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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 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Molecular Understanding of Charge Storage in MoS 2 Supercapacitors with Ionic Liquids

Owing to high electrical conductivity and ability to reversibly host a variety of inserted ions, 2D metallic molybdenum disulfide (1T-MoS 2 ) has demonstrated promising energy storage performance when used as a supercapacitor electrode. However, its charge storage mechanism is still not fully understood, in particular, how the interlayer spacing of 1T-MoS 2 would affect its capacitive performance. In this work, molecular dynamics simulations of 1T-MoS 2 with interlayer spacing ranging from 0.615 to 1.615 nm have been performed to investigate the resulting charge storage capacity in ionic liquids. Simulations reveal a camel-like capacitance-potential relation, and MoS 2 with an interlayer spacing of 1.115 nm has the highest volumetric and gravimetric capacitance of 118 F cm –3 and 42 F g –1 , respectively. Although ions in MoS 2 with an interlayer spacing of 1.115 nm diffuse much faster than with interlayer spacings of 1.365 and 1.615 nm, the MoS 2 with larger interlayer spacing has a much faster-charging process. Our analyses reveal that the ion number density and its charging speed, as well as ion motion paths, have significant impacts on the charging response. Here, this work helps to understand how the interlayer spacing affects the interlayer ion structures and the capacitive performance of MoS 2 , which is important for revealing the charge storage mechanism and designing MoS 2 supercapacitor.

25 ENERGY STORAGE↗
DOE OSTI2021

Computational study of the effect of core–skin structure on the mechanical properties of carbon nanofibers

The effect of the core–skin structure on the mechanical properties of carbon nanofibers is investigated in large-scale molecular dynamics simulations of tensile deformation of carbon nanofibers with the core–skin and homogeneous structures. Contrary to an established notion of the deleterious effect of the skin layer on the strength of carbon fibers, the presence of a high-quality skin layer is found to increase both the Young’s modulus and tensile strength of the nanofiber. A detailed analysis of the fracture process indicates that the nanofiber strengthening is related to the ability of skin layer to suppress crack nucleation at the core–skin interface. Furthermore, the computational predictions suggest that the design of new approaches to carbon fiber manufacturing and processing leading to the generation of a high-quality skin layer while avoiding the introduction of structural defects at the core–skin interface may yield a significant enhancement of the mechanical properties of carbon fibers.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Macroscale properties and atomic-scale mechanisms of ash removal in low-temperature hydrothermal carbonization

Biogenic ash is a significant impediment to the utilization of agricultural residues in biofuel production. Such challenge can be addressed by various treatments, as demonstrated in this study on the experimental and computational mechanisms involved in the hydrothermal treatment (HT) of wheat straw. A combination of classical (all-atom) molecular dynamics simulations of cellulose carrying silica and calcium species, along with first principles quantum chemical calculations, indicates the dissociation of inorganics from the cellulose with increased HT temperature. Here, this observation is confirmed by experimental evidence of effective ash removal by HT, showing at least 50% removal of sulfur, chlorine, potassium, and calcium, and 12.5% of silica, leading to a reduced total ash content (from 6.7% to 4.2%).Changes in structural features upon HT, such as surface cellular structure and porosity, were revealed, accompanied by an increased specific surface area (from 1.17 to 6.34 m 2 /g). Our simulations suggest that silica binds tightly to the hydrophobic face of cellulose at room temperature, but HT significantly reduces the binding free energy of association with both hydrophobic and hydrophilic surfaces. Most significantly, ash removal leads to an increased calorific value, rising from approximately 16 MJ/kg to about 19 MJ/kg, along with improved thermal behavior. The improved integration combustion index parameter S indicates that the combustion properties improve with ash removal efficiency. The proposed atomic-level mechanism for the observed removal of inorganics during mild HT underscores the potential of such treatment in producing energy-dense wheat straw, a widely available agricultural residue.

