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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 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Convective and Turbulent Motions in Nonprecipitating Cu. Part II: LES Simulated Cloud Represented by a Starting Plume

The dynamic structure of a small trade wind cumulus (Cu) is analyzed using a novel approach. Cu developing in a shear-free environment is simulated by 10-m-resolution LES model with spectral bin microphysics. The aim is to clarify the dynamical nature of cloud updraft zone (CUZ) including entrainment and mixing in growing Cu. The validity of concept stating that a cloud at developing state can be represented by a parcel or a jet is tested. To investigate dynamical entrainment in CUZ performed by motions with scales larger than the turbulence scales, the modeled fields of air velocity were filtered by wavelet filter that separated convective motions from turbulent ones. Two types of objects in developing cloud were investigated: small volume ascending at maximal velocity (point parcel) and CUZ. It was found that the point parcel representing the upper part of cloud core is adiabatic. The motion of the air in this parcel ascending from cloud base determines cloud-top height. The top-hat (i.e., averaged) values of updraft velocity and adiabatic fraction in CUZ are substantially lower than those in the point parcel. Evaluation of the terms in the dynamical equation typically used in 1D cloud parcel models show that this equation can be applied for calculation of vertical velocities at the developing stage of small Cu, at least up to the heights of the inversion layer. Dynamically, the CUZ of developing cloud resembles the starting plume with the tail of nonstationary jet. Both the top-hat vertical velocity and buoyancy acceleration linearly increase with the height, at least up to the inversion layer. An important finding is that lateral entrainment of convective (nonturbulent) nature has a little effect on the top-hat CUZ velocity and cannot explain the vertical changes of conservative variables qt and θl. In contrast, entrained air lifting inside CUZ substantially decreases top-hat liquid water content and its adiabatic fraction. Possible reasons of these effects are discussed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

OC6 project Phase IV: validation of numerical models for novel floating offshore wind support structures

Abstract. This paper provides a summary of the work done within Phase IV of the Offshore Code Comparison Collaboration, Continued with Correlation and unCertainty (OC6) project, under International Energy Agency Wind Technology Collaboration Programme Task 30. This phase focused on validating the loading on and motion of a novel floating offshore wind system. Numerical models of a 3.6 MW horizontal-axis wind turbine atop the TetraSpar floating support structure were compared using measurement data from a 1:43-Froude-scale test performed in the University of Maine's Alfond Wind–Wave (W2) Ocean Engineering Laboratory. Participants in the project ran a series of simulations, including system equilibrium, surge offsets, free-decay tests, wind-only conditions, wave-only conditions, and a combination of wind and wave conditions. Validation of the models was performed by comparing the aerodynamic loading, floating support structure motion, tower base loading, mooring line tensions, and keel line tensions. The results show a relatively good estimation of the aerodynamic loading and a reasonable estimation of the platform motion and tower base fore–aft bending moment. However, there is a significant dispersion in the dynamic loading for the upwind mooring line. Very good agreement was observed between most of the numerical models and the experiment for the keel line tensions.

17 WIND ENERGY↗
DOE OSTI2024

Simulating Wind-Driven Loading on PV Systems

As PV modules continue to trend toward larger, thinner, and more flexible forms they grow more susceptible to damage from dynamic wind loading. As a result, understanding the impact of wind on PV systems, particularly when mounted on compliant solar-tracking hardware, and identifying robust, stable array layouts and stow strategies is becoming increasingly important for the PV community. We are developing an open-source software package, PVade (PV aerodynamic design engineering), to simulate the cascading fluid-structure interaction that occurs within single-axis, solar-tracking arrays to enable researchers to test hardware, layout, and tracker control changes, leading to enhanced stability and a reduction in wind-driven damage. We will give an overview of the PVade software and present the latest outcomes from our ongoing validation campaign in which we compare time series and statistical structural responses with field data. From there, we will present simulated results from a larger, multi-row array and highlight the effect of varying tracker angles on stability and the differences between positive and negative tilt angles.

