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All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

The Potosi Reservoir Model 2013c, Property Modeling Update

As part of a larger project co-funded by the United States Department of Energy (US DOE) to evaluate the potential of formations within the Cambro-Ordovician strata above the Mt. Simon as potential targets for carbon sequestration in the Illinois and Michigan Basins, the Illinois Clean Coal Institute (ICCI) requested Schlumberger to evaluate the potential injectivity and carbon dioxide (CO2) plume size of the Cambrian Potosi Formation. The evaluation of this formation was accomplished using wireline data, core data, pressure data, and seismic data from this project as well as two other separately funded projects: the US DOE-funded Illinois Basin–Decatur Project (IBDP) being conducted by the Midwest Geological Sequestration Consortium (MGSC) in Macon County, Illinois, and the Illinois Industrial Carbon Capture and Sequestration (ICCS) project funded through the American Recovery and Reinvestment Act. In 2010, technical performance evaluations on the Cambrian Potosi Formation were performed through reservoir modeling. The data included formation tops from mud logs, well logs from the Verification Well #1 (VW1) and the Injection Well (CCS1), structural and stratigraphic formation from three dimensional (3D) seismic data, and field data from several waste water injection wells for Potosi Formation. The intention was for 2.2 million tons per annum (2 million tonnes per annum [MTPA]) of CO2 to be injected for 20 years. In the Task Error! Reference source not found., the 2010 Potosi heterogeneous model (referred to as the "Potosi Dynamic Model 2010") was re-run using a new injection scenario of 3.5 million tons per annum (3.2 MTPA) for 30 years. The extent of the Potosi Dynamic Model 2010, however, appeared too small for the new injection target. The models size was insufficient to accommodate the evolution of the plume. The new model, Potosi Dynamic Model 2013a, was built by extending the Potosi Dynamic Model 2010 grid to 30 by 30 mi (48 by 48 km), while preserving all property modeling workflows and layering. This model was retained as the base case. In the preceding Task [1], the Potosi reservoir model was updated to take into account the new data from the Verification Well #2 (VW2) which was drilled in 2012. The porosity and permeability modeling was revised to take into account the log data from the new well. Revisions of the 2010 modeling assumptions were also done on relative permeability, capillary pressures, formation water salinity, and the maximum allowable well bottomhole pressure. Dynamic simulations were run using the injection target of 3.5 million tons per annum (3.2 MTPA) for 30 years. This dynamic model was named Potosi Dynamic Model 2013b. In this Task, a new property modeling workflow was applied, where seismic inversion data guided the porosity mapping and geobody extraction. The static reservoir model was fully guided by PorosityCube interpretations and derivations coupled with petrophysical logs from three wells. The two main assumptions are: porosity features in the PorosityCube that correlate with lost circulation zones represent vugular zones, and that these vugular zones are laterally continuous. Extrapolation was done carefully to populate the vugular facies and their corresponding properties outside the seismic footprint up to the boundary of the 30 by 30 mi (48 by 48 km) model. Dynamic simulations were also run using the injection target of 3.5 million tons per annum (3.2 MTPA) for 30 years. This new dynamic model was named Potosi Dynamic Model 2013c. Reservoir simulation with the latest model gives a cumulative injection of 43 million tons (39 MT) in 30 years with a single well, which corresponds to 40% of the injection target. The injection rate is approx. 3.2 MTPA in the first six months as the well is injecting into the surrounding vugs, and declines rapidly to 1.8 million tons per annum (1.6 MTPA) in year 3 once the surrounding vugs are full and the CO2 start to reach the matrix. After, the injection rate declines gradually to 1.2 million tons per annum (1.1 MTPA) in year 18 and stays constant. This implies that a minimum of three (3) wells could be required in the Potosi to reach the injection target. The injectivity evaluated in this Task was higher compared to the preceding Task, since the current facies modeling (guided by the porosity map from the seismic inversion) indicated a higher density of vugs within the vugular zones. 5 As the CO2 follows the paths where vugs interconnection exists, a reasonably large and irregular plume extent was created. After 30 years of injection, the plume extends 13.7 mi (22 km) in E-W and 9.7 mi (16 km) in N-S directions. After injection finishes, the plume continues to migrate laterally, mainly driven by the remaining pressure gradient. After 60 years post-injection, the plume extends 14.2 mi (22.8 km) in E-W and 10 mi (16 km) in N-S directions, and remains constant as the remaining pressure gradient has become very low. Should the targeted cumulative injection of 106 million tons (96 MT) be achieved; a much larger plume extent could be expected. The increase of reservoir pressure at the end of injection is approximately 1,200 psia (8,274 kPa) around the injector and gradually decreases away from the well. The reservoir pressure increase is less than 10 psia (69 kPa) beyond 14 mi (23 km) away from injector. Should the targeted cumulative injection of 106 million tons (96 MT) be achieved; a much larger areal pressure increase could be expected. The reservoir pressure declines rapidly during the first 30 years post injection and the initial reservoir pressure is nearly restored after 100 years post-injection. The present evaluation is mainly associated with uncertainty on the vugs permeability and interconnectivity. The use of porosity mapping from seismic inversion might have reduced the uncertainty on the lateral vugs body distributions. However, major uncertainties on the Potosi vugs permeability remains. Therefore, injection test and pressure interference test among the wells could be considered to evaluate the local vugs permeability, extent, and interconnectivity. Facies modeling within the Potosi has yet to be thoroughly addressed. The carbonates during the time of deposition are believed to be regionally extensive. However, it may be worth delineating the reservoir with other regional wells or modern day analogues to understand the extent of the Potosi. More specifically, the model could incorporate lateral changes or trends if deemed necessary to represent facies transition. Data acquisitions to characterize the fracture pressure gradient, the formation water properties, the relative permeability, and the capillary pressure could also be considered in order to allow a more rigorous evaluation of the Potosi storage performance. A simulation using several injectors could also be considered to determine the required number of wells and appropriate spacing to achieve the injection target while taking into account the pressure interference.

