ethanol, as well as of the complexation of quinone imines and thiophenol with these solvents were calculated by quantum chemical methods (DFT calculations at the PBE/cc-pVDZ level of theory) and in terms of the additive-multiplicative model. Both approaches give consistent results. The formation of molecular complexes in quinone imine–thiphenol systems is accompanied by a 10–30 kJ mol{sup –1} decrease in enthalpy and has only a slight effect on the reaction mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Spin transition characteristics of molecular solvates of Cu{sup II} complexes with nitroxides: sensitivity to the packing type

A method for the synthesis of solvates of dinuclear heterospin complexes of bis(hexafluoroacetylacetonato)copper(II) with 2-(4-methylpyridin-3-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyl (L{sup Me}) and 2-(4-ethylpyridin-3-yl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-3-oxide-1-oxyl (L{sup Et}) of the composition [Cu(hfac){sub 2}L{sup R}]{sub 2} · Solv (Solv = benzene, bromobenzene, toluene, o-xylene, p-xylene) was developed. It was found that a decrease in temperature induces structural transformations of the solid phases of the complexes followed by significant changes in the distances between the paramagnetic centers in the intramolecular exchange clusters {Cu"2"+-O"·-} from 2.321 to 1.974 Å. As a result, the temperature dependences of the effective magnetic moment μ{sub eff}(T) exhibit magnetic features similar to spin transitions. An analysis of the shape of the μ{sub eff}(T) curves suggested that the magnetic properties of the compounds under study depend primarily on the molecular packing. A comparison of the magneto-structural correlations typical of the [Cu(hfac){sub 2}L{sup R}]{sub 2} · Solv complexes studied in this work with the data obtained earlier for analogous solvates of heterospin polymer chain complexes showed that the spin transition characteristics of the [Cu(hfac){sub 2}L{sup R}]{sub 2} · Solv systems are much less sensitive to the change of the solvent than the corresponding characteristics of the heterospin polymers containing solvate molecules in the interchain space. The magnetic characteristics of the heterospin dimer molecules depend primarily on which cavity between the dimers is filled with solvate molecules. For solvates with monoclinic symmetry, changes in the solvent molecules occupying same-type cavities have almost no effect on the spin transition characteristics in the heterospin exchange cluster.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Structural-Phase Features of Low-Stability Pre-Transitional States of BCC-Alloys with Complexes of Planar Defects (Antiphase Boundaries)

Using the Monte Carlo method, the influence of the complexes of antiphase boundaries (APBs) (a pair of shear APBs and a pair of thermal APBs) on the low-stability, pre-transitional states of BCC-alloys is considered by the example of a conventional copper alloy CuZn and an intermetallic compound NiAl. It is shown that in the region of low-stability structural-phase states the energy of formation of a complex of thermal APBs is higher than that of shear APBs. The contribution of APBs into disordering is appreciable up to the structural-phase transition temperature. The most significant factor in terms of the long-range order is the formation of the defect itself; the differences in the APB type or the plane of their occurrence do not so much affect the longrange order behavior with the temperature variation. The type of APBs however appreciably affects the structural-energy characteristics of the system at the temperatures below the phase transformation temperature. Logically, a system with structural defects is less ordered than a defect-free system. The presence of a defect favors the onset of disordering at lower temperatures: it starts at lower temperatures in the case of thermal APBs (TAPBs) compared to shear APBs (TAPBs). In a BCC-system with a complex of TAPBs the first signs of disordering invariably appear near the phase boundary in the neighborhood of large atoms (Zn–Zn in the CuZn alloy or Al–Al in the NiAl intermetallide). In the alloy with a complex of shear APBs the distortion of ordering at low temperatures is observed in the regions where the boundaries cross. The presence of antiphase boundaries affects the alloy stability under heating. It is shown that disordering is accompanied by smearing of the boundaries and their faceting. It follows from a comparative analysis of the peculiarities of disordering in the BCC-system under study (classical alloy CuZn and intermetallide NiAl) under conditions of higher temperatures in the region of low-stability, pre-transitional states that the order – disorder phase transition in the CuZn alloy takes place as a result of disordering of the system, while in the intermetallide NiAl the change of long-range order results from the structural-phase transition.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Photodissociative Cross-Linking of Non-covalent Peptide-Peptide Ion Complexes in the Gas Phase