fluid↗
DOE OSTI2020

In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations

Subsurface microbial communities mediate the transformation and fate of redox sensitive materials including organic matter, metals and radionuclides. Few studies have explored how changing geochemical conditions influence the composition of groundwater microbial communities over time. We temporally monitored alterations in abiotic forces on microbial community structure using 1L in-field bioreactors receiving background and contaminated groundwater at the Oak Ridge Reservation, TN. Planktonic and biofilm microbial communities were initialized with background water for 4 days to establish communities in triplicate control reactors and triplicate test reactors and then fed filtered water for 14 days. On day 18, three reactors were switched to receive filtered groundwater from a contaminated well, enriched in total dissolved solids relative to the background site, particularly chloride, nitrate, uranium, and sulfate. Biological and geochemical data were collected throughout the experiment, including planktonic and biofilm DNA for 16S rRNA amplicon sequencing, cell counts, total protein, anions, cations, trace metals, organic acids, bicarbonate, pH, Eh, DO, and conductivity. We observed significant shifts in both planktonic and biofilm microbial communities receiving contaminated water. This included a loss of rare taxa, especially amongst members of the Bacteroidetes, Acidobacteria, Chloroflexi, and Betaproteobacteria, but enrichment in the Fe- and nitrate- reducing Ferribacterium and parasitic Bdellovibrio. These shifted communities were more similar to the contaminated well community, suggesting that geochemical forces substantially influence microbial community diversity and structure. These influences can only be captured through such comprehensive temporal studies, which also enable more robust and accurate predictive models to be developed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Distributed Acoustic Sensing for Whale Vocalization Monitoring: A Vertical Deployment Field Test

Abstract There is growing interest in floating offshore wind turbine (FOWT) technology, where turbines are installed on floating structures anchored to the seabed, allowing wind energy development in areas unsuitable for traditional fixed-platform turbines. Responsible development requires monitoring the impact of FOWTs on marine wildlife, such as whales, throughout the operational lifecycle of the turbines. Distributed acoustic sensing (DAS)—a technology that transforms fiber-optic cables into vibration sensor arrays—has been demonstrated for acoustic monitoring of whales using seafloor telecommunications cables. However, no studies have yet evaluated DAS performance in dynamic, engineered environments, such as floating platforms or moving vessels with complex, dynamic strain loads, despite their relevance to FOWT settings. This study addresses that gap by deploying DAS aboard a boat in Monterey Bay, California, where a fiber-optic cable was lowered using a weighted and suspended mooring line, enabling vertical deployment. Humpback whale vocalizations were captured and identified in the DAS data, noise sources were identified, and DAS data were compared to audio captured by a standalone hydrophone attached to the mooring line and a nearby hydrophone on a cabled observatory. This study is unique in: (1) deploying DAS in a vertical deployment mode, where noise from turbulence, cable vibrations, and other sources posed additional challenges compared to seafloor DAS applications; (2) demonstrating DAS in a dynamic, nonstationary setup, which is uncommon for DAS interrogators typically used in more stable environments; and (3) leveraging looped sections of the cable to reduce the noise floor and mitigate the effects of excessive cable vibrations and strain. This research demonstrates DAS’s ability to capture whale vocalizations in challenging environments, highlighting its potential to enhance underwater acoustic monitoring, particularly in the context of renewable energy development in offshore environments.

Saw, Jaewon↗
DOE OSTI2017

Type I Shell Galaxies as a Test of Gravity Models

Shell galaxies are understood to form through the collision of a dwarf galaxy with an elliptical galaxy. Shell structures and kinematics have been noted to be independent tools to measure the gravitational potential of the shell galaxies. We compare theoretically the formation of shells in Type I shell galaxies in different gravity theories in this work because this is so far missing in the literature. We include Newtonian plus dark halo gravity, and two non-Newtonian gravity models, MOG and MOND, in identical initial systems. We investigate the effect of dynamical friction, which by slowing down the dwarf galaxy in the dark halo models limits the range of shell radii to low values. Under the same initial conditions, shells appear on a shorter timescale and over a smaller range of distances in the presence of dark matter than in the corresponding non-Newtonian gravity models. If galaxies are embedded in a dark matter halo, then the merging time may be too rapid to allow multi-generation shell formation as required by observed systems because of the large dynamical friction effect. Starting from the same initial state, the observation of small bright shells in the dark halo model should be accompanied by large faint ones, while for the case of MOG, the next shell generation patterns iterate with a specific time delay. The first shell generation pattern shows a degeneracy with the age of the shells and in different theories, but the relative distance of the shells and the shell expansion velocity can break this degeneracy.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Ectopic Organogenesis after Allotransplantation of Freshly Removed or Cryopreserved Neonatal Testicle under the Renal Capsule in Rats