Adushita, Yasmin↗
NASA NTRS2011

CLVTOPS Liftoff and Separation Analysis Validation Using Ares I-X Flight Data

CLVTOPS is a multi-body time domain flight dynamics simulation tool developed by NASA s Marshall Space Flight Center (MSFC) for a space launch vehicle and is based on the TREETOPS simulation tool. CLVTOPS is currently used to simulate the flight dynamics and separation/jettison events of the Ares I launch vehicle including liftoff and staging separation. In order for CLVTOPS to become an accredited tool, validation against other independent simulations and real world data is needed. The launch of the Ares I-X vehicle (first Ares I test flight) on October 28, 2009 presented a great opportunity to provide validation evidence for CLVTOPS. In order to simulate the Ares I-X flight, specific models were implemented into CLVTOPS. These models include the flight day environment, reconstructed thrust, reconstructed mass properties, aerodynamics, and the Ares I-X guidance, navigation and control models. The resulting simulation output was compared to Ares I-X flight data. During the liftoff region of flight, trajectory states from the simulation and flight data were compared. The CLVTOPS results were used to make a semi-transparent animation of the vehicle that was overlaid directly on top of the flight video to provide a qualitative measure of the agreement between the simulation and the actual flight. During ascent, the trajectory states of the vehicle were compared with flight data. For the stage separation event, the trajectory states of the two stages were compared to available flight data. Since no quantitative rotational state data for the upper stage was available, the CLVTOPS results were used to make an animation of the two stages to show a side-by-side comparison with flight video. All of the comparisons between CLVTOPS and the flight data show good agreement. This paper documents comparisons between CLVTOPS and Ares I-X flight data which serve as validation evidence for the eventual accreditation of CLVTOPS.

Burger, Ben↗
NASA NTRS1988

Application of similitude principle to the numerical simulation of solar atmospheric dynamics

Numerical simulation has become an essential part of solar physics because the complex nonlinear characteristics of solar phenomena makes analytical solutions difficult to obtain. Realistic simulation of the birth and decay of an active region still is not possible because of the wide range of spatial and time scales that must be considered. Therefore, proper scaling rules must be recognized for the development of appropriate models. In this paper, the similitude principle is applied to develop scaling rules. It is found that these rules are highly dependent on the physical nature of the specific problem under consideration. A set of 'similitude critiques' is presented for some specific physical conditions. Numerical examples of coronal dynamic response and active region dynamics are used to demonstrate these ideas.

