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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 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Solar enhanced oxygen evolution reaction with transition metal telluride

The photo-enhanced electrocatalytic method of oxygen evolution reaction (OER) shows promise for enhancing the effectiveness of clear energy generation through water splitting by using renewable and sustainable source of energy. However, despite benefits of photoelectrocatalytic (PEC) water splitting, its uses are constrained by its low efficiency as a result of charge carrier recombination, a large overpotential, and sluggish reaction kinetics. Here, we illustrate that Nickel telluride (NiTe) synthesized by hydrothermal methods can function as an extremely effective photo-coupled electrochemical oxygen evolution reaction (POER) catalyst. In this study, NiTe was synthesized by hydrothermal method at 145°C within just an hour of reaction time. In dark conditions, the NiTe deposited on carbon cloth substrate shows a small oxygen evolution reaction overpotential (261 mV) at a current density of 10 mA cm –2 , a reduced Tafel slope (65.4 mV dec -1 ), and negligible activity decay after 12 h of chronoamperometry. By virtue of its enhanced photo response, excellent light harvesting ability, and increased interfacial kinetics of charge separation, the NiTe electrode under simulated solar illumination displays exceptional photoelectrochemical performance exhibiting overpotential of 165 mV at current density of 10 mA cm -2 , which is about 96 mV less than on dark conditions. In addition, Density Functional Theory investigations have been carried out on the NiTe surface, the results of which demonstrated a greater adsorption energy for intermediate -OH on the catalyst site. Since the -OH adsorption on the catalyst site correlates to catalyst activation, it indicates the facile electrocatalytic activity of NiTe owing to favorable catalyst activation. DFT calculations also revealed the facile charge density redistribution following intermediate -OH adsorption on the NiTe surface. This work demonstrates that arrays of NiTe elongated nanostructure are a promising option for both electrochemical and photoelectrocatalytic water oxidation and offers broad suggestions for developing effective PEC devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Mass transport in a highly immiscible alloy on extended shear deformation

Forced mixing to a single phase or supersaturated solid solution (SSS) and its prerequisite microstructure evolution in immiscible systems has been a focus of research for both fundamental science and a variety of applications. Controlling the formation of SSS by shear deformation assisted processing could enable a material design beyond conventional equilibrium microstructure in immiscible systems. Here, a highly immiscible (mixing enthalpy of ~ 20 kJ·mol -1 ) Cu-50 at. % Cr binary alloy was employed to investigate the microstructure evolution and localized tendencies of SSS during severe shear deformation. The present results demonstrate distinctive microstructure refinement process in each phase and how they lead to localized SSS as a function of shear strain. Preferential dynamic recrystallization occurs in the softer Cu phase due to strain localization, leading to substantial grain refinement. The refinement of Cr phase in the top-most layer, however, is enabled by the progressive evolution of grain lamination, splitting, and fragmentation as a function of shear strain. The eventual SSS is found to be strongly dependent on the local environments that affect the dislocation activity, including the level of microstructure refinement, the interfacial orientation relationship, hardness difference, and supposed stability of oxidation. Ab initio simulations comfirm that it is more favorable to oxidize Cr than Cu at incoherent Cu/Cr interfaces which then limits the mass transport on an incoherent boundary. Our results shed light on the underpinning mechanism for non-equilibrium mass transport in immiscible systems upon severe deformation that can be applicable to a variety of processing techniques aimed at producing immiscible alloys with superior mechanical properties.

36 MATERIALS SCIENCE↗
DOE OSTI2021

The onset of alloying in Cu-Ni powders under high-shear consolidation

Friction consolidation (FC) is a solid phase processing methodology that densifies a material through high-shear deformation and pressure at elevated temperature. The method has garnered interest in the scientific community because of its ability to produce extremely refined and homogeneous microstructures, off-axis texture development, and improved material properties. This manuscript presents an investigation of Cu and Ni material mixing via evaluation of morphological evolution, grain boundary characterization, and compositional analysis to provide insights on the operational alloying mechanisms occurring under high shear and elevated temperature. Using correlative microscopy techniques, we show alloying progresses via a combination of grain boundary diffusion and interfacial roughening at heterophane boundaries. Evidence supporting Cu infiltration along Ni-Ni grain boundaries along with asymmetric diffusion of Cu into Ni grains is highlighted. The resultant, consolidated microstructure was produced directly from a powder compact in ~30 s and exhibited a submicron, equiaxed grain size.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Aerosol Optical Tweezers Elucidate the Chemistry, Acidity, Phase Separations, and Morphology of Atmospheric Microdroplets