In experiments on white outbred male rats, a freshly removed (20 experiments) or cryopreserved (10 experiments) testicle from newborn rats (1-2 days after birth) was transplanted under the renal capsule after bilateral orchiectomy. In all experiments with transplantation of freshly removed testicle, it was engrafted. In 3 months, histological examination revealed the formation of mature seminiferous tubules, but spermatogenesis was blocked at the stage of spermatogonia; groups of proliferating Leydig cells in the loose connective tissue between the tubules were also seen. In 6 and 12 months, the status of the seminiferous tubules remained unchanged, but structures typical of the epididymis and developing vas deferens were revealed. The number of proliferating Leydig cells increased. The initially low testosterone concentration in the blood of castrated males increased significantly as soon as in 1 month after transplantation and grew up to 3 months, remaining at a level ~50% of normal. Engraftment of cryopreserved neonatal testicular tissue was observed in 60% cases, however, engrafted tissue, similar to the fresh one, retained the ability for organogenesis with the formation of mature seminiferous tubules, epididymis, and groups of proliferating Leydig cells. The dynamics of blood testosterone concentration in rats with cryopreserved and fresh transplantation was similar. Subcapsular transplantation did not adversely affect the kidneys, which was seen from normal histological structure of the kidneys and creatinine and urea concentrations in the blood.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Deformation Mechanisms of Vertically Stacked WS 2 /MoS 2 Heterostructures: The Role of Interfaces

Here, the mechanical and optical properties generated due to the stacking of different atomically thin materials have made it possible to tune and engineer these materials for next-generation electronics. The understanding of the interlayer interactions in such stacked structures is of fundamental interest for structure and property correlation. Here, a combined approach of in situ Raman spectroscopy and mechanical straining along with molecular dynamics (MD) simulations has been used to probe one such interface, namely, the WS 2 /MoS 2 heterostructure. Vertical heterostructures on poly(methyl methacrylate), when flexed, showed signs of decoupling at 1.2% strain. Theoretical calculations showed strain-induced stacking changes at 1.75% strain. The sliding characteristics of layers were also investigated using scanning probe microscopy based nanoscratch testing, and the results are further supported by MD simulations. The present study could be used to design future optoelectronic devices based on WS 2 /MoS 2 heterostructures.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

Characterization and Diversification of AraC/XylS Family Regulators Guided by Transposon Sequencing

In this study, we explored the development of engineered inducible systems. Publicly available data from previous transposon sequencing assays were used to identify regulators of metabolism in Pseudomonas putida KT2440. For AraC family regulators (AFRs) represented in these data, we posited AFR/promoter/inducer groupings. Twelve promoters were characterized for a response to their proposed inducers in P. putida, and the resultant data were used to create and test nine two-plasmid sensor systems in Escherichia coli. Several of these were further developed into a palette of single-plasmid inducible systems. From these experiments, we observed an unreported inducer response from a previously characterized AFR, demonstrated that the addition of a P. putida transporter improved the sensor dynamics of an AFR in E. coli, and identified an uncharacterized AFR with a novel potential inducer specificity. Finally, targeted mutations in an AFR, informed by structural predictions, enabled the further diversification of these inducible plasmids.

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

Species traits and network structure predict the success and impacts of pollinator invasions

Species invasions constitute a major and poorly understood threat to plant–pollinator systems. General theory predicting which factors drive species invasion success and subsequent effects on native ecosystems is particularly lacking. We address this problem using a consumer–resource model of adaptive behavior and population dynamics to evaluate the invasion success of alien pollinators into plant–pollinator networks and their impact on native species. We introduce pollinator species with different foraging traits into network models with different levels of species richness, connectance, and nestedness. Among 31 factors tested, including network and alien properties, we find that aliens with high foraging efficiency are the most successful invaders. Networks exhibiting high alien–native diet overlap, fraction of alien-visited plant species, most-generalist plant connectivity, and number of specialist pollinator species are the most impacted by invaders. Our results mimic several disparate observations conducted in the field and potentially elucidate the mechanisms responsible for their variability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Predicting Instability and the Effect of Wind Loading on Single-Axis Trackers

As PV modules continue to trend toward larger, thinner, and more flexible forms they grow more susceptible to damage from dynamic wind loading. As a result, understanding the impact of wind on PV systems, particularly when mounted on solar-tracking hardware, and identifying robust, stable array layouts and stow strategies is becoming increasingly important for the PV community. In our ongoing DuraMAT project, we are developing an open-source software package, PVade (PV aerodynamic design engineering), to simulate the cascading fluid-structure interaction that occurs within solar-tracking arrays to enable researchers to test hardware, layout, and tracker control changes, leading to enhanced stability and a reduction in wind-driven damage. We will give an overview of the PVade software, highlighting recent user-interface and algorithm developments, before presenting the latest outcomes from our ongoing validation campaign in which we analyze and compare with experimental data obtained from a DuraMAT 1 project. From there, we will present simulated results from a larger, multi-row array and highlight relationships between varying tracker angles and stability as measured by different experimentally validated metrics.

