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Results for “molecular dynamic (MD) simulation”

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At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Hub stability in the calcium calmodulin-dependent protein kinase II

The calcium calmodulin protein kinase II (CaMKII) is a multi-subunit ring assembly with a central hub formed by the association domains. There is evidence for hub polymorphism between and within CaMKII isoforms, but the link between polymorphism and subunit exchange has not been resolved. Here, we present near-atomic resolution cryogenic electron microscopy (cryo-EM) structures revealing that hubs from the α and β isoforms, either standalone or within an β holoenzyme, coexist as 12 and 14 subunit assemblies. Single-molecule fluorescence microscopy of Venus-tagged holoenzymes detects intermediate assemblies and progressive dimer loss due to intrinsic holoenzyme lability, and holoenzyme disassembly into dimers upon mutagenesis of a conserved inter-domain contact. Molecular dynamics (MD) simulations show the flexibility of 4-subunit precursors, extracted in-silico from the β hub polymorphs, encompassing the curvature of both polymorphs. The MD explains how an open hub structure also obtained from the β holoenzyme sample could be created by dimer loss and analysis of its cryo-EM dataset reveals how the gap could open further. An assembly model, considering dimer concentration dependence and strain differences between polymorphs, proposes a mechanism for intrinsic hub lability to fine-tune the stoichiometry of αβ heterooligomers for their dynamic localization within synapses in neurons.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Mechanistic insights into a heterobifunctional degrader-induced PTPN2/N1 complex

PTPN2 (protein tyrosine phosphatase non-receptor type 2, or TC-PTP) and PTPN1 are attractive immuno-oncology targets, with the deletion of Ptpn1 and Ptpn2 improving response to immunotherapy in disease models. Targeted protein degradation has emerged as a promising approach to drug challenging targets including phosphatases. We developed potent PTPN2/N1 dual heterobifunctional degraders (Cmpd-1 and Cmpd-2) which facilitate efficient complex assembly with E3 ubiquitin ligase CRL4 CRBN , and mediate potent PTPN2/N1 degradation in cells and mice. To provide mechanistic insights into the cooperative complex formation introduced by degraders, we employed a combination of structural approaches. Our crystal structure reveals how PTPN2 is recognized by the tri-substituted thiophene moiety of the degrader. We further determined a high-resolution structure of DDB1-CRBN/Cmpd-1/PTPN2 using single-particle cryo-electron microscopy (cryo-EM). This structure reveals that the degrader induces proximity between CRBN and PTPN2, albeit the large conformational heterogeneity of this ternary complex. The molecular dynamic (MD)-simulations constructed based on the cryo-EM structure exhibited a large rigid body movement of PTPN2 and illustrated the dynamic interactions between PTPN2 and CRBN. Together, our study demonstrates the development of PTPN2/N1 heterobifunctional degraders with potential applications in cancer immunotherapy. Furthermore, the developed structural workflow could help to understand the dynamic nature of degrader-induced cooperative ternary complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Graphene-extracted membrane lipids facilitate the activation of integrin α v β 8

Despite the remarkable electrochemical properties of graphene, strong van der Waals attraction between graphene and biomolecules often causes cytotoxicity, which hinders its applications in the biomedical field. Unfortunately, surface passivation of graphene might stimulate undesired immune response as the nanomaterial triggers cytokine production through membrane receptor activation. In this work, we use all-atom Molecular Dynamics (MD) simulations to unravel the underlying mechanism of graphene-induced inside-out activation of integrin αvβ8, a prominent membrane receptor expressed in immune cells. We model the transmembrane (TM) domains of integrin αvβ8 in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer and observe the structural changes in the integrin–membrane complex when interacting with a graphene nanosheet across the membrane. We find that the β8 TM domain interacts with the graphene nanosheet directly or indirectly through extracted lipids, facilitating the pulling of a β8 subunit away from an αv subunit and thus leading to the disruption of the TM domain association by breaking the hydrophobic cluster in the cytoplasmic domains of the αv and β8 subunits. Alanine substitution of two conserved phenylalanine residues on the αv subunit at this hydrophobic cluster further reveals the importance of a stable T-shaped structure in retaining integrin in its inactive state. Our results agree with previous studies on the interactions between other integrin subtypes and their endogenous activators, suggesting an intriguing role that the graphene nanosheet may play in the integrin-related signal transduction during its interaction with the membrane.