Wu, S. T.↗
DOE OSTI2023

ReaxFF reactive force field model enables accurate prediction of physiochemical and mechanical properties of crystalline and amorphous shape‐memory polyurethane

Abstract We investigate reactive force field (ReaxFF) prediction of physiochemical and mechanical properties, and stimuli response behavior of a shape‐memory polyurethane (SMPU) rigid segment. We used SMPUs as a platform to link the rigid/hard segment domain crystallinity with properties that can also be experimentally measured. Specifically, we developed models for crystalline and amorphous forms of a common rigid segment of SMPUs, for example, 4,4′‐diphenylmethane diisocyanate (MDI) with n‐butanediol (BDO), denoted as MDI‐BDO. ReaxFF molecular dynamics simulations with equilibrium dynamics are performed by controlling mass, temperature, and pressure or volume to predict the structural and physiochemical properties of crystalline and amorphous rigid segments of SMPU systems, followed by simulating their XRD and FTIR patterns, respectively. Non‐equilibrium ReaxFF simulations are implemented by using uniaxial box deformation technique to study response‐behavior of crystalline SMPU under tensile loading and during stress‐relaxation. The model and simulation scheme presented in this study demonstrates a robust theoretical pathway toward application‐dictated, on‐demand design of high‐performance SMPUs in applications such as soft robotics.

Afroz, Mohammad M.↗
DOE OSTI2024

Simulating water dynamics related to pedogenesis across space and time: Implications for four-dimensional digital soil mapping

Digital soil mapping (DSM) relies on machine-learning and geostatistics to represent soil property observations across space. DSM techniques are powerful but often empirical, being limited to the quality and density of point samples. Water dynamics are closely related to soil variability, and the physics that govern water movement are well known. Hydrological properties can hence be simulated by physical models through space and time, unveiling key characteristics about soils. We propose the use of hydrologic models to map soils across the surface (2D), depth (1D), and time (1D)–which provides a 4D approach to digital soil mapping (4DSM). The Distributed Hydrology Soil Vegetation Model (DHSVM) was applied to a watershed currently under pasture. Moisture sensors and wells were installed at different depths in the watershed on summit, sideslope and toeslope positions to validate the model. DHSVM simulations of soil moisture distribution and depth to saturation were performed during the hydrological year (October 2008-September 2009). Clusters of similar pixels based on soil moisture values were determined using Dynamic Time Warping (DTW) to align temporal data and K-means. Clustering was performed both seasonally and for the entire year. Temporal patterns simulated by DHSVM matched measurements given by moisture sensors and wells. Seasonal clusters differed from the annual cluster. Distinct clusters were observed for each season and with depth, showing that spatiotemporal soil variability is lost when statically assessing soils. Spatiotemporal clusters corroborated field observations of fragipan occurrence not explicitly spatially mapped by Soil Survey Geographic Database (SSURGO). If a connection can be made between water and soils, static and dynamic soil variability can be predicted using physically based hydrologic models. Hydrologic models can benefit soil mapping by enabling reliable 4D simulation of water dynamics, which are fundamental to soil variability and soil classification and directly relate to biological, physical and chemical soil processes not captured by typical soil sampling protocols.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1989

OMV mission simulator

The Orbital Maneuvering Vehicle (OMV) will be remotely piloted during rendezvous, docking, or proximity operations with target spacecraft from a ground control console (GCC). The real-time mission simulator and graphics being used to design a console pilot-machine interface are discussed. A real-time orbital dynamics simulator drives the visual displays. The dynamics simulator includes a J2 oblate earth gravity model and a generalized 1962 rotating atmospheric and drag model. The simulator also provides a variable-length communication delay to represent use of the Tracking and Data Relay Satellite System (TDRSS) and NASA Communications (NASCOM). Input parameter files determine the graphics display. This feature allows rapid prototyping since displays can be easily modified from pilot recommendations. A series of pilot reviews are being held to determine an effective pilot-machine interface. Pilots fly missions with nominal to 3-sigma dispersions in translational or rotational axes. Console dimensions, switch type and layout, hand controllers, and graphic interfaces are evaluated by the pilots and the GCC simulator is modified for subsequent runs. Initial results indicate a pilot preference for analog versus digital displays and for two 3-degree-of-freedom hand controllers.