We report a gas-phase UV photodissociation study investigating non-covalent interactions between neutral hydrophobic pentapeptides and peptide ions incorporating a diazirine-tagged photoleucine residue. Phenylalanine (Phe) and proline (Pro) were chosen as the conformation-affecting residues that were incorporated into a small library of neutral pentapeptides. Gas-phase ion-molecule complexes of these peptides with photo-labeled pentapeptides were subjected to photodissociation. Selective photocleavage of the diazirine ring at 355 nm formed short-lived carbene intermediates that underwent cross-linking by insertion into H–X bonds of the target peptide. The cross-link positions were established from collision-induced dissociation tandem mass spectra (CID-MS{sup 3}) providing sequence information on the covalent adducts. Effects of the amino acid residue (Pro or Phe) and its position in the target peptide sequence were evaluated. For proline-containing peptides, interactions resulting in covalent cross-links in these complexes became more prominent as proline was moved towards the C-terminus of the target peptide sequence. The photocross-linking yields of phenylalanine-containing peptides depended on the position of both phenylalanine and photoleucine. Density functional theory calculations were used to assign structures of low-energy conformers of the (GLPMG + GLL*LK + H){sup +} complex. Born-Oppenheimer molecular dynamics trajectory calculations were used to capture the thermal motion in the complexes within 100 ps and determine close contacts between the incipient carbene and the H–X bonds in the target peptide. This provided atomic-level resolution of potential cross-links that aided spectra interpretation and was in agreement with experimental data. .

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Mesoscopic-scale complexity in macroscopically-uniform plastic flow of an Al 0.3 CoCrFeNi high-entropy alloy

The concept of a smooth and homogeneous plastic flow of solids is nowadays constantly challenged by various observations of the self-organization of crystal defects on mesoscopic scales pertaining, e.g., to acoustic emission or the evolution of the local strain field. Such investigations would be of particular interest for High-Entropy Alloys (HEAs) characterized by extremely complex microstructures. However, the complexity of their deformation has been only studied in relation to the jerky flow. The present work explores a mesoscale complexity of the macroscopically-smooth plastic flow of an Al 0.3 CoCrFeNi alloy. Here, an inclusive approach involving various experimental methods and complementary nonlinear analyses allowed to reveal transitions between distinct dynamical regimes, which may be assimilated with noises of different colors, in particular the blue noise that is rarely observed in complex systems, and various kinds of reddened behavior. Such findings provide significant new insights into the micro/macro transition in the deformation behavior of HEAs.

36 MATERIALS SCIENCE↗
DOE OSTI2021

A three-step model of high harmonic generation using complex classical trajectories

Highlights: • Rigorous trajectory formulation of strong field physics and high harmonic generation. • The Coulomb ground state is represented by an ensemble of complex trajectories. • Trajectories transition seamlessly from the ground state to ionization or recollision. • The ionized wavepacket is reproduced well from the complex trajectories. • Classically allowed and forbidden processes are treated in a single framework. We present a new trajectory formulation of high harmonic generation that treats classically allowed and classically forbidden processes within a single dynamical framework. Complex trajectories orbit the nucleus, producing the stationary Coulomb ground state. When the field is turned on, these complex trajectories continue their motion in the field-dressed Coulomb potential and therefore tunnel ionization, unbound evolution and recollision are described within a single, seamless framework. The new formulation can bring mechanistic understanding to a broad range of strong field physics effects.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Moore vs. Murphy: Tradeoffs between complexity and reliability in distributed energy system scheduling using software-as-a-service

