Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SEARCH · Engineering Papers
Results for “TiMo”
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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Generating Protein Structures for Pathway Discovery Using Deep Learning
Resolving the intricate details of biological phenomena at the molecular level is fundamentally limited by both length- and time scales that can be probed experimentally. Molecular dynamics (MD) simulations at various scales are powerful tools frequently employed to offer valuable biological insights beyond experimental resolution. However, while it is relatively simple to observe long-lived, stable configurations of, for example, proteins, at the required spatial resolution, simulating the more interesting rare transitions between such states often takes orders of magnitude longer than what is feasible even on the largest supercomputers available today. One common aspect of this challenge is pathway discovery, where the start and end states of a scientific phenomenon are known or can be approximated, but the mechanistic details in between are unknown. Here, we propose a representation-learning-based solution that uses interpolation and extrapolation in an abstract representation space to synthesize potential transition states, which are automatically validated using MD simulations. The new simulations of the synthesized transition states are subsequently incorporated into the representation learning, leading to an iterative framework for targeted path sampling. Our approach is demonstrated by recovering the transition of a RAS-RAF protein domain (CRD) from membrane-free to interacting with the membrane using coarse-grain MD simulations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Capturing Biologically Complex Tissue-Specific Membranes at Different Levels of Compositional Complexity
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Enhanced Exploration of Protein Conformational Space through Integration of Ultra-Coarse-Grained Models to Multiscale Workflows
Not Available
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
THD-C Sheet: A Novel Nonbenzenoid Carbon Allotrope with Tetra-, Hexa-, and Dodeca-Membered Rings
Here, we propose a novel two-dimensional carbon-based structure with tetra-, hexa-, and dodeca-membered rings, which we refer to by the abbreviated name, THD-C. The structure presents a mixture of sp–sp 2 hybridization and can potentially be synthesized by the topological assembly of 4-ethynyldiphenylacetylene molecules. By employing first-principles calculations, the stability and ease of synthesis of the sheet are investigated and compared with various C-allotropes. We predict its metallic behavior and excellent kinetic and dynamic stability. Due to the crystal structure of the sheet, a strong mechanical anisotropy is observed. The effects of functionalization on the electronic properties of the material are also studied, and different semiconducting systems are obtained. The potential of THD-C for energy storage in metal-based batteries, hydrogen storage, and catalysis is also investigated, and we find a superior performance in comparison to graphite and other allotropes. The quantum confinement effect is investigated by constructing nanoribbons and nanotubes of various sizes. For ribbons, we find that tailor-made electronic and magnetic properties can be obtained and explored in potential spintronic devices. Additionally, we observe that nanotubes are conducting irrespective of their chirality and can potentially be used for capture, storage, and separation of industrially relevant small gas molecules.
36 MATERIALS SCIENCE↗
Flexible MOFs as Pressure-Tunable Filters for Hydrocarbon Separation
Metal–organic frameworks (MOFs) hold significant promise for separating gas mixtures, especially hydrocarbons. While the main focus in the field is the development of new adsorbents for specific separations of binary mixtures, a preferable situation would be using a single framework for separating various species. This has been achieved in some flexible MOFs, where ternary mixtures can be separated at different temperatures. Here, we propose a simple yet fascinating way of utilizing the flexibility of MOFs to create tunable filters as a function of external pressure. We thus replace the more costly temperature-driven tunability with a cost-efficient external-pressure tunability. As a proof-of-concept, we select the CaMOF flexible framework for C6 hydrocarbon separation, however, our results are applicable to other flexible framework and gas molecules. Furthermore, our findings provide mechanistic insight and guidelines to engineer separation filters by designing flexible pores with critical sizes that can be effectively manipulated by external pressure.
36 MATERIALS SCIENCE↗
Open-Source and FAIR Research Software for Proteomics
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.