Cok, Keith E.↗
DOE OSTI2017

Cluster Dynamics Modeling with Bubble Nucleation, Growth and Coalescence

The topic of this communication pertains to defect formation in irradiated solids such as plasma-facing tungsten submitted to helium implantation in fusion reactor com- ponents, and nuclear fuel (metal and oxides) submitted to volatile ssion product generation in nuclear reactors. The purpose of this progress report is to describe ef- forts towards addressing the prediction of long-time evolution of defects via continuum cluster dynamics simulation. The di culties are twofold. First, realistic, long-time dynamics in reactor conditions leads to a non-dilute di usion regime which is not accommodated by the prevailing dilute, stressless cluster dynamics theory. Second, long-time dynamics calls for a large set of species (ideally an in nite set) to capture all possible emerging defects, and this represents a computational bottleneck. Extensions beyond the dilute limit is a signi cant undertaking since no model has been advanced to extend cluster dynamics to non-dilute, deformable conditions. Here our proposed approach to model the non-dilute limit is to monitor the appearance of a spatially localized void volume fraction in the solid matrix with a bell shape pro le and insert an explicit geometrical bubble onto the support of the bell function. The newly cre- ated internal moving boundary provides the means to account for the interfacial ux of mobile species into the bubble, and the growth of bubbles allows for coalescence phenomena which captures highly non-dilute interactions. We present a preliminary interfacial kinematic model with associated interfacial di usion transport to follow the evolution of the bubble in any number of spatial dimensions and any number of bubbles, which can be further extended to include a deformation theory. Finally we comment on a computational front-tracking method to be used in conjunction with conventional cluster dynamics simulations in the non-dilute model proposed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

RF Gap Transformation in PARMILA

The PARMILA (Phase And Radial Motion in Ion Linear Accelerators) code is used to design ion linacs and simulate the beam dynamics therein. The original code was developed in the 1960’s and later the Los Alamos Accelerator Code Group developed a PC version that has been used worldwide. Recently, in an effort to modernize the code and use it as the basis for a high-performance beam dynamics simulator with the LANSCE linac, the details of the code have come under additional scrutiny. PARMILA is a “z code” that uses various transformations to approximately represent the effect of the beam line element on the beam. In the case of the RF gap, it treats the particle dynamics inside the gap as a combination of drift + kick at the mid-plane + drift. Recently, we uncovered an undocumented keyword “off-exact” in PARMILA that enables the code to use the full modified-Bessel functions instead of low-order approximations in the RF gap transformation. This change improved the accuracy of the transformation for off-axis particles. However, a discrepancy between the analytical formula and the code was found for the transformation of the transverse coordinates. The purpose of this tech note is to document the derivation of the gap transformation and the related DTL cell length calculation used in the PARMILA code.

43 PARTICLE ACCELERATORS↗
DOE OSTI2016

Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions

Here, we investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been “extended” and considered as a prototype reaction-diffusion system. These results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the “well-mixed” approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Anomalous fast atomic dynamics in bulk metallic glasses

It is believed that the strong glass formers tend to be dense packing and have rather slow atomic dynamics. Here, we report that the anomalous fast atomic dynamics exist in an Au 55 Cu 20 Ag 5 Si 20 metallic glass (MG) with good glass forming ability (GFA) by combining X-ray photon correlation spectroscopy measurements with ab initio molecular dynamics simulations. The fast dynamics are mainly originated from the increased mobility of Cu atoms by Ag addition. Ag atoms are inclined to locate at Cu-centered <0, 2, 8, 1> motifs, which slow or accelerate the dynamics of shell Cu atoms, depending on whether Ag atoms appear at the first shells or not, leading to the formation of structural heterogeneity at the atomic level. The results enrich the understanding of atomic dynamics in Cue-Ag-containing MGs and will trigger more studies on the dynamics-GFA relationship in MGs.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2021

Structure–Capacitance Relationships of Graphene/Ionic Liquid Electrolyte Double Layers