Software-based optimization of building control strategies, including scheduling, has the potential to improve the performance of existing complex heating, ventilation, and air conditioning (HVAC), storage, and other systems—especially if temporally variable energy production, such as solar thermal or photovoltaics, is included. If reductions in energy bills can be achieved using optimized control strategies that take advantage of cost-saving opportunities, such as time-of-use pricing, the additional bill savings can cover further efficiency investment costs. As computer processing becomes cheaper over time (Moore's Law), opportunities to perform complex control optimization become more abundant, and these can be performed remotely as software-as-a-service (SaaS). However, by “perfecting” our control strategies, we run an increased risk that when something unexpected happens (Murphy's Law), the consequences of failure are greater. This study used simulation to explore the potential benefits of HVAC schedule optimization, delivery, and implementation using a SaaS paradigm, at various levels of complexity. Implementing optimal schedules in a model of an efficient building's HVAC system, the study predicts energy cost savings of up to 10% compared to the naïve reference control strategy. Optimizing more system control variables increases the potential energy cost savings; however, these savings could be compromised by failures in communication inherent in delivering schedules via SaaS. The additional cost of energy resulting from the risk of increased demand charges generally increased with increased communication failure to a much larger extent than the risk of increased energy use charges. This work suggests that moderate improvements in performance, achieved at low cost by simple means, may be more effective than highly optimized schemes, which are more susceptible to failure due to their dependence on complex interactions between systems.

42 ENGINEERING↗
DOE OSTI2018

Structure of a benzylidene derivative of 9(10H)-anthracenone in complex with tubulin provides a rationale for drug design

Highlights: • The first crystal structure of an anthracenone family agent complexed with tubulin. • Comparison of the binding mode between different agents reveals the inhibition mechanism. • This structure helps understand the results of the structure-activity-relationship (SAR) studies. Microtubules are composed of αβ-tubulin heterodimers and have been treated as highly attractive targets for antitumor drugs. A broad range of agents bind to tubulin and interfere with microtubule assembly, including colchicine binding site inhibitors (CBSIs). Tubulin Polymerization Inhibitor I (TPI1), a benzylidene derivative of 9(10H)-anthracenone, is a CBSI that inhibits the assembly of microtubules. However, for a long time, the design and development of anthracenone family drugs have been hindered by the lack of structural information of the tubulin-agent complex. Here we report a 2.3 Å crystal structure of tubulin complexed with TPI1, the first structure of anthracenone family agents. This complex structure reveals the interactions between TPI1 and tubulin, and thus provides insights into the development of new anthracenone derivatives targeting the colchicine binding site.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

The malaria parasite RhopH protein complex interacts with erythrocyte calmyrin identified from a comprehensive erythrocyte protein library

Highlights: • WGCFS generated protein libraries are useful in identification of host receptors. • Mouse calmyrin is PyRhopH complex RBC receptor in rodent malaria model, P. yoelii. • WGCFS and AlphaScreen technology are invaluable to post-genome malaria research. Malaria merozoite apical organelles; microneme and rhoptry secreted proteins play functional roles during and following invasion of host erythrocytes. Among numerous proteins, the rhoptries discharge high molecular weight proteins known as RhopH complex. Recent reports suggest that the RhopH complex is essential for growth and survival of the malaria parasite within erythrocytes. However, an in-depth understanding of the host-parasite molecular interactions is indispensable. Here we utilized a comprehensive mouse erythrocyte protein library consisting of 443 proteins produced by a wheat germ cell-free system, combined with AlphaScreen technology to identify mouse erythrocyte calmyrin as an interacting molecule of the rodent malaria parasite Plasmodium yoelii RhopH complex (PyRhopH). The PyRhopH interaction was dependent on the calmyrin N-terminus and divalent cation capacity. The finding unveils a recommendable and invaluable usefulness of our comprehensive mouse erythrocyte protein library together with the AlphaScreen technology in investigating a wide-range of host-parasite molecular interactions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Cationic lipid/DNA complexes manufactured by microfluidics and bulk self-assembly exhibit different transfection behavior