fluid structure interaction↗
DOE OSTI2022

Substructure in the stellar halo near the Sun: II. Characterisation of independent structures

In an accompanying paper, we present a data-driven method for clustering in ‘integrals of motion’ space and apply it to a large sample of nearby halo stars with 6D phase-space information. The algorithm identified a large number of clusters, many of which could tentatively be merged into larger groups. The goal here is to establish the reality of the clusters and groups through a combined study of their stellar populations (average age, metallicity, and chemical and dynamical properties) to gain more insights into the accretion history of the Milky Way. To this end, we developed a procedure that quantifies the similarity of clusters based on the Kolmogorov–Smirnov test using their metallicity distribution functions, and an isochrone fitting method to determine their average age, which is also used to compare the distribution of stars in the colour–absolute magnitude diagram. Also taking into consideration how the clusters are distributed in integrals of motion space allows us to group clusters into substructures and to compare substructures with one another. We find that the 67 clusters identified by our algorithm can be merged into 12 extended substructures and 8 small clusters that remain as such. The large substructures include the previously known Gaia-Enceladus, Helmi streams, Sequoia, and Thamnos 1 and 2. We identify a few over-densities that can be associated with the hot thick disc and host a small metal-poor population. Especially notable is the largest (by number of member stars) substructure in our sample which, although peaking at the metallicity characteristic of the thick disc, has a very well populated metal-poor component, and dynamics intermediate between the hot thick disc and the halo. We also identify additional debris in the region occupied by Sequoia with clearly distinct kinematics, likely remnants of three different accretion events with progenitors of similar masses. Although only a small subset of the stars in our sample have chemical abundance information, we are able to identify different trends of [Mg/Fe] versus [Fe/H] for the various substructures, confirming our dissection of the nearby halo. We find that at least 20% of the halo near the Sun is associated to substructures. When comparing their global properties, we note that those substructures on retrograde orbits are not only more metal-poor on average but are also older. We provide a table summarising the properties of the substructures, as well as a membership list that can be used for follow-up chemical abundance studies for example.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2017

High-Pressure, High-Temperature Thermal Hydraulic Test Facility for Nuclear-Renewable Hybrid Energy System Studies; Facility Design Description and Status Report

A high-pressure, high-temperature water flow loop has been designed at Idaho National Laboratory (INL) for deployment in the INL Dynamic Energy Transport and Integration Laboratory (DETAIL) within the Energy Systems Laboratory (ESL) D100 northwest high bay. This loop is the first of three thermally coupled flow loops that will comprise the Advanced Reactor Technology Integral System Test (ARTIST) facility. The ARTIST facility will ultimately include a high temperature helium loop and a liquid salt loop, in addition to the PWR loop. The high-pressure water loop will operate at Pressurized Water Reactor (PWR) conditions. It will support experimental research on nuclear-renewable hybrid energy systems as well as advanced reactor technology topics. Within DETAIL, the water flow loop will also serve as a thermal energy source, emulating a reactor system. The loop will be thermally integrated with co-located energy systems including a thermal energy transport loop, thermal energy storage system, and a 25 kW high-temperature electrolysis system for hydrogen production. DETAIL will include additional energy systems such as an integrated microgrid and renewable energy systems including solar photovoltaics. The electrically heated flow loop will be dynamically controlled to simulate nuclear fuel behavior under normal and off-normal operating conditions. DETAIL will be designed for characterization of complex system dynamics. The various components will be interfaced with Digital Real-Time Simulators for supervisory control and dynamic simulation of complete systems. The design and assembly of the high-pressure water flow loop and supporting systems has been subdivided into two Phases. Phase 1, which will be completed by the end of FY17, includes installation of cable trays and supports, electrical conduit, DI water system, drain lift station and the concrete pad for the chiller located outside of the laboratory. Phase 2 includes the detailed design and final assembly of the flow loop, supporting structures and personnel platforms, the chiller and associated piping. As of September, 2017, the final detailed design of the flow loop is complete. Funding for Phase 2 procurement, assembly, system operability checkout, shakedown testing and initial operation of the flow loop is requested for FY18.