The differential capacitance profile of electrochemical interfaces reflects the physical properties of the double layer. For carbon electrodes and ionic liquid based electrolytes, these capacitance profiles are not fully understood. In this work, we utilize constant voltage molecular dynamics simulations to compute differential capacitance profiles of ionic liquids [BMIm + ][BF 4 - ] and [BMIm + ][TFSI - ] mixed with acetonitrile and 1,2-dichloroethane, at model graphene electrodes. We find that both pure and 10% mole fraction ionic liquid electrolytes exhibit camel shaped capacitance profiles with two peaks on either side of a minimum centered at the potential of zero charge. This profile shape results from electric field induced rearrangement of ion structure within the inner layer closest to the electrode interface. At low potential, the ionic liquid inner layer is concentrated with non-polar tri-fluoromethyl and butyl functional groups of the anions and cations, corresponding to the minimum of the capacitance profiles. With increasing voltage, electrostatic interactions of polar/charged functional groups with the electrode surface compete with these non-polar interactions, leading to ion rearrangement that increases the inner layer charge density and results in higher capacitance. After the ion restructuring is complete, the response saturates and capacitance diminishes. The presence of organic solvent significantly changes the composition of the inner layer. For example, strong non-polar interactions between dichloroethane molecules and the graphene surface substantially block ion/electrode contact at moderate potentials. Overall, our simulations highlight the dynamic nature of the inner region of organic electrolyte double layers, and the sensitive dependence on electrolyte composition and applied voltage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Ab Initio Predictions of Hexagonal Zr(B,C,N) Polymorphs for Coherent Interface Design

Density functional theory calculations are used to explore hexagonal (HX) NiAs-like polymorphs of Zr(B,C,N) and compare with corresponding Zr(B,C,N) Hagg-like face-centered cubic rocksalt (B1) phases. While all predicted compounds are mechanically stable according to the Born-Huang criteria, only HX Zr(C,N) are found dynamically stable from ab initio molecular dynamics simulations and lattice dynamics calculations. HX ZrN emerges as a candidate structure with ground state energy, elastic constants, and extrinsic mechanical parameters comparable with those of B1 ZrN. Ab initio band structure and semi-classical Boltzmann transport calculations predict a metallic character and a monotonic increase in electrical conductivity with the number of valence electrons. Electronic structure calculations indicate that the HX phases gain their stability and mechanical attributes by Zr d- non-metal p hybridization and by broadening of Zr d bands. Furthermore, it is shown that the HX ZrN phase provides a low-energy coherent interface model for connecting B1 ZrN domains, with significant energetic advantage over an atomistic interface model derived from high resolution transmission electron microscopy images. The ab initio characterizations provided herein should aid the experimental identification of non-Hagg-like hard phases. Furthermore, the results can also enrich the variety of crystalline phases potentially available for designing coherent interfaces in superhard nanostructured materials and in materials with multilayer characteristics.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Coherent Dynamics of Mixed Frenkel and Charge-Transfer Excitons in Dinaphtho[2,3- b :2'3'- f ]thieno[3,2- b ]-thiophene Thin Films: The Importance of Hole Delocalization

Charge-transfer states in organic semiconductors play crucial roles in processes such as singlet fission and exciton dissociation at donor/acceptor interfaces. Recently, a time-resolved spectroscopy study of dinaphtho[2,3-b:2'3'-f]thieno[3,2-b]-thiophene (DNTT) thin films provided evidence for the formation of mixed Frenkel and charge-transfer excitons after the photoexcitation. In this study, we investigate optical properties and excitation dynamics of the DNTT thin films by combining ab initio calculations and a stochastic Schrödinger equation. Our theory predicts that the low-energy Frenkel exciton band consists of 8–47% CT character. The quantum dynamics simulations show coherent dynamics of Frenkel and CT states in 50 fs after the optical excitation. Lastly, we demonstrate the role of charge delocalization and localization in the mixing of CT states with Frenkel excitons as well as the role of their decoherence.

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

Anomalous Nanoscale Optoacoustic Phonon Mixing in Nematic Mesogens

Recent inelastic X-ray scattering (IXS) experiments on mesogens have shown entirely new capabilities with regards to their nanoscale phonon-assisted heat management. Mesogens such as nematic liquid crystals (LCs) are appealing systems for study because their structure and morphology can easily be tuned. We report on Q-resolved ultra-high-resolution IXS, X-ray diffraction, and THz time-domain spectroscopy experiments combined with large-scale all-atom molecular dynamics simulations on the dynamic properties of 5CB LCs. For the first time, we observe a strong mixing of phonon excitations originating from independent in-phase and out-of-phase van-der-Waals-mediated displacement patterns. The coexistence of transverse acoustic and optical modes of 5CB LCs at near room temperature is revealed through the emergent transverse phonon gap and THz light–phonon coupling taking place within the same energy range. Moreover, our experimental observations are supported by analysis showing correlations of spontaneous fluctuations of LCs on picosecond time scales. These findings are significant for the design of a new generation of soft molecular vibration-sensitive nanoacoustic and optomechanical applications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Multivalent Polymer–Peptide Conjugates: A General Platform for Inhibiting Amyloid Beta Peptide Aggregation