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

CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

Cryoelectron microscopy requires molecular modeling for refinement of structures. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins. Here, we introduce CryoFold, a pipeline of molecular dynamics simulations that determines ensembles of protein structures by integrating density data of varying sparsity at 3–5 Å resolution with sequence information and coarse-grained topological knowledge of the protein folds. We present six examples, folding proteins between 72 and 2,000 residues, including large membrane and multi-domain systems, and results from two Electron Microscopy Data Bank (EMDB) competitions. Driven by data from a single state, CryoFold discovers ensembles of common low-energy models together with rare low-probability structures that capture the equilibrium distribution of proteins constrained by the density maps. Many of these conformations are experimentally validated and functionally relevant. We arrive at a set of best practices for data-guided protein folding that are controlled using a Python graphical user interface (GUI).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Platinum nanoparticle compression: Combining in situ TEM and atomistic modeling

The mechanical behavior of nanoparticles governs their performance and stability in many applications. However, the small sizes of technologically relevant nanoparticles, with diameters in the range of 10 nm or less, significantly complicate experimental examination. These small nanoparticles are difficult to manipulate onto commercial test platforms and deform at loads that are below the typical noise floor of the testing instruments. Here, we synthesized small platinum nanoparticles directly onto a mechanical tester and used a modified nanomanipulator to enhance load resolution to the nanonewton scale. We demonstrated the in situ compression of an 11.5-nm platinum nanoparticle with simultaneous high-resolution measurements of load and particle morphology. Molecular dynamics simulations were performed on similarly sized particles to achieve complementary measurements of load and morphology, along with atomic resolution of dislocations. The experimental and simulation results revealed comparable values for the critical resolved shear stress for failure, 1.28 and 1.15 GPa, respectively. Altogether, this investigation demonstrated the promise of, and some initial results from, the combination of atomistic simulations and in situ experiments with an unprecedented combination of high spatial resolution and high load resolution to understand the behavior of metal nanoparticles under compression.

42 ENGINEERING↗
DOE OSTI2024

Anisotropic interactions for continuum modeling of protein–membrane systems

In this work, a model for anisotropic interactions between proteins and cellular membranes is proposed for large-scale continuum simulations. The framework of the model is based on dynamic density functional theory, which provides a formalism to describe the lipid densities within the membrane as continuum fields while still maintaining the fidelity of the underlying molecular interactions. Within this framework, we extend recent results to include the anisotropic effects of protein–lipid interactions. As applications, we consider two membrane proteins of biological interest: a RAS–RAF complex tethered to the membrane and a membrane embedded G protein-coupled receptor. A strong qualitative and quantitative agreement is found between the numerical results and the corresponding molecular dynamics simulations. Combining the scope of continuum level simulations with the details from molecular level particle simulations enables research into protein–membrane behaviors at a more biologically relevant scale, which crucially can also be accessed via experiment.

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

Mechanical properties of heterogeneous metallic glasses: Insights from brick-and-mortar designs

The brick-and-mortar architectural paradigm is commonly applied in structural design to achieve an exceptional combination of strength and plasticity due to its highly tunable mechanical attributes. This study applies molecular dynamics simulations of tensile loading to investigate the mechanical properties and failure mechanisms of brick-and-mortar metallic glasses (BMMGs). The focus is primarily on the implications of the aspect ratio of the bricks and interlayer thickness on the strength, plasticity, and deformation mechanisms. Results indicate that the failure mode is typified by multiple shear bands localized within the softer mortar regions, creating a staggered network under smaller aspect ratios that significantly enhances plastic deformation. However, a transition to a single dominant SB occurs when the aspect ratio exceeds 4.1. In addition, results indicate that a concurrent improvement in strength and plasticity can be achieved by modulating the distance between brick layers in BMMGs. This enhancement originates from the extensive generation and interaction of shear transformation zones. Furthermore, this study highlights that a desirable balance between strength and plasticity can be obtained in BMMGs with appropriate brick aspect ratios and interlayer thicknesses, providing a potential design strategy for the advancement of novel metallic glasses with superior properties.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Effect of iron redox ratio on the structures of boroaluminosilicate glasses