Aerosol particles represent unique chemical environments because of their high surface area-to-volume ratio that promotes the effects of interfacial chemistry in confined environments. Properties such as viscosity, diffusivity, water content, pH, and morphology—following liquid–liquid phase separation—can strongly alter how a particle interacts with condensable vapors and reactive trace gases, thus modifying its continual evolution and environmental effects. Our understanding of this chemical evolution of atmospheric particulate matter and its environmental impacts is largely limited by our ability to directly observe how these critical particle properties respond to the addition or reactive uptake of new chemical components. Aerosol optical tweezers (AOT) stably trap particles in focused laser beams, providing positional control and the retrieval of many of these critical properties required to understand and predict the chemistry of aerosolized microdroplets. The analytical power of the AOT stems from the retrieval of the cavity-enhanced Raman spectrum induced by the trapping laser. Analysis of the whispering gallery modes (WGMs) that resonate as a standing wave around the droplet’s interface, provide high accuracy measurements of the droplet’s size, refractive index (and thus a measurement of composition), and can distinguish between core–shell, partially engulfed, and homogeneous morphologies. In this study, we have advanced the ability to determine the properties of the core and shell phases in biphasic droplets, including obtaining high-accuracy pH measurements. These capabilities were applied to perform AOT physical chemistry experiments on authentic secondary organic aerosol (SOA) produced directly in the AOT chamber by ozonolysis of terpene vapors. The propensity of the SOA to phase separate as a shell from a wide range of nonpolar to polar core phases was observed, along with the discovery of a stable emulsified state of SOA particles in an aqueous salt droplet. Micron-thick SOA shells did not impede the gain or loss of water or squalane from the core to the surrounding air, indicating no significant diffusional limitations to condensational growth or partitioning even under dry conditions. These experiments formed the foundation of a new framework that predicts how the phase-separated morphology of complex aerosols containing organic carbon evolves during continual atmospheric oxidation processes. Increases in oxidation state will quickly drive conversion from a partially engulfed to core–shell morphology that has dramatically different chemical reactivity since the core phase is completely concealed by the shell. The recent advances in the experimental capabilities of the AOT technique such as presented here enable novel experimental methodologies that provide insights into the chemistry and multidimensional properties of aerosol microdroplets, and how these coevolve and respond to continual chemical reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Fundamental mechanistic insights into the catalytic reactions of Li-S redox by Co single-atom electrocatalysts via operando methods

Lithium-sulfur batteries represent an attractive option for energy storage applications. A deeper understanding of the multistep lithium-sulfur reactions and the electrocatalytic mechanisms are required to develop advanced, high-performance batteries. We have systematically investigated the lithium-sulfur redox processes catalyzed by a cobalt single-atom electrocatalyst (Co-SAs/NC) via operando confocal Raman microscopy and x-ray absorption spectroscopy (XAS). The real-time observations, based on potentiostatic measurements, indicate that Co-SAs/NC efficiently accelerates the lithium-sulfur reduction/oxidation reactions, which display zero-order kinetics. Under galvanostatic discharge conditions, the typical stepwise mechanism of long-chain and intermediate-chain polysulfides is transformed to a concurrent pathway under electrocatalysis. In addition, operando cobalt K-edge XAS studies elucidate the potential-dependent evolution of cobalt’s oxidation state and the formation of cobalt-sulfur bonds. Our work provides fundamental insights into the mechanisms of catalyzed lithium-sulfur reactions via operando methods, enabling a deeper understanding of electrocatalysis and interfacial dynamics in electrical energy storage systems.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Identifying Dense NiSe 2 /CoSe 2 Heterointerfaces Coupled with Surface High-Valence Bimetallic Sites for Synergistically Enhanced Oxygen Electrocatalysis