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

Reversible electrowetting transitions on superhydrophobic surfaces

An electric field applied across the interface has been shown to enable transitions from the Cassie to the Wenzel state on superhydrophobic surfaces with miniature corrugations. Molecular dynamics (MD) simulations manifest the possibility of reversible cycling between the two states when narrow surface wells support spontaneous expulsion of water in the absence of the field. With approximately 1 nm sized wells between the surface asperities, the response times to changes in the electric field are of O(0.1) ns, allowing up to GHz frequency of the cycle. Because of the orientation preferences of interfacial water in contact with the solid, the phenomenon depends on the polarity of the field normal to the interface. The threshold field strength for the Cassie-to-Wenzel transition is significantly lower for the field pointing from the aqueous phase to the surface; however, once in the Wenzel state, the opposite field direction secures tighter filling of the wells. Considerable hysteresis revealed by the delayed water retraction at decreasing field strength indicates the presence of moderate kinetic barriers to expulsion. Known to scale approximately with the square of the length scale of the corrugations, these barriers preclude the use of increased corrugation sizes while the reduction of the well diameter necessitates stronger electric fields. Field-controlled Cassie-to-Wenzel transitions are therefore optimized by using superhydrophobic surfaces with nanosized corrugations. Abrupt changes indicate a high degree of cooperativity reflecting the correlations between the wetting states of interconnected wells on the textured surface.

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

Structure of water-in-salt and water-in-bisalt electrolytes

We report a systematic diffraction study of two “water-in-salt” electrolytes and a “water-in-bisalt” electrolyte combining high-energy X-ray diffraction (HEXRD) with polarized and unpolarized neutron diffraction (ND) on both H 2 O and D 2 O solutions. The measurements provide three independent combinations of correlations between the different pairs of atom types that reveal the short- and intermediate-range order in considerable detail. The ND interference functions show pronounced peaks around a scattering vector Q ~ 0.5 Å -1 that change dramatically with composition, indicating significant rearrangements of the water network on a length scale around 12 Å. The experimental results are compared with two sets of Molecular Dynamics (MD) simulations, one including polarization effects and the other based on a non-polarizable force field. The two simulations reproduce the general shapes of the experimental structure factors and their changes with concentration, but differ in many detailed respects, suggesting ways in which their force fields might be modified to better represent the actual systems.

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

Catalytic production of tetrahydropyran (THP): a biomass-derived, economically competitive solvent with demonstrated use in plastic dissolution

Tetrahydropyran (THP) is a five-carbon heterocyclic ether that is non-carcinogenic, non-peroxide forming, biodegradable, and economically competitive with tetrahydrofuran (THF) as a solvent. In this work, THP has been synthesized from renewable biomass at >99.8% selectivity and 98% yield via hydrogenation of furfural-derived 3,4-dihydropyran (DHP) over Ni/SiO 2 in a continuous flow reactor at 150–200 °C. The apparent activation energy of THP formation is 31 kJ mol -1 , and the reaction orders with respect to the partial pressures of H 2 , DHP, and THP are: 2, 1, and -0.3. The kinetic data has been fitted to a Hougen–Watson model where the rate limiting step is the hydrogenation of adsorbed DHP. Ni/SiO 2 is shown to have a low deactivation rate constant of 0.012 h -1 over 100 h time on stream and can be regenerated in situ. As a performance advantage, THP is shown to be resistant to ring opening polymerization under strongly acidic conditions that THF is not, revealing it to be a superior solvent. Further, the minimum selling price of THP is competitive with the market price of THF ($$900 – 1400 per ton ) at a DHP feedstock cost of $1000 per ton. Conductor-like Screening Model for Real Solvents (COSMO-RS) and molecular dynamics (MD) simulations with 1008 solvents and 8 common plastics have demonstrated that THP can serve as an alternative solvent to THF, 2-methyltetrahydrofuran (MeTHF), and cyclopentyl methyl ether (CPME) for plastic dissolution, especially low-density polyethylene (LDPE), polypropylene (PP), polystyrene (PS) and polyvinyl chloride (PVC). This work establishes THP as a green solvent with excellent thermal, chemical and peroxidative stability that can be used for numerous applications, including waste plastic recycling.