Iron oxide is commonly found in natural or industrial glass compositions and can exist as ferrous (Fe 2+ ) or ferric (Fe 3+ ) species, with their ratios depending on glass composition, temperature, pressure and the redox reactions during the glass forming process. The iron redox ratio plays an important role on silicate glass structures and consequently various properties. This work aims to study the effect of iron oxide, and particularly the iron redox ratio, on the structures of borosilicate and boroaluminosilicate glasses using molecular dynamics simulations with newly developed iron potential parameters that are compatible with the borosilicate potentials. The results provide detailed cation coordination states of both iron species and the effect of redox ratio on boron coordination and other structural features. Particularly, competition for charge compensating modifier cations (such as Na + ) among the fourfold-coordinated cations such as B 3+ , Al 3+ , and Fe 3+ is investigated by calculating the cation–cation pair distribution functions and coordination preferential ratios. The results show that the trivalent ferric ions, with a shorter Fe–O bond distance and better defined first coordiation shell with mainly four-fold coordination, act as a glass former whereas the divalent ferrous ions mainly play the role of glass modifier. The ferrous/ferric ratio (Fe 2+ /Fe 3+ ) was found to affect the glass chemistry and hence glass properties by regulating the amount of four-coordinated boron, the fraction of non-briding oxygen and other features. Finally, the results are compared with available experimental data to gain insights of the complex structures and charge compensation schemes of the glass system.

36 MATERIALS SCIENCE↗
DOE OSTI2021

CASTELO: clustered atom subtypes aided lead optimization—a combined machine learning and molecular modeling method

Background: Drug discovery is a multi-stage process that comprises two costly major steps: pre-clinical research and clinical trials. Among its stages, lead optimization easily consumes more than half of the pre-clinical budget. We propose a combined machine learning and molecular modeling approach that partially automates lead optimization workflow in silico, providing suggestions for modification hot spots. Results: The initial data collection is achieved with physics-based molecular dynamics simulation. Contact matrices are calculated as the preliminary features extracted from the simulations. To take advantage of the temporal information from the simulations, we enhanced contact matrices data with temporal dynamism representation, which are then modeled with unsupervised convolutional variational autoencoder (CVAE). Finally, conventional and CVAE-based clustering methods are compared with metrics to rank the submolecular structures and propose potential candidates for lead optimization. Conclusion: With no need for extensive structure-activity data, our method provides new hints for drug modification hotspots which can be used to improve drug potency and reduce the lead optimization time. It can potentially become a valuable tool for medicinal chemists.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Concentric core-shell tracks and spectroscopic properties of SrTiO 3 under intense electronic excitation

A deeper understanding of the intrinsic link between the irradiation-induced microstructures and the corresponding spectroscopic properties is becoming increasingly attractive for the research fields of materials science, physics, and information technology. In this work, the structural damage response, spectroscopic features, and associated physical mechanisms of SrTiO 3 single crystals under swift heavy ion irradiation were comparatively analyzed using a combination of experimental and theoretical approaches. Corresponding to 0.11–5.00 MeV/u ion irradiation with electronic energy loss ranging from 4.0 to 29.3 keV/nm, the inelastic thermal spike calculations combined with molecular dynamics simulations are compared with the experimental observations, revealing the track fine structures (individual spherical defects with a disordered region, and discontinuous and continuous tracks consisting of an amorphous core and a disordered outer shell) and demonstrating the dominant effects of the deposition energy and lattice temperature on track damage formation and evolution; thus, two essential thresholds for defect formation of ~0.60 eV/atom and amorphous region formation of ~1.81 eV/atom were identified to better describe the concentric core-shell track structure. The enhanced nanohillock formation in the surface region is attributed to the combined action of kinetic and potential energy depositions, and the fluence dependence in regulating the hillock dimensions is also presented. The measured refractive index profiles along different crystal axes further indicate the anisotropy of irradiation-induced lattice expansion. With increasing ion fluence and damage level, the intrinsic bandgap gradually decreased, and the concentration of additional radiative recombination centers (1.81 eV, 2.31 eV, and 2.42 eV) accordingly increased in the SrTiO 3 crystal, providing the possibility of regulating related defects to achieve tunable/selective photon emission for more critical technological applications.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2022