Constructing heterostructures with abundant interfaces is essential for integrating the multiple functionalities in single entities. Herein, the synthesis of NiSe 2 /CoSe 2 heterostructures with different interfacial densities via an innovative strategy of successive ion injection is reported. The resulting hybrid electrocatalyst with dense heterointerfaces exhibits superior electrocatalytic properties in an alkaline electrolyte, superior to other benchmarks and precious metal catalysts. Advanced synchrotron techniques, post structural characterizations, and density functional theory (DFT) simulations reveal that the introduction of atomic-level interfaces can lower the oxidation overpotential of bimetallic Ni and Co active sites (whereas Ni$^{2+}$ can be more easily activated than Co$^{2+}$) and induce the electronic interaction between the core selenides and surface in situ generated oxides/hydroxides, which play a critical role in synergistically reducing energetic barriers and accelerating reaction kinetics for catalyzing the oxygen evolution. Hence, the heterointerface structure facilitates the catalytic performance enhancement via increasing the intrinsic reactivity of metallic atoms and enhancing the synergistic effect between the inner selenides and surface oxidation species. This work not only complements the understanding on the origins of the activity of electrocatalysts based on metal selenides, but also sheds light on further surface and interfacial engineering of advanced hybrid materials.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Dynamic Evolution of Palladium Single Atoms on Anatase Titania Support Determines the Reverse Water–Gas Shift Activity

Research interest in single-atom catalysts (SACs) has been continuously rising. However, the lack of understanding of the dynamic behaviors of SACs during applications hinder catalyst development and mechanistic understanding. Herein, we report on the evolution of active sites over Pd/TiO 2 -anatase SAC (Pd 1 /TiO 2 ) in the reverse water-gas shift (rWGS) reaction. Combining kinetics, in-situ characterization, and theory, we show that at T ≥ 350 °C, the reduction of TiO 2 by H 2 alters the coordination environment of Pd, creating Pd sites with partially cleaved Pd-O interfacial bonds and a unique electronic structure that exhibit high intrinsic rWGS activity through the carboxyl pathway. The activation by H 2 is accompanied by the partial sintering of single Pd atoms (Pd 1 ) into disordered, flat, ~1 nm diameter clusters (Pd n ). The highly active Pd sites in the new coordination environment under H 2 are eliminated by oxidation, which, when performed at high temperature, also re-disperses Pd n and facilitates the reduction of TiO 2 . In contrast, Pd 1 sinters into crystalline, ~5 nm particles (Pd NP ) during CO treatment, deactivating Pd 1 /TiO 2 . During the rWGS reaction, the two Pd evolution pathways co-exist. The activation by H 2 dominates, leading to the increasing rate with time-on-stream, and steady-state Pd active sites similar with the ones formed under H 2 . Finally, this work demonstrates how the coordination environment and nuclearity of metal sites on a SAC evolve during catalysis and pre-treatments, and how their activity is modulated by these behaviors. These insights on SAC dynamics and structure-function relationship are valuable to mechanistic understanding and catalyst design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2013

Effect of Residual Noncondensables on Pressurization and Pressure Control of a Zero-Boil-Off Tank in Microgravity

The Zero-Boil-Off Tank (ZBOT) Experiment is a small-scale experiment that uses a transparent ventless Dewar and a transparent simulant phase-change fluid to study sealed tank pressurization and pressure control with applications to on-surface and in-orbit storage of propellant cryogens. The experiment will be carried out under microgravity conditions aboard the International Space Station in the 2014 timeframe. This paper presents preliminary results from ZBOT's ground-based research that focuses on the effects of residual noncondensable gases in the ullage on both pressurization and pressure reduction trends in the sealed Dewar. Tank pressurization is accomplished through heating of the test cell wall in the wetted and un-wetted regions simultaneously or separately. Pressure control is established through mixing and destratification of the bulk liquid using a temperature controlled forced jet flow with different degrees of liquid jet subcooling. A Two-Dimensional axisymmetric two-phase CFD model for tank pressurization and pressure control is also presented. Numerical prediction of the model are compared to experimental 1g results to both validate the model and also indicate the effect of the noncondensable gas on evolution of pressure and temperature distributions in the ullage during pressurization and pressure control. Microgravity simulations case studies are also performed using the validated model to underscore and delineate the profound effect of the noncondensables on condensation rates and interfacial temperature distributions with serious implications for tank pressure control in reduced gravity.