Highlights: • Transfection efficiency of lipid/DNA complexes manufactured by microfluidics is low. • Lipid/DNA complexes prepared by microfluidics have a minor impact on cell viability. • Optimized microfluidic manufacture will produce effective and not toxic lipoplexes. Recent advances in biochemical and biophysical research have been achieved through the employment of microfluidic devices. Microfluidic mixing of therapeutic agents with biomaterials yields systems with finely tuned physical-chemical properties for applications in drug and gene delivery. Here, we investigate the role of preparation technology (microfluidic mixing vs. bulk self-assembly) on the transfection efficiency (TE) and cytotoxicity of multicomponent cationic liposome/DNA complexes (lipoplexes) in live Chinese hamster ovarian (CHO) cells. Decoupling TE and cytotoxicity allowed us to combine them in a unique coherent vision. While bulk self-assembly produces highly efficient and highly toxic MC lipoplexes, microfluidics manufacture leads to less efficient, but less cytotoxic complexes. This discrepancy is ascribed to two main factors controlling lipid-mediated cell transfection, i.e. the lipoplex concentration at the cell surface and the lipoplex arrangement at the nanoscale. Further research is required to optimize microfluidic manufacturing of lipoplexes to obtain highly efficient and not cytotoxic gene delivery systems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

The C-terminus of Ubl4A is critical for pro-death activity and association with the Arp2/3 complex

Highlights: • The Ubl4A C-terminus has a pro-death function. • Ubl4A interacts with the Arp2/3 complex through its C-terminus. • A single mutation in Ubl4A C-terminus abolishes its association with Arp2/3. • The D122A mutation also diminishes Ubl4A cytotoxicity in cancer cells. Ubl4A is a small ubiquitin-like protein involved in diverse cellular functions. We have shown that Ubl4A is critical for survival of the starvation-mediated cell death in vivo. The underlying mechanism for this is through interaction with the actin-related protein Arp2/3 complex and promotion of actin branching. Interestingly, “put-back” of Ubl4A to Ubl4A-deficient cells also results in cell death. Removal of the Ubl4A N-terminus significantly enhances its cytotoxicity, indicating that the pro-death activity of Ubl4A is mainly from its C-terminal region. In vitro protein pull-down assays show that the C-terminal region of Ubl4A can directly interact with the Arp2/3 complex. The single point mutation of an aspartic acid to alanine (D122A) in the Ubl4A C-terminus abolishes its ability to bind the Arp2/3 complex. This mutation also destabilizes Ubl4A proteins susceptible to protease degradation. Importantly, ectopic expression of wild-type Ubl4A can induce cell death in colon cancer cells, but such pro-death activity is diminished in the D122A mutant. These data suggest that Ubl4A C-terminus, especially D122, is critical for Ubl4A-Arp2/3 interaction and its pro-death function.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Cell survival regulation during receptor-mediated endocytosis of chemically-modified lipoproteins associated to the formation of an Amphiphysin 2 (Bin1)/c-Myc complex

Highlights: • Cells under oxidative stress form a complex between amphiphysin 2(Bin1) and c-Myc. • The complex provides cells with a novel survival state established between proliferation and cell death. • Novel clones of amphiphysin 2 are described. Amphiphysin 2 and members of the BAR-domain family of proteins participate in a wide array of cellular processes including cell cycle and endocytosis. Given that amphiphysin 2 is related to diverse cell responses as a result of metabolic stress, we investigated in macrophages whether oxidative stress originated by the internalization of oxidized low density lipoproteins (oxLDL) affect both, the expression of amphiphysin 2 and its binding partner c-Myc. Here we report that under oxidative stress, a complex formation between amphiphysin 2(Bin1) and c-Myc allows the cell to develop a novel survival equilibrium state established between cell proliferation and cell death. We propose that under conditions of oxidative stress given by the internalization of oxLDL, macrophages employ the formation of the amphiphysin 2(Bin1)/c-Myc complex as a control mechanism to initially avoid the process of cell death in an attempt to prolong cell survival.

60 APPLIED LIFE SCIENCES↗
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↗