42 ENGINEERING↗
DOE OSTI2016

Study of the internal structure, instabilities, and magnetic fields in the dense Z-pinch

Z-pinches are sources of hot dense plasma which generates powerful x-ray bursts and can been applied to various areas of high-energy-density physics (HEDP). The 26-MA Z machine is at the forefront of many of these applications, but important aspects of HEDP have been studied on generators at the 1 MA current level. Recent development of laser diagnostics and upgrade of the Leopard laser at Nevada Terawatt Facility (NTF) give new opportunities for the dense Z-pinch study. The goal of this project is the investigation of the internal structure of the stagnated Z pinch including sub-mm and micron-scale instabilities, plasma dynamics, magnetic fields, and hot spots formation and initiation. New plasma diagnostics will be developed for this project. A 3D structure and instabilities of the pinch will be compared with 3D MHD and spectroscopic modeling and theoretical analysis. The structure and dynamics of stagnated Z pinches has been studied with x-ray self-radiation diagnostics which derive a temperature map of the pinch with a spatial resolution of 70-150 µm. The regular laser diagnostics at 532 nm does not penetrate in the dense pinch due to strong absorption and refraction in trailing plasma. Recent experiments at NTF showed that shadowgraphy at the UV wavelength of 266 nm unfolds a fine structure of the stagnated Z-pinch with unprecedented detail. We propose to develop laser UV diagnostics for Z pinches with a spatial resolution <5 μm to study the small-scale plasma structures, implement two-frame shadowgraphy/interferometry, and develop methods for investigation of strong magnetic fields. New diagnostics will help to understand better basic physical processes in Z pinches. A 3D internal structure of the pinch and characteristic instabilities will be studied in wire arrays with different configurations and compared with 3D MHD simulations and analytical models. Mechanisms of “enhanced heating” of Z-pinch plasma will be studied. Fast dynamics of stagnated plasma will be studied to estimate its contribution to the Doppler broadening of x-ray lines. Development of “necks” and “hot spots” will be studied with high-resolution UV diagnostics, an x-ray streak camera, and x-ray spectroscopy. Laser initiation of hot spots in Z pinches will be tested. A Faraday rotation diagnostic at 266 nm will be applied to 1-10 MG magnetic fields. For magnetic fields B>20 MG, suggested in micropinches, Cotton-Mouton and cutoff diagnostics will be applied. A picosecond optical Kerr shutter will be tested to increase a sensitivity of UV methods for application at multi-MA Z pinches. The proposal is based on the experimental capability of NTF. The Zebra generator produces 1-1.7 MA Z-pinches with electron plasma density of 10 20 -10 21 cm -3 , electron temperature of 0.5-1 keV, and magnetic fields >10 MG. The Leopard laser was upgraded to energy of 90-J at 0.8 ns. This regime will be used for laser initiation of hot spots. A further upgrade to energy of 250-J is suggested for laser-Z-pinch interaction. A picosecond regime will be used for optical gating. A 10-TW Tomcat laser at NTF is available for the high energy UV laser probing of the Z-pinch. Two graduate students will develop new optical and x-ray diagnostics, carry out experiments, and process experimental data. Other students will be involved in the design and fabrication of loads, supporting regular optical and x-ray diagnostics, and data processing. The new plasma diagnostics may be applied to HEDP experiments at NTF and other multi-MA generators. The feasibility of the research plan is based on the experience of the scientific team in Z-pinch plasma physics, laser physics, development of new plasma diagnostics, and the experimental capability of NTF. The experimental group of Dr. V. V. Ivanov (UNR) collaborates with a group for Z pinch MHD modeling of Dr. J. P. Chittenden (Imperial College, London), and theoretical group of Dr. D. D. Ryutov (LLNL). The suggested research ideas are supported by preliminary experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2021

On the computational solution of vector-density based continuum dislocation dynamics models: A comparison of two plastic distortion and stress update algorithms