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

Feasibility study of Mg storage in a bilayer silicene anode via application of an external electric field

With the goal of developing a Si-based anode for Mg-ion batteries (MIBs) that is both efficient and compatible with the current semiconductor industry, the current research utilized classical Molecular Dynamics (MD) simulation in investigating the intercalation of a Mg 2+ ion under an external electric field (E-field) in a 2D bilayer silicene anode (BSA). First principles density functional theory calculations were used to validate the implemented EDIP potentials. Our simulation shows that there exists an optimum E-field value in the range of 0.2–0.4 V Å –1 for Mg 2+ intercalation in BSA. To study the effect of the E-field on Mg 2+ ions, an exhaustive spread of investigations was carried out under different boundary conditions, including calculations of mean square displacement (MSD), interaction energy, radial distribution function (RDF), and trajectory of ions. Our results show that the Mg 2+ ions form a stable bond with Si in BSA. The effects of E-field direction and operating temperature were also investigated. In the X–Y plane in the 0°–45° range, 15° from the X-direction was found to be the optimum direction for intercalation. The results of this work also suggest that BSA does not undergo drastic structural changes during the charging cycles with the highest operating temperature being ~300 K

25 ENERGY STORAGE↗
DOE OSTI2024

Visualizing the SEI formation between lithium metal and solid-state electrolyte

The solid electrolyte interphase (SEI) is regarded as the most important factor affecting the durability of lithium-metal anode in all-solid-state batteries (ASSBs). Despite its significance, the nucleation and growth mechanism of SEI is not yet well understood. Here, we elucidate the thermodynamics and kinetics governing SEI formation at the Li|β-Li 3 PS 4 interface at the atomic scale via thermodynamic phase equilibrium analysis and machine-learning-potential-assisted molecular dynamics (MD) simulations. An accurate moment tensor potential using the machine-learning method is developed for a reactive model of Li|β-Li 3 PS 4 . This potential enabled us to perform large-scale MD simulations with the model size expanded to the experimental dimensions (~40 nm) while maintaining the same level of accuracy as density functional theory calculations. The results reveal a four-stage evolution process at the Li|β-Li 3 PS 4 interface, namely (i) fast ion diffusion, (ii) nucleation, (iii) Li 2 S growth, and (iv) stabilization. Notably, we demonstrate that the SEI can be categorized into crystalline and amorphous regions. The simulated SEI thickness, structure, and composition closely match experimental findings, validating the accuracy of the MD simulations. We further disclose the significant impact of ion diffusion kinetic limitations on the phase formation and crystallization of interfacial products. Furthermore, we shed light on the detailed potential energy (PE) distribution of lithium along the direction perpendicular to the interface. Finally, this information is crucial for better understanding interfacial ion mobility.