Bacterial Membranes Are More Perturbed by the Asymmetric Versus Symmetric Loading of Amphiphilic Molecules

Characterizing the biophysical properties of bacterial membranes is critical for understanding the protective nature of the microbial envelope, interaction of biological membranes with exogenous materials, and designing new antibacterial agents. Presented here are molecular dynamics simulations for two cationic quaternary ammonium compounds, and the anionic and nonionic form of a fatty acid molecule interacting with a Staphylococcus aureus bacterial inner membrane. The effect of the tested materials on the properties of the model membranes are evaluated with respect to various structural properties such as the lateral pressure profile, lipid tail order parameter, and the bilayer’s electrostatic potential. Conducting asymmetric loading of molecules in only one leaflet, it was observed that anionic and cationic amphiphiles have a large impact on the Staphylococcus aureus membrane’s electrostatic potential and lateral pressure profile as compared to a symmetric distribution. Nonintuitively, we find that the cationic and anionic molecules induce a similar change in the electrostatic potential, which points to the complexity of membrane interfaces, and how asymmetry can induce biophysical consequences. Finally, we link changes in membrane structure to the rate of electroporation for the membranes, and again find a crucial impact of introducing asymmetry to the system. Understanding these physical mechanisms provides critical insights and viable pathways for the rational design of membrane-active molecules, where controlling the localization is key.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Columnar Grain-driven Plasticity and Cracking in Nanotwinned FCC Metals

The mechanisms of strengthening and plasticity in columnar-grained metals with preferentially oriented nano-sized twins have been examined traditionally by considering dislocation processes, but rarely from the perspective of grain boundary (GB) deformation. Here, the effects of GB strain accommodation on plastic deformation in four different columnar-grained nanocrystalline nanotwinned (nt) face-centered-cubic metals (Cu, Ag, Al, and Ni) were studied by large-scale molecular dynamics simulations. It is observed that in tensile deformation parallel to coherent twin boundaries (CTBs), the dislocation mechanisms in each metal are identical and associated with GB emissions of jog and threading dislocations at small and large CTB spacings, respectively. However, CTB strengthening effects are increasingly more pronounced in columnar-grained nt metals as their shear modulus increases, which is rationalized by the dependence of GB stress concentrations on twin size, metal type and strain rate. Also, while flow stresses in nt-Cu, nt-Ag, and nt-Al metals increase linearly with decreasing CTB spacing, a maximum strength limit is reached in nt-Ni below a critical CTB spacing of 6 nm. The strength limit in nt-Ni results from columnar GB cracking induced by prominent GB sliding. For columnar-grained microstructures, GB sliding is equivalent in nt-Ag and nt-Al and slightly lower in nt-Cu but markedly higher in nt-Ni. These findings underscore the importance of new GB deformation mechanisms on plasticity and fracture in columnar-grained nt metals and enrich our understanding of CTB strengthening in fcc metals synthesized in the literature.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Intrinsic and extrinsic effects on the fracture toughness of ductile metallic glasses

The potential application of metallic glasses (MGs) as structural materials demands accurate measurements of their toughness and the understanding of the underlying factors affecting it. Currently, it is challenging to precisely measure the toughness of MGs, especially ductile MGs. Measured toughness values are widely scattered, even for MGs with identical compositions. That is attributed to the combined effect of intrinsic and extrinsic factors including processing, sample geometries, and loading conditions. A fundamental understanding of the influences of these elements is thus of great significance. In the present study, molecular dynamics simulations are performed to investigate the influence of intrinsic and extrinsic effects on the fracture toughness of CuZr MGs. In particular, focused is placed on the effects of cooling rate, notch shape and size, strain rate, and temperature. The results indicate that the fracture toughness of a MG scales with the cooling rate used to prepare it. This is attributed to increased free volume content generated at high cooling rates, which enhances plastic deformation and amplifies the associated energy dissipation during plastic deformation events. Fracture toughness also increases with the strain rate, arguably due to strain rate-induced crack extension delay. Overall, the results demonstrate that the largest fracture toughness are achieved when MG samples are fabricated at high cooling rates and subjected to high strain rate deformation. In addition, results suggest that the fracture toughness decreases with increasing temperature, due to the significant decrease in strength. Here, the correlations revealed between these crucial intrinsic and extrinsic parameters and the calculated MG fracture toughness support the development of a framework to understand the root of the discrepancies in the measurement of the toughness of MGs and provide insights into the design of tough MGs for structural applications.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Mechanism of ion pairing–induced co-ion penetration into the stern layer