97 MATHEMATICS AND COMPUTING↗
Electronic Coherence and Coherent Dephasing in the Optical Control of Electrons in Graphene
Electronic coherence is of utmost importance for the access and control of quantum-mechanical solid-state properties. Using a purely electronic observable, the photocurrent, we measure a lower bound of the electronic coherence time of 22 ± 4 fs in graphene. The photocurrent is ideally suited to measure electronic coherence, as it is a direct result of coherent quantum-path interference, controlled by the delay between two ultrashort two-color laser pulses. The maximum delay for which interference between the population amplitude injected by the first pulse interferes with that generated by the second pulse determines the electronic coherence time. In particular, numerical simulations reveal that the experimental data yields a lower bound on the electronic coherence time, masked by coherent dephasing due to the broadband absorption in graphene. Overall, we expect that our results will significantly advance the understanding of coherent quantum control in solid-state systems ranging from excitation with weak fields to strongly driven systems.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Flexible Zn-MOF with Rare Underlying scu Topology for Effective Separation of C6 Alkane Isomers
Adsorptive separation by porous solids provides an energy-efficient alternative for the purification of important chemical species compared to energy-intensive distillations. Particularly, the separation of linear hexane isomers from its branched counterparts is crucial to produce premium grade gasoline with high research octane number (RON). Herein, we report the synthesis of a new, flexible zinc-based metal-organic framework, [Zn 5 (μ 3 -OH) 2 (adtb) 2 (H 2 O) 5 ·5 DMA] (Zn-adtb), constructed from a butterfly shaped carboxylate linker with underlying (4,8)-connected scu topology capable of separating the C6 isomers nHEX, 3MP, and 23DMB. The sorbate-sorbent interactions and separation mechanisms were investigated and analyzed through in situ FTIR, solid state NMR measurements and computational modeling. Here these studies reveal that Zn-adtb discriminates the nHEX/3MP isomer pair through a kinetic separation mechanism and the nHEX/23DMB isomer pair through a molecular sieving mechanism. Column breakthrough measurements further demonstrate the efficient separation of linear nHEX from the mono- and dibranched isomers.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Loss and Isotopic Fractionation of Alkali Elements during Diffusion-Limited Evaporation from Molten Silicate: Theory and Experiments
Moderately volatile elements (MVEs) are variably depleted in planetary bodies, reflecting the imprints of nebular and planetary processes. Among MVEs, Na, K, and Rb are excellent tracers for unraveling the history of MVE depletion in planetary bodies because they have similar geochemical behaviors but can be chemically fractionated by evaporation and condensation processes. Furthermore, K and Rb are amenable to high-precision isotopic analyses, which can help constrain the conditions of evaporation and condensation. To quantitatively understand why Na, K, and Rb are depleted in planetary bodies, we have carried out vacuum evaporation experiments from basaltic melt at 1200 and 1400 °C to study their evaporation kinetics and isotopic fractionations. We chose this composition because it is relevant to evaporation from small differentiated planetesimals. The Rb isotopic compositions of the evaporation residues were measured by multicollector inductively coupled plasma mass spectrometry (MC-ICPMS), and the K isotopic compositions were measured along profiles across the residues by secondary ion mass spectrometry (SIMS). In the 1400 °C run products, we found that the concentrations of both K and Rb in the run products decreased from core to rim, which was accompanied by a heavy K isotope enrichment near the surface. This indicates that, in this run, evaporation was limited by diffusion. To use those data quantitatively, we derive analytical equations that describe the evaporation rate and isotopic fractionation associated with diffusion-limited evaporation from a sphere, slab, and cylinder in transient and quasi-steady state regimes. This model is used to tease out the roles that diffusive transport in the melt and evaporation at the melt/gas interface play in setting the elemental depletion and isotopic composition of the residue. Under our experimental conditions, volatility decreases in the order of Na, Rb, and K. Using our experimental results in a thermodynamic model, we have estimated the product γΓ of activity coefficients × evaporation coefficients of Na, Rb, and K. The measured isotopic compositions of the residues are well explained using Rayleigh distillations, whereby the relative volatilities of K and Rb isotopes are given by the square root of their masses. We use our results and previously published data to predict how K and Rb could have been lost as a function of temperature, melt composition, oxygen fugacity, and saturation degree relevant to Vesta’s building blocks. We find that the K and Rb depletions, K/Rb elemental fractionation, and δ 41 K and δ 87 Rb isotopic fractionations of Vesta (as sampled by howardite-eucrite-diogenite (HED) meteorites) are best explained by evaporation of submillimeter size objects for 0.1-10 years at moderate temperatures (~1050 °C) in a medium ~98.8% saturated.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A Water-Resistant Hydrogen-Bonded Organic Framework for Ethane/Ethylene Separation in Humid Environments