25 ENERGY STORAGE↗
DOE OSTI2023

Quantifying selective solvent transport under an electric field in mixed-solvent electrolytes

Electrolytes in lithium-ion batteries comprise solvent mixtures, but analysis of ion transport is always based on treating the solvents as a single-entity. We combine electrophoretic NMR (eNMR) measurements and molecular dynamics (MD) simulations to quantify electric-field-induced transport in a concentrated solution containing LiPF 6 salt dissolved in an ethylene carbonate/ethyl methyl carbonate (EC/EMC) mixture. The selective transport of EC relative to EMC is reflected in the difference between two transference numbers, defined as the fraction of current carried by cations relative to the velocity of each solvent species. This difference arises from the preferential solvation of cations by EC and its dynamic consequences. The simulations reveal the presence of a large variety of transient solvent-containing clusters which migrate at different velocities. Rigorous averaging over different solvation environments is essential for comparing simulated and measured transference numbers. Our study emphasizes the necessity of acknowledging the presence of four species in mixed-solvent electrolytes.

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

Metadynamics investigation of lanthanide solvation free energy landscapes and insights into separations energetics

Lanthanide ion solvation chemistry in nonaqueous phases is key to understanding and developing effective separation processes for these critical materials. Due to the complexity and inherent disorder of the solution phase, a comprehensive picture of the solvated metal ion is often difficult to generate solely from conventional spectroscopic approaches and electronic structure calculations, particularly in the extractant phase. In this work, we use classical molecular dynamics (MD) simulation with an advanced sampling technique, metadynamics, supplemented by experimental spectroscopy and speciation analysis, to measure lanthanide solvation free energy landscapes. We define coordination-based collective variables to probe the entire range of solvation configurations in the organic phase of lanthanum (La), europium (Eu), and lutetium (Lu) nitrate salts bound with a commonly used extractant, N,N′-dimethyl, N,N′-dioctylhexylethoxymalonamide (DMDOHEMA). The known lanthanide extraction trend of La ≈ Eu > Lu is readily explained by the measured free energy surfaces, which show consistent DMDOHEMA coordination from La to Eu, followed by loss of DMDOHEMA coordination from Eu to Lu. These simulations suggest how ligand crowding at the metal center can control selectivity, in this case resulting in the opposite extraction trend as observed with other conventional extractants, where the enthalpic contribution from increasing lanthanide charge density across the series dominates the extraction energetics. We also find that the presence of inner-sphere water, verified by time-resolved fluorescence, diversifies the accessible solvation structures. As a result, understanding solvation requires consideration of an entire thermodynamic ensemble, rather than the single dominant lowest-energy structure, as is often considered out of necessity in interpretation of spectroscopic data or in electronic structure-based ligand design approaches. In general, we demonstrate how metadynamics uniquely enables investigation of complex, multidimensional solvation energetic landscapes, and how it can explain selectivity trends where extraction is controlled by more complex mechanisms than simple charge density-based selectivity.

Wang, Xiaoyu↗
DOE OSTI2025

Teacher-student training improves the accuracy and efficiency of machine learning interatomic potentials

Machine learning interatomic potentials (MLIPs) are revolutionizing the field of molecular dynamics (MD) simulations. Recent MLIPs have tended towards more complex architectures trained on larger datasets. The resulting increase in computational and memory costs may prohibit the application of these MLIPs to perform large-scale MD simulations. Herein, we present a teacher-student training framework in which the latent knowledge from the teacher (atomic energies) is used to augment the students' training. We show that the light-weight student MLIPs have faster MD speeds at a fraction of the memory footprint compared to the teacher models. Remarkably, the student models can even surpass the accuracy of the teachers, even though both are trained on the same quantum chemistry dataset. Our work highlights a practical method for MLIPs to reduce the resources required for large-scale MD simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Application-specific machine-learned interatomic potentials: exploring the trade-off between DFT convergence, MLIP expressivity, and computational cost