Marangoni and Natural Convection↗
NASA NTRS2015

Modeling of Non-Isothermal Cryogenic Fluid Sloshing

A computational fluid dynamic model was used to simulate the thermal destratification in an upright self-pressurized cryostat approximately half-filled with liquid nitrogen and subjected to forced sinusoidal lateral shaking. A full three-dimensional computational grid was used to model the tank dynamics, fluid flow and thermodynamics using the ANSYS Fluent code. A non-inertial grid was used which required the addition of momentum and energy source terms to account for the inertial forces, energy transfer and wall reaction forces produced by the shaken tank. The kinetics-based Schrage mass transfer model provided the interfacial mass transfer due to evaporation and condensation at the sloshing interface. The dynamic behavior of the sloshing interface, its amplitude and transition to different wave modes, provided insight into the fluid process at the interface. The tank pressure evolution and temperature profiles compared relatively well with the shaken cryostat experimental test data provided by the Centre National D'Etudes Spatiales.

Cryogenics↗
DOE OSTI2023

Fluctuating hydrodynamics and the Rayleigh–Plateau instability

The Rayleigh–Plateau instability occurs when surface tension makes a fluid column become unstable to small perturbations. At nanometer scales, thermal fluctuations are comparable to interfacial energy densities. Consequently, at these scales, thermal fluctuations play a significant role in the dynamics of the instability. These microscopic effects have previously been investigated numerically using particle-based simulations, such as molecular dynamics (MD), and stochastic partial differential equation–based hydrodynamic models, such as stochastic lubrication theory. In this paper, we present an incompressible fluctuating hydrodynamics model with a diffuse-interface formulation for binary fluid mixtures designed for the study of stochastic interfacial phenomena. An efficient numerical algorithm is outlined and validated in numerical simulations of stable equilibrium interfaces. We present results from simulations of the Rayleigh–Plateau instability for long cylinders pinching into droplets for Ohnesorge numbers of Oh = 0.5 and 5.0. Both stochastic and perturbed deterministic simulations are analyzed and ensemble results show significant differences in the temporal evolution of the minimum radius near pinching. Short cylinders, with lengths less than their circumference, were also investigated. As previously observed in MD simulations, we find that thermal fluctuations cause these to pinch in cases where a perturbed cylinder would be stable deterministically. Finally, we show that the fluctuating hydrodynamics model can be applied to study a broader range of surface tension–driven phenomena.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2003

Membrane peptides and their role in protobiological evolution

How simple membrane peptides performed such essential protocellular functions as transport of ions and organic matter across membranes separating the interior of the cell from the environment, capture and utilization of energy, and transduction of environmental signals, is a key question in protobiological evolution. On the basis of detailed, molecular-level computer simulations we explain how these peptides fold at water-membrane interfaces, insert into membranes, self-assemble into higher-order structures and acquire functions. We have investigated the interfacial behavior and folding of several peptides built of leucine and glutamine residues and have demonstrated that many of them tend to adopt ordered structures. Further, we have studied the insertion of an alpha-helical peptide containing leucine (L) and serine (S) of the form (LSLLLSL)3 into a model membrane. The transmembrane state is metastable, and approximately 15 kcal mol(-1) is required to insert the peptide into the membrane. Investigations of dimers formed by (LSLLLSL)3 and glycophorin A demonstrate how the favorable free energy of helix association can offset the unfavorable free energy of insertion, leading to self-assembly of peptide helices in the membrane. An example of a self-assembled structure is the tetrameric transmembrane pore of the influenza virus M2 protein, which is an efficient and selective voltage-gated proton channel. Our simulations explain the gating mechanism and provide guidelines how to re-engineer the channel to act as a simple proton pump. In general, emergence of integral membrane proteins appears to be quite feasible and may be easier to envision than the emergence of water-soluble proteins.

Models, Chemical↗
DOE OSTI2025

Minimization of Cathode|Solid-Electrolyte Interfacial Delamination through the Application of Interphase Layers

Next-generation lithium-ion batteries are expected to use solid electrolytes (SEs) to enable higher energy density and extreme fast-charge capabilities. One major mode of degradation at the cathode|SE interface is delamination between the cathode active materials and SEs, which leads to performance decay. Experimental observations indicate that implementation of interphase layers can minimize the cathode|SE delamination induced capacity fade. A multiscale computational methodology is developed here to investigate the applicability of boron substituted lithium carbonate (Li 2+x B x C 1–x O 3 , x = 0.5, or LBCO) to minimize the delamination at the cathode|SE interface. Atomistic simulations indicate that the fracture energies at both the cathode|LBCO and LBCO|SE interfaces are higher than those at the cathode|SE interface, which reduces the extent of delamination. Mesoscale simulations indicate that, apart from increasing the fracture energy, decreasing the evolution of strain energy by lowering the elastic modulus of the interphase layer can also minimize the extent of delamination at the cathode|SE interface. However, the adoption of an interphase layer with high ionic conductivity is necessary to minimize the ohmic losses during operation at higher current densities. This study provides guidance on selecting interphase layers with specific properties and thicknesses to minimize both interfacial delamination and impedance growth.