Continuum dislocation dynamics models of mesoscale plasticity consist of dislocation transport-reaction equations coupled with crystal mechanics equations. The coupling between these two sets of equations is such that dislocation transport gives rise to the evolution of plastic distortion (strain), while the evolution of the latter fixes the stress from which the dislocation velocity field is found via a mobility law. Earlier solutions of these equations employed a staggered solution scheme for the two sets of equations in which the plastic distortion was updated via time integration of its rate, as found from Orowan's law. In this work, we show that such a direct time integration scheme can suffer from accumulation of numerical errors. We introduce an alternative scheme based on field dislocation mechanics that ensures consistency between the plastic distortion and the dislocation content in the crystal. The new scheme is based on calculating the compatible and incompatible parts of the plastic distortion separately, and the incompatible part is calculated from the current dislocation density field. Stress field and dislocation transport calculations were implemented within a finite element based discretization of the governing equations, with the crystal mechanics part solved by a conventional Galerkin method and the dislocation transport equations by the least squares method. A simple test was first performed to show the accuracy of the two schemes for updating the plastic distortion, which shows that the solution method based on field dislocation mechanics is more accurate. This method then was used to simulate an austenitic steel crystal under uniaxial loading and multiple slip conditions. By considering dislocation interactions caused by junctions, a hardening rate similar to discrete dislocation dynamics simulation results was obtained. Finally, the simulations show that dislocations exhibit some self-organized structures as the strain is increased.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Demonstration of femtosecond X-ray pump X-ray probe diffraction on protein crystals

The development of X-ray free-electron lasers (XFELs) has opened the possibility to investigate the ultrafast dynamics of biomacromolecules using X-ray diffraction. Whereas an increasing number of structures solved by means of serial femtosecond crystallography at XFELs is available, the effect of radiation damage on protein crystals during ultrafast exposures has remained an open question. We used a split-and-delay line based on diffractive X-ray optics at the Linac Coherent Light Source XFEL to investigate the time dependence of X-ray radiation damage to lysozyme crystals. For these tests, crystals were delivered to the X-ray beam using a fixed-target approach. The presented experiments provide probe signals at eight different delay times between 19 and 213 femtoseconds after a single pump event, thereby covering the time-scales relevant for femtosecond serial crystallography. Even though significant impact on the crystals was observed at long time scales after exposure with a single X-ray pulse, the collected diffraction data did not show significant signal reduction that could be assigned to beam damage on the crystals in the sampled time window and resolution range. This observation is in agreement with estimations of the applied radiation dose, which in our experiment was clearly below the values expected to cause damage on the femtosecond time scale. The experiments presented here demonstrate the feasibility of time-resolved pump-multiprobe X-ray diffraction experiments on protein crystals.

43 PARTICLE ACCELERATORS↗
DOE OSTI2017

Frustration-guided motion planning reveals conformational transitions in proteins

Proteins exist as conformational ensembles, exchanging between substates to perform their function. Advances in experimental techniques yield unprecedented access to structural snapshots of their conformational landscape. However, computationally modeling how proteins use collective motions to transition between substates is challenging owing to a rugged landscape and large energy barriers. Here in this paper, we present a new, robotics-inspired motion planning procedure called dCCRRT that navigates the rugged landscape between substates by introducing dynamic, interatomic constraints to modulate frustration. The constraints balance non-native contacts and flexibility, and instantaneously redirect the motion towards sterically favorable conformations. On a test set of eight proteins determined in two conformations separated by, on average, 7.5Å root mean square deviation (RMSD), our pathways reduced the Cα atom RMSD to the goal conformation by 78%, outperforming peer methods. Additionally, we then applied dCC-RRT to examine how collective, small-scale motions of four side-chains in the active site of cyclophilin A propagate through the protein. dCC-RRT uncovered a spatially contiguous network of residues linked by steric interactions and collective motion connecting the active site to a recently proposed, non-canonical capsid binding site 25Å away, rationalizing NMR and multi-temperature crystallography experiments. In all, dCC-RRT can reveal detailed, all-atom molecular mechanisms for small and large amplitude motions.Source code and binaries are freely available at https://github.com/ExcitedStates/KGS/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS)

Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are emerging as a valuable avenue for predicting, understanding and designing microbial communities. Computation of microbial ecosystems in time and space (COMETS) extends dynamic flux balance analysis to generate simulations of multiple microbial species in molecularly complex and spatially structured environments. Here we describe how to best use and apply the most recent version of COMETS, which incorporates a more accurate biophysical model of microbial biomass expansion upon growth, evolutionary dynamics and extracellular enzyme activity modules. In addition to a command-line option, COMETS includes user-friendly Python and MATLAB interfaces compatible with the well-established COBRA models and methods, as well as comprehensive documentation and tutorials. Overall, this protocol provides a detailed guideline for installing, testing and applying COMETS to different scenarios, generating simulations that take from a few minutes to several days to run, with broad applicability to microbial communities across biomes and scales.

59 BASIC BIOLOGICAL SCIENCES↗