The separation of ethane (C 2 H 6 ) and ethylene (C 2 H 4 ) represents a crucial process for the production of polymer-grade C 2 H 4 , and adsorptive separation holds enormous promise for this industrially important but challenging task. Furthermore we report a new hydrogen-bonded organic frameworks (HIAM-102) with suitable channel and superhydrophobicity for preferential adsorption of C 2 H 6 over C 2 H 4 . HIAM-102 shows a C 2 H 6 /C 2 H 4 IAST selectivity of 1.9 and C 2 H 6 uptake of 48.25 cm 3 /g at 1 bar and 298 K. Benefitted from the hydrophobic pore surface, it can well-separate C 2 H 6 and C 2 H 4 under highly humid conditions as confirmed by experimental column breakthrough measurements. Computational calculations provide additional support for the experimental observations that the nonpolar channel of HIAM-102 interact favorably with C 2 H 6 over C 2 H 4 .
36 MATERIALS SCIENCE↗
Full Exclusion of Branched Hexanes from Their Linear Isomer by a Robust Aluminum Metal–Organic Framework with Tailored Pore Structure
High-efficiency separation of hexane isomers through selective molecular exclusion represents an important yet challenging task in the petrochemical industry. It has stringent requirements on the adsorbents' pore shape and dimensions. Here we report the complete exclusion of branched hexanes from their linear isomer by an aluminum metal-organic framework, CAU-21-ODB (ODB = 4,4'-oxydibenzoate) with high stability. The unique gourd-shaped channels with suitable pore aperture lead to substantial uptake of nHEX (141 mg/g at 30 °C) but negligible adsorption of its branched isomers under identical conditions. Furthermore, the capability of CAU-21-ODB for the separation of hexane isomers has been verified by multicomponent breakthrough experiments. DFT calculations further confirm the size-exclusion based separation mechanism.
36 MATERIALS SCIENCE↗
Nickel Isonicotinate Framework with Optimal Pore Structure for Complete Discrimination of Hexane Isomers
Efficient separation of physicochemically similar alkanes is of vital importance. Adsorptive separation utilizing porous materials such as metal–organic frameworks with tunable pore structure and surface functionality represents an energy-efficient technology. In this study, we demonstrate successful separation of alkanes with varying degree of branching using a microporous nickel isonicotinate framework, Ni(4-PyC) 2 . Its 2-fold interpenetrated diamondoid structure with well-suited pore size enables selective adsorption of linear and monobranched hexane isomers, while excluding dibranched isomer. Breakthrough experiments validated its capability to completely discriminate all three hexane isomers. Ab initio calculations combined with in situ infrared spectroscopic analysis unveiled the nature of host–guest interactions and differences in the binding energies and diffusion barriers among the isomers. Furthermore, having well-balanced adsorption uptakes (146 and 79 mg g –1 of nHEX and 3MP), high nHEX/DMB uptake ratio (12.2) and fast kinetics, Ni(4-PyC) 2 stands out as a promising adsorbent for complete separation of hexane isomers under ambient conditions.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Discrimination of Hexane Isomers by Temperature Swing Adsorption in a Rigid Aluminum Metal–Organic Framework
The efficient separation of alkane isomers with similar physicochemical properties remains a persistent challenge for the petrochemical industry. Adsorptive separation using metal− organic frameworks (MOFs) offers an energy-efficient alternative to conventional distillation. Herein, we report temperature swing discrimination of hexane isomers with different degrees of branching using MIL-120, a rigid aluminum pyromellitate-based MOF. MIL-120 features uniform one-dimensional channels with an aperture of ∼5.5 Å. At 30 °C, it selectively adsorbs linear and monobranched hexanes while excluding the dibranched isomer. Upon heating to 120 °C, both mono- and dibranched isomers are completely excluded, whereas linear hexane remains strongly adsorbed. Breakthrough experiments validate the temperature swing separation performance. Adsorption heat analysis combined with ab initio calculations provides a quantitative measure of distinct differences in adsorption enthalpies, binding energies, and diffusion barriers responsible for the observed separation efficiency, highlighting the potential of this MOF for efficient separation of alkane isomers via temperature swing adsorption.