In classical electric double layer (EDL) theory, co-ions—ions carrying the same charge as the electrode—are assumed to be excluded from the Stern layer because of electrostatic repulsion. However, ion pairing with adsorbed counterions may enable co-ions to access the EDL, a phenomenon that remains underexplored. Key questions therefore remain unresolved, including how deeply co-ions penetrate, how ion-specific properties govern them, and how ion pairing within the EDL differs from bulk solution. Here, in this study, we employ molecular dynamics simulations combined with well-tempered metadynamics to quantify co-ion penetration and ion-pairing thermodynamics at positively charged Mg-Al layered double hydroxide interfaces (σ = +20.6 μC/cm 2 ) in aqueous chloride electrolytes across 0.005–3 M range. We reveal a concentration-driven crossover: at dilute conditions, counterion–co-ion contact ion pairing (CIP) is thermodynamically unfavorable or only weakly favorable (ΔG CIP = +0.12 kcal/mol for Li + to −0.42 kcal/mol for K + ), leading to co-ion exclusion. As concentration increases (≥0.5 M), enhanced screening reduces surface repulsion and stabilizes CIP thermodynamics (ΔG CIP = −0.89 kcal/mol for Li + to −1.05 kcal/mol for K + at 3 M), enabling monovalent co-ions to penetrate the Stern layer following the hydration hierarchy K + > Na + > Li + , while divalent co-ions (Mg 2+ , Ca 2+ ) remain in the diffuse layer, forming only solvent-separated pairs. Comparison with bulk solution shows interfacial ion pairing is suppressed at low concentrations but converges to bulk-like thermodynamics at high concentrations, indicating surface effects vanish under strong screening. These results establish a quantitative framework linking ion-pairing thermodynamics to co-ion penetration and providing strategies to design electrochemical interfaces.

Co-ion penetration↗
DOE OSTI2026

Substrate-Directed Dimensional and Phase Control of Peptide Assemblies on Two-Dimensional van der Waals Materials

Understanding and controlling biomolecular self-assembly on van der Waals (vdW) materials has the potential to advance hybrid bioelectronic devices by enabling precise tuning of the interface and modulation of the resulting electronic properties of the biomolecule-vdW heterostructure. However, how surface properties of vdW materials direct biomolecule assembly remains poorly understood. To fill this knowledge gap, we investigated the assembly of a peptide known to assemble into two-dimensional (2D) crystalline films on MoS 2 on three representative vdW surfaces: WS 2 , MoS 2 , and highly oriented pyrolytic graphite (HOPG). Using in situ atomic force microscopy (AFM), we find that assembly is substrate-dependent, resulting in multilayers on WS 2 , monolayers on MoS 2 , and multiple coexisting phases on HOPG. WS 2 exhibits a higher negative charge, strong long-range electrostatic interactions, and extensive hydration layering that may promote multilayer stacking. In contrast, MoS 2 has stronger short-range interactions with the peptides but much weaker long-range interactions and hydration structure, which may favor monolayer formation. Molecular dynamics simulations predict a corresponding switch from monolayer to multilayer aggregates of the adsorbed monomers, reflected in their relative mobilities. On hydrophobic HOPG, the peptides bind most strongly and remain as monomers with high surface mobility. The peptide dimers comprising the basic unit of the crystals are more compact on HOPG, which has a smaller lattice constant than WS 2 or MoS 2 , suggesting strain contributes to stabilizing multiple phases. Our results provide mechanistic insights into how surface charge and hydration structure, and the lattice structure of the substrates governs peptide assembly on vdW materials, offering a framework to rationally control the 2D peptide-vdW heterostructures.