Machine-learned interatomic potentials (MLIPs) are revolutionizing computational materials science and chemistry by offering an efficient alternative to ab initio molecular dynamics (MD) simulations. However, fitting high-quality MLIPs remains a challenging, time-consuming, and computationally intensive task where numerous trade-offs have to be considered, e.g., How much and what kind of atomic configurations should be included in the training set? Which level of ab initio convergence should be used to generate the training set? Which loss function should be used for fitting the MLIP? Which machine learning architecture should be used to train the MLIP? The answers to these questions significantly impact both the computational cost of MLIP training and the accuracy and computational cost of subsequent MLIP MD simulations. In this study, we use a configurationally diverse beryllium dataset and quadratic spectral neighbor analysis potential. We demonstrate that joint optimization of energy versus force weights, training set selection strategies, and convergence settings of the ab initio reference simulations, as well as model complexity can lead to a significant reduction in the overall computational cost associated with training and evaluating MLIPs. This opens the door to computationally efficient generation of high-quality MLIPs for a range of applications which demand different accuracy versus training and evaluation cost trade-offs.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Charge state-dependent ion condensation near conjugated polymer backbones

Despite the technological appeal of polymeric organic mixed ionic/electronic conductors (OMIECs) for diverse applications, a deep understanding of the fundamentals of mixed charge transport in these materials, especially regarding the complex interplay between polymer, ion and solvent structure in determining transport, is lacking. Herein, extensive molecular dynamics (MD) simulations of a model OMIEC representing various electrochemically gated states are reported that reveal charge state-dependent counterion condensation. X-ray diffraction simulations based on the MD data predict a measurable change in the scattering intensity at the counterion absorption edge, indicative of counterion repositioning with charging. We leverage an operando resonant X-ray scattering technique to experimentally corroborate the simulated scattering and report excellent agreement between predicted and experimental data, confirming that counterions preferentially reside in the lamellar mid-plane of crystallites at low doping, and near the polymer backbone at higher doping. Driving forces for ion type-dependent spatial repositioning and implications thereof are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Genetic control of morphological transitions in a coacervating protein template

Nature routinely exploits liquid–liquid phase separation (LLPS) of proteins to control the assembly and mineralization of hybrid materials. Here, we show that fusion of the Car9 silica-binding peptide to an elastin-like polypeptide (ELP) yields temperature- and sequence-programmable soft matter templates for the synthesis of silicified architectures ranging in size from nanometers to micrometers. Specifically, we demonstrate unprecedented control over the diameter of silica nanoparticles (SiNP) in the 30–60 nm range with 4 nm precision, show that a single arginine residue (R4) in the Car9 sequence underpins the transition from micelles to proteinosomes, and find that substitutions in other basic residues modulate electrostatic repulsion and solvation to enable access to kinetically trapped species. These structures, which include interconnected micelles, small (∼200 nm) and large (>5 µm) vesicles, are readily visualized by SEM imaging following silicification. Molecular dynamics (MD) simulations and AlphaFold predictions reveal that mutations in positively charged residues alter interfacial packing, hydration, and conformational freedom of the silica-binding segments. Overall, our results establish sequence and thermal energy as synergistic levers for morphological control across length scales using solid-binding ELPs and establish mineralization as a powerful tool to visualize the structure of dynamic soft matter assemblies.

hierarchy↗
DOE OSTI2025

Atomistic characterization of hydration-dependent fuel cell ionomer nanostructure: validation by vibrational spectroscopy