LBCO↗
DOE OSTI2024

Unraveling the multi-step crystallization mechanism of polytetrafluoroethylene, modified polytetrafluoroethylene, and their nanocomposites with boron nitride nanobarbs: Experimental insights and theoretical analysis

The non-isothermal crystallization behavior and kinetics of polytetrafluoroethylene (PTFE) composites with boron nitride nanobarb (BNNB), a new generation nanostructure with unique surface morphology and mechanical “barbs” have been analyzed, understanding these properties is essential for their high-end applications as thermal interface materials (TIM) for microwave, 5G and microelectronic devices. The analysis of the crystallization parameters includes crystallization onset, peak and end temperatures, crystallization half-life and overall crystallinity of PTFE, modified PTFE and their BNNB composites. The results were further analyzed using theoretical models such as the combined Avrami-Ozawa model. It was found that BNNB supports crystallization in the modified PTFE but shows minimal effect on the crystallization of PTFE. Due to the limitation of the classical theoretical models used above in fully characterizing the multi-step crystallization process of PTFE, an in-depth analysis using the model-free advanced isoconversional computation was used to characterize the PTFE crystallization based on the evolution of activation energy with fractional crystallinity and for the first time with temperature. Three kinetic regions were identified in the crystallization mechanism. Here, this study investigated the molecular organization and microstructural evolution of PTFE, modified PTFE and their composites during non-isothermal crystallization using advanced X-ray scattering measurements. An insight into the changes undergone by the material's microstructural units including crystallite size and morphology, lamellar thickness and lamellar interfacial layer thickness, and crystallographic phase dynamics during non-isothermal cooling from the melt, was provided here in this work. The effect of copolymer modification of PTFE and the inclusion of pristine and functionalized BNNB (a thermally conductive and electrically insulating ceramic) are both new investigations that provide valuable knowledge for the development of materials with strong matrix-nanofiller interaction and guidance for optimizing sintering and cooling cycles, two key steps in PTFE processing that largely affect the material microstructural features. Overall, the result of the three-part investigation demonstrates that BNNB supports crystallization in the modified PTFE up to 20 wt% concentration and at low and high cooling rates typically used in the industrial processing of PTFE.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Two-Phase Fluid Flow Properties of Rough Fractures With Heterogeneous Wettability: Analysis With Lattice Boltzmann Simulations

Fractures are conduits for fluid flow in low-permeability geological formations. Multiphase flow properties of fractures are important in natural processes and in engineering applications such as the evaluation of the sealing capacity of caprocks and productivity of hydrocarbon-bearing tight rocks. Investigations of flow and transport through fractures typically focus on the effects of fracture geometric and mechanical factors such as aperture, roughness, and compressibility. The wettability of the fracture surfaces and its influence on microscale interfacial phenomena and macroscale effective transport properties are seldom studied. In this study, we investigated the effect of heterogeneous wetting properties on the displacement of water by supercritical CO2 through a series of lattice Boltzmann method simulations. The results show the evolution of the CO2 plume within a fracture is controlled by both the roughness of the aperture field and the wetting distribution. We combined these factors into a capillary pressure map that can be related to the macroscopic flow behavior of the fracture. We observed that heterogeneous wetting distributions promote the residual trapping of water where lower capillary pressures allowed for isolated water pockets in higher capillary pressure zones. Analysis of fracture unsteady relative permeability shows the effect of wetting on permeability evolution and provides support for the viscous-coupling relative permeability model. Finally, analysis of the steady-state relative permeability and saturation demonstrates a strong correlation between permeability and the standard deviation of the capillary pressure field. Thus, characterizing the distribution of wetting properties of fractures is crucial to understanding multiphase fracture flow and transport properties.