Molecular dynamics simulations↗
DOE OSTI2025

Binding and Translocation of Substrate Allosterically Promotes Functional Interactions Within the AlkB–AlkG Electron Transfer Complex

The alkane monooxygenase AlkB and rubredoxin AlkG form an electron transfer complex that hydroxylates terminal alkanes to produce alcohols. The recent cryoEM study of Fontimonas thermophila AlkB-AlkG complex revealed its architecture, including a dodecane (D12) substrate at the active site. However, FtAlkBG molecular mechanism of action of remains unknown. Here, in this study, we examined its dynamics and interactions by multiscale computations, including molecular dynamics simulations, elastic network models, and QM/MM of the oxygen activation mechanism at the AlkB catalytic site. D12 maintained stable interactions within the catalytic site during two MD runs, coordinated by hydrophobic residues L263-L264, I267, I133. A third extended run revealed that D12 could translocate to a membrane-exposed site near S49/F46 along a hydrophobic channel gated by I54. During this translocation, D12 was temporarily stabilized at intermediate sites IS1 (lined by I27/L30-G31/G50/L53-I54/P59/S124/A127-V128) and IS2 (I33-G34/L37/L45-F46/S49) before nearly exiting the protein, and diffused back to the active site, assisted by L30. Substrate binding and translocation across those intermediate sites affects the coupling between the iron centers in AlkBG, and interfacial interactions between AlkB-AlkG. The channel was further connected to the cytosol, near two surface-exposed arginines, potentially allowing for O 2 passage. The allosteric effects between D12 putative entry site, catalytic site and AlkB-AlkG interface were analyzed by ENM-based methods which confirmed the cooperative perturbation-responses and strongly correlated movements of residues belonging to those distal regions. Our study provides new mechanistic insights into key sites and their interactions that could be targeted for developing AlkB-variants with desirable alkane conversion functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Protein folding from heterogeneous unfolded state revealed by time-resolved X-ray solution scattering

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Structural determination of a full-length plant cellulose synthase informed by experimental and in silico methods

Three-dimensional structure determination and prediction of proteins with intrinsically disordered regions, unstructured regions, conformational flexibility, and lacking homologous structures are challenging. We previously predicted and refined an in silico structure of a plant cellulose synthase from cotton (GhCESA1), and more recently, cryo-electron microscopy (cryo-EM) has resolved a majority of the lengths of two CESA structures from poplar (PttCESA8) and cotton (GhCESA7). However, 26–30% of these cryo-EM structures remain unresolved, including the N-terminal domain, half of the class-specific region, the gating loop region, and the C-terminal domain. Here, we describe the generation and evaluation of a full-length hybrid GhCESA1 model based on this cryo-EM PttCESA8 structure, with unresolved regions completed using this in silico refined GhCESA1 model. All-atom molecular dynamics simulations and subsequent energy minimizations were performed for the in silico and hybrid GhCESA1 models in a lipid bilayer-water-ion environment, and structural stability, dynamics, energetics, contacts, and quality were evaluated. The unresolved regions were found to be the most dynamic, in agreement with their poor electron density with cryo-EM. The hybrid model exhibited a higher total secondary structure content, more favorable intra-protein and protein-lipid interaction energies, and improved quality metrics. Moreover, hydrogen bonding was revealed to be a primary mechanism for intra-protein and protein-lipid contacts. These results demonstrate that in silico structure prediction and refinement may be useful to augment experimental structure determination, especially for disordered and unstructured regions. Furthermore, this hybrid model can serve as a steppingstone to derive full-length homology models of other CESAs found in more experimentally tractable organisms.

59 BASIC BIOLOGICAL SCIENCES↗