The development of Nafion alternatives for fuel cells and electrolyzers requires a fundamental understanding of hydration-dependent ion-exchange site acid/base chemistry. We present here reactive force field (ReaxFF) molecular dynamics (MD) simulations of Nafion at varying molar water/ion-exchange-site ratios (λ), which we correlate to our experimental and density functional theory-based vibrational spectra. ReaxFF describes the formation and breaking of covalent bonds, enabling simulations of proton exchange between sulfonic acid/sulfonate groups and water/hydronium. Our MD simulations determine the λ-dependent equilibrium proportions of protonated and deprotonated sites. We find that protonated sites persist across all λ from 0 to 20, challenging the widely accepted notion that all sites are ionized above a threshold λ value (e.g., 3 or 4). Our simulations generate hundreds of realistic exchange site environments, the characterization of which are based on 6 Å radii sulfur-centered ‘inner-spheres’. These inner- and outer-sphere regions elucidate an interplay of stereoelectronic factors that influence protonation states, including the number of inner-sphere waters (Λ). Our simulations produce broad λ-dependent distributions of Λ values, representing non-uniform exchange site hydration. Moreover, we demonstrate that these distributions are specific to both protonated and deprotonated sites, with significant overlap between the two distributions for all non-zero λ. These distributions underpin the IR spectra of hydrated membranes, with each exchange site contributing an IR spectrum characteristic of its protonation state and Λ. We expect that these nanostructural characterizations of Nafion exchange sites will contribute to the development of new ionomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Synthesis challenges, thermodynamic stability, and growth kinetics of La–Si–P ternary compounds

Although many new compounds have been recently predicted with the help of machine learning, the successful experimental synthesis of these compounds remains challenging. Computational insights about the thermodynamic stability and phase formation kinetics among the ground state and competing metastable phases are highly desirable to rationalize and attempt to overcome synthesis challenges experimentally. In this work, we explore synthetic challenges within ternary La–Si–P compounds through feedback between experimental and computational studies. We discuss the experimental challenges in forming three computationally predicted ternary phases (La 2 SiP, La 5 SiP 3 , and La 2 SiP 3 ). To understand the synthetic challenges, we performed molecular dynamics (MD) simulations using an accurate and efficient artificial neural network machine learning (ANN-ML) interatomic potential. We study the phase stability and formation kinetics of these ternary phases in relation to the reported and synthesized La 2 SiP 4 phase. While the growth of the La 2 SiP 4 phase can be reproduced by our MD simulation, our results indicate that the rapid formation of a Si-substituted LaP crystalline phase is a major barrier to the synthesis of the predicted La 2 SiP, La 5 SiP 3 , and La 2 SiP 3 ternary compounds, agreeing well with experimental observations. Our simulations also suggest that there is a narrow temperature window in which the La 2 SiP 3 phase can be grown from the solid–liquid interface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Strong Effect of Nonpolar Solvent Molecular Structure on CdSe Nanoplatelet Stacking

We report a drastic difference in stacking behavior of oleic acid-stabilized 4-monolayer (4 ML) CdSe nanoplatelets (NPLs) in toluene and methylcyclohexane (MCH), two nonpolar solvents that differ in the conformational flexibility of their molecules. Using liquid cell transmission electron microscopy (TEM) and small angle scattering (SAXS) techniques, we show that NPLs form microns-long ribbons consisting of 4 ML CdSe NPLs in toluene, the solvent widely used to form stable colloidal solutions of a broad range of quasi-spherical nanoparticles. In contrast, 4 ML CdSe NPLs are well dispersed in MCH. The difference in stacking behavior of NPLs in toluene and MCH suggests that the conformational flexibility of the solvent molecules, such as the ability to adopt multiple chair conformations, modulates nanoplatelet interactions. Molecular dynamics (MD) simulations reveal that solvent molecules subtly alter the structure of the organic ligand shell. These solvent-dependent changes propagate to the inorganic core, modulating the degree of CdSe nanoplatelet (NPL) twisting and, consequently, the properties of the nanoparticles. We show that toluene better solvates oleate ligands while MCH induces a bimodal oleate span distribution, which can lead to increased solubility of CdSe NPLs. In addition, the solvent can also influence the inorganic core, which, in turn, can modify the nanoparticle properties. We demonstrate that destabilization of toluene solution containing ribbons of 4 ML CdSe NPLs without CdS shells results in the formation of NPL assemblies with amplified spontaneous emission (ASE) with a low threshold of 14 µJ cm−2 that is comparable with that of CdSe/CdS core/shell NPLs. Our results emphasize that the solvent plays a major role in mediating interactions between NPLs and hence their processability for fabrication of functional structures.

CdSe↗