58 GEOSCIENCES↗
DOE OSTI2021

Tool-workpiece stick-slip conditions and their effects on torque and heat generation rate in the friction stir welding

Friction stir welding (FSW) has found increased applications in automotive and aerospace industries due to its advantages of solid-state bonding, no fusion and melting, and versatility in various working conditions and material combinations. However, the relationship among processing parameters, material properties, and bonding extent and fidelity remains largely empirical, primarily because of the lack of the mechanistic understanding of the tool-workpiece frictional behavior that affects our subsequent understanding of microstructural evolution and interface bonding formation. While the tool-workpiece stick-slip condition is believed to dictate the resulting torque and heat generation rate during the welding process, it remains rare and elusive to conduct a quantitative experimental measurement of such interfacial field. On the other hand, numerical simulations based on Computational Fluid Dynamics (CFD) rely on ad hoc assumptions of interfacial pressure and shear-stress conditions, but predictions can only be validated via the medium- and far-range temperature field which is known to be insensitive to the interfacial frictional behavior. This work first presents a comparison among two CFD-based simulation methodologies and the Coupled Eulerian Lagrangian (CEL) model in finite element method, the last of which uses the Coulomb friction so that the stick-slip is naturally developed. Based on the Hill-Bower similarity relationship in the contact analysis, an analytical model is developed here to prove why a constant stick-slip fraction will be developed in the steady state, to correlate the stick-slip fraction to processing parameters such as the tool spin rate, and further to derive dimensionless functions for torque and heat-generation-rate predictions. Pros and cons of various numerical approaches in predicting stick-slip are discussed, and our analytical model has been found to agree well with our numerical simulation and literature experimental results. These analyses provide the critical strain-rate and temperature fields that are needed for the bonding analysis in our future work.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Resolving protein-mineral interfacial interactions during in vitro mineralization by atom probe tomography

Organic macromolecules exert remarkable control over the nucleation and growth of inorganic crystallites during (bio)mineralization, as exemplified during enamel formation where the protein amelogenin regulates the formation of hydroxyapatite (HAP). However, it is poorly understood how fundamental processes at the organic-inorganic interface, such as protein adsorption and/or incorporation into minerals, regulates nucleation and crystal growth due to technical challenges in observing and characterizing mineral-bound organics at high-resolution. Here, atom probe tomography techniques were developed and applied to characterize amelogenin-mineralized HAP particles in vitro, revealing distinct organic-inorganic interfacial structures and processes at the nanoscale. Specifically, visualization of amelogenin across the mineralized particulate demonstrates protein can become entrapped during HAP crystal aggregation and fusion. Identification of protein signatures and structural interpretations were further supported by standards analyses, i.e., defined HAP surfaces with and without amelogenin adsorbed. These findings represent a significant advance in the characterization of interfacial structures and, more so, interpretation of fundamental organic-inorganic processes and mechanisms influencing crystal growth. Ultimately, this approach can be broadly applied to inform how potentially unique and diverse organic-inorganic interactions at different stages regulates the growth and evolution of various biominerals.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Graphic contrastive learning analyses of discontinuous molecular dynamics simulations: Study of protein folding upon adsorption

A comprehensive understanding of the interfacial behaviors of biomolecules holds great significance in the development of biomaterials and biosensing technologies. In this work, we used discontinuous molecular dynamics (DMD) simulations and graphic contrastive learning analysis to study the adsorption of ubiquitin protein on a graphene surface. Our high-throughput DMD simulations can explore the whole protein adsorption process including the protein structural evolution with sufficient accuracy. Contrastive learning was employed to train a protein contact map feature extractor aiming at generating contact map feature vectors. Subsequently, these features were grouped using the k-means clustering algorithm to identify the protein structural transition stages throughout the adsorption process. The machine learning analysis can illustrate the dynamics of protein structural changes, including the pathway and the rate-limiting step. Our study indicated that the protein–graphene surface hydrophobic interactions and the π–π stacking were crucial to the seven-stage adsorption process. Upon adsorption, the secondary structure and tertiary structure of ubiquitin disintegrated. The unfolding stages obtained by contrastive learning-based algorithm were not only consistent with the detailed analyses of protein structures but also provided more hidden information about the transition states and pathway of protein adsorption process and structural dynamics. Our combination of efficient DMD simulations and machine learning analysis could be a valuable approach to studying the interfacial behaviors of biomolecules.

97 MATHEMATICS AND COMPUTING↗