Protein aggregation is implicated in multiple deposition diseases including Alzheimer's Disease, which features the formation of toxic aggregates of amyloid beta (Aβ) peptides. Many inhibitors have been developed to impede or reverse Aβ aggregation. Multivalent inhibitors, however, have been largely overlooked despite the promise of high inhibition efficiency endowed by the multivalent nature of Aβ aggregates. In this work, we report the success of multivalent polymer peptide conjugates (mPPCs) as a general class of inhibitors of the aggregation of Aβ 40 . Significantly delayed onset of fibril formation was realized using mPPCs prepared with three peptide/peptoid ligands covering a range of polymer molecular weights (MWs) and ligand loadings. Dose dependence studies showed that the nature of the ligands is a key factor in mPPC inhibition potency. The negatively charged ligand LPFFD leads to more efficient mPPCs compared to mPPCs with the neutral ligands, and is most effective at 7% ligand loading across different MWs. Molecular dynamics simulations along with dynamic light scattering experiments suggest that mPPCs form globular structures in solution due to ligand ligand interactions. Such interactions are key to the spatial proximity of ligands and thus to the multivalency effect of mPPC inhibition. Finally, excess ligand ligand interactions, however, reduce the accessibility of mPPC ligands to Aβ peptides, and impair the overall inhibition potency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B

The APOBEC3B (A3B) single-stranded DNA (ssDNA) cytosine deaminase has important roles in innate immunity but is also a major endogenous source of mutations in cancer. Previous structural studies showed that the C-terminal catalytic domain of human A3B has a tightly closed active site, and rearrangement of the surrounding loops is required for binding to substrate ssDNA. Here we report structures of the A3B catalytic domain in a new crystal form that show alternative, yet still closed, conformations of active site loops. All-atom molecular dynamics simulations support the dynamic behavior of active site loops and recapitulate the distinct modes of interactions that maintain a closed active site. Replacing segments of A3B loop 1 to mimic the more potent cytoplasmic deaminase APOBEC3A leads to elevated ssDNA deaminase activity, likely by facilitating opening of the active site. These data collectively suggest that conformational equilibrium of the A3B active site loops, skewed toward being closed, controls enzymatic activity by regulating binding to ssDNA substrates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Acoustic force spectroscopy reveals subtle differences in cellulose unbinding behavior of carbohydrate-binding modules

Protein adsorption to solid carbohydrate interfaces is critical to many biological processes, particularly in biomass deconstruction. To engineer more-efficient enzymes for biomass deconstruction into sugars, it is necessary to characterize the complex protein–carbohydrate interfacial interactions. A carbohydrate-binding module (CBM) is often associated with microbial surface-tethered cellulosomes or secreted cellulase enzymes to enhance substrate accessibility. However, it is not well known how CBMs recognize, bind, and dissociate from polysaccharides to facilitate efficient cellulolytic activity, due to the lack of mechanistic understanding and a suitable toolkit to study CBM–substrate interactions. Our work outlines a general approach to study the unbinding behavior of CBMs from polysaccharide surfaces using a highly multiplexed single-molecule force spectroscopy assay. Here, we apply acoustic force spectroscopy (AFS) to probe a Clostridium thermocellum cellulosomal scaffoldin protein (CBM3a) and measure its dissociation from nanocellulose surfaces at physiologically relevant, low force loading rates. An automated microfluidic setup and method for uniform deposition of insoluble polysaccharides on the AFS chip surfaces are demonstrated. The rupture forces of wild-type CBM3a, and its Y67A mutant, unbinding from nanocellulose surfaces suggests distinct multimodal CBM binding conformations, with structural mechanisms further explored using molecular dynamics simulations. Applying classical dynamic force spectroscopy theory, the single-molecule unbinding rate at zero force is extrapolated and found to agree with bulk equilibrium unbinding rates estimated independently using quartz crystal microbalance with dissipation monitoring. However, our results also highlight critical limitations of applying classical theory to explain the highly multivalent binding interactions for cellulose–CBM bond rupture forces exceeding 15 pN.

09 BIOMASS FUELS↗