Adsorption↗
Discovery and Characterization of a Metastable Cubic Interstitial Nickel–Carbon System with an Expanded Lattice
Metastable, i.e., kinetically favored but thermodynamically not stable, interstitial solid solutions of carbon in iron are well-understood. Carbon can occupy the interstitial atoms of the host metal, altering its properties. Alloying of the host metal results in the stabilization of the FeC x phases, widening its application. Pure nickel finds niche applications, mainly focusing on catalysis, while nickel alloys are widely applied, e.g., in gas turbines, reactors, and seawater piping. Nickel carbide (Ni 3 C) is the well-known stable Ni–C system displaying a rhombohedral (R3̅c) crystal structure. Some reports describe an elusive cubic Ni–C system, observed during certain catalytic reactions occurring on nickel and formed by the occupation of the interstitials of the metal with carbon: to date, the stabilization and characterization of this phase have not been accomplished. Hereby, we report on the synthesis of a cubic metastable NiC x phase using chemical vapor deposition of methane on supported nickel nanoparticles. The structure was predicted by DFT/ReaxFF, synthesized and monitored with in situ time-resolved synchrotron XRD, and experimentally confirmed by Rietveld refinement and (S)TEM-EELS under ambient conditions. The results show an Fm3̅m phase with a lattice parameter of a = 3.749 ± 0.037 Å at room temperature, with the highest ever reported atomic percentage of carbon occupying the octahedral interstices of 23.1%, resulting in a NiC 0.3 phase. The degree of occupation of the interstitial voids by carbon can be controlled, enabling the tuning of the host metal’s d-spacing and composition, highlighting the applicability of this synthesis route for catalytic nanoparticle preparation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ultrafast Strong-Field Electron Emission and Collective Effects at a One-Dimensional Nanostructure
Not provided.
Materials Science↗
Porous Ti-MOF-74 Framework as a Strong-Binding Nitric Oxide Scavenger
Combining synthesis, infrared spectroscopy, and ab initio modeling we show that the titanium-based porous framework Ti-MOF-74 has potential as an environmental nitric oxide (NO) scavenger, exhibiting an extraordinarily strong binding affinity and selectivity over other flue-gas components. The robustness upon exposure to water vapor and high flue-gas stack temperatures suggests that this material can perform well in an industrial environment. In-depth analysis of the Ti-NO bond indicates that the NO forms a strong covalent bond with the Ti. The process of this NO bond formation involves a reaction with the OH- capping groups of the Ti to form NO x groups, after which the excess NO binds to the open Ti metal sites. Ti-MOF-74 thus becomes, to the best of our knowledge, the first known porous framework that binds NO significantly stronger than water, providing novel avenues for environmental and physiological scavenging applications.
36 MATERIALS SCIENCE↗