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At least 685 records · Page 38

Mapping the structural–mechanical landscape of amorphous carbon with ReaxFF molecular dynamics

We use ReaxFF molecular dynamics (MD) to investigate the relationship between structural and mechanical properties in bulk and nanostructured amorphous carbon (a-C). The liquid-quench MD method is used to generate isotropic bulk samples with mass densities ranging from 0.96 to 3.29 g/cm3. Structural analysis identifies two types of structures with distinct short- and medium-range order: lower-density sp2-dominated a-C, which is characterized by a bimodal ring-size distribution, and higher-density sp3-dominated tetrahedral amorphous carbon (ta-C), exhibiting a unimodal ring-size distribution. Stress–strain MD simulations and analysis reveal how an atomistic structure impacts elastic properties and post-yield atomic rearrangements. All stretched structures demonstrate elastic isotropy and plasticity driven by a ring-size expansion mechanism reflected in changes in ring statistics. The plastic region is substantially larger in ta-C than in a-C due to the post-yield shift from sp3 to sp2 C dominant bonding. In both a-C and ta-C, ultimate failure occurs when a reactive crack, traversed by long sp chains, forms and propagates predominantly perpendicular to the direction of the applied strain. Oxygen infiltration into the fractured region significantly reduces stress resistance, primarily through the early rupture of long sp chains. MD simulations and analysis are extended to a-C slabs, a-C nanotubes, and partially a-C nanotubes. The latter nanostructure highlights the differences between the elastically isotropic a-C walls, which develop circumferential cracking, and the crystalline walls, which tear along crystallographic directions. These results provide a strong foundation for further computational characterization of a-C materials.

Dernov, A. (ORCID:0009000004220973)↗

Tuning the Functionalities of Porous Liquids for Emergent Gas-Capture Properties

Type 3 Porous Liquids (PLs) are a class of materials with the potential to revolutionize gas capture, storage, and utilization. These PLs are formed by suspending sorbent nanoparticles (e.g., metal−organic frameworks) in sterically excluded solvents, creating permanent porosity for gas capture in a processable, low-viscosity phase. Herein, a computational study revealed sorbent surface functionalization strategies to enhance CO 2 sorption, and the molecular structural signatures underpinning the enhancements in gas uptake. PLs composed of a ZIF-8 surface functionalized with 3-amino-1,2,4-triazole (Atz) in glyceryl triacetate were targeted for emergent CO 2 capture, exceeding that of the unfunctionalized ZIF-8 PL. ZIF-8 was surface functionalized with Atz at various surface coverage fractions (f), and classical molecular dynamics simulations predicted an increase in CO 2 sorption capacity with increasing f, up to f = 0.75. Additionally, detailed structural analyses revealed that solvent orientational order, derived from the solvent triplet-angle distribution, can identify the gas-capture potential of a PL without requiring computationally expensive direct modeling of the CO 2 sorption. Combined with experimental validation, initial computational screening of PL compositions promises to accelerate the discovery of PL compositions for novel gas separation materials platforms.

gas capture↗

Edge Segregated Polymorphism in 2D Molybdenum Carbide

Molybdenum carbide (Mo 2 C), a class of unterminated MXene, is endowed with rich polymorph chemistry, but the growth conditions of the various polymorphs are not understood. Other than the most commonly observed T-phase Mo 2 C, little is known about other phases. Here, Mo 2 C crystals are successfully grown consisting of mixed polymorphs and polytypes via a diffusion-mediated mechanism, using liquid copper as the diffusion barrier between the elemental precursors of Mo and C. By controlling the thickness of the copper diffusion barrier layer, the crystal growth can be controlled between a highly uniform AA-stacked T-phase Mo 2 C and a “wedding cake” like Mo 2 C crystal with spatially delineated zone in which the Bernal -stacked Mo 2 C predominate. The atomic structures, as well as the transformations between distinct stackings, are simulated and analyzed using density functional theory (DFT)-based calculations. Bernal -stacked Mo 2 C has a d band closer to the Fermi energy, leading to a promising performance in catalysis as verified in hydrogen evolution reaction (HER).

36 MATERIALS SCIENCE↗

Synthesis of Operable Process Intensification Systems—Steady-State Design with Safety and Operability Considerations

In this work, we present an integrated approach to synthesize process intensification systems with guaranteed flexibility and safety performances. The synthesis of intensified equipment/flowsheets is addressed through the Generalized Modular Representation Framework (GMF), which utilizes an aggregation of multifunctional mass/heat exchange modules to represent chemical processes. Thus, the optimal design options are investigated as mass- and heat-transfer opportunities using superstructure-based optimization techniques without a prepostulation of plausible configurations. To ensure that the designs can be operated under a specified range of uncertain parameters, a multiperiod GMF representation is developed based on the critical operating conditions identified by flexibility test. Risk assessment, accounting for equipment failure frequency and consequence severity, is incorporated as a constraint into this synthesis model to derive inherently safer designs. The resulting safely operable intensified systems, which are represented via phenomenological modules, are then identified as corresponding equipment-based flowsheets and validated with steady-state simulation. We demonstrate the proposed approach through a case study for the production of methyl tert-butyl ether. Here, the results indicate that safety and operability considerations can result in significant changes in the structural and operating parameters of the optimal intensified design configuration.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A two-dimensional type I superionic conductor

Superionic conductors (SICs) possess liquid-like ionic diffusivity in the solid state, finding wide applicability from electrolytes in energy storage to materials for thermoelectric energy conversion. Type I SICs (e.g., AgI, Ag 2 Se, etc.) are defined by a first-order transition to the superionic state and have so far been found exclusively in three-dimensional crystal structures. Here, we reveal a two-dimensional type I SIC, α-KAg 3 Se 2 by scattering techniques and complementary simulations. Quasi-elastic neutron scattering and ab initio molecular dynamics simulations confirm that the superionic Ag + ions are confined to sub-nanometre sheets, with the simulated local structure validated by experimental X-ray powder pair-distribution-function analysis. Finally, we demonstrate that the phase transition temperature can be controlled by chemical substitution of the alkali metal ions that comprise the immobile charge-balancing layers. Our work thus extends the known classes of SICs and will facilitate the design of new materials with tailored ionic conductivities and phase transitions.

36 MATERIALS SCIENCE↗

Defect-Free Growth of Decagonal Quasicrystals around Obstacles

Quasicrystals are aperiodic solids with exotic physical properties. The mechanisms driving their growth are far from understood, particularly in the presence of rigid obstacles. Here, using in situ synchrotron x-ray tomography and molecular dynamics simulations, we investigate the interaction between decagonal quasicrystals and obstacles (shrinkage pores) during solidification of an Al 79 ⁢Co 6 ⁢Ni 15 alloy. The results reveal defect-free quasicrystal growth around the pores, independent of pore size and geometry. Our findings point to a universal feature of aperiodic solids: their ability to accommodate structural disruptions due to additional (phasonic) degrees of freedom. This Letter opens new possibilities for synthesizing large-scale, single quasicrystals from a liquid metal precursor.

alloys↗

Flow behavior in liquid molding

The liquid molding (LM) process for manufacturing polymer composites with structural properties has the potential to significantly lower fabrication costs and increase production rates. LM includes both resin transfer molding and structural reaction injection molding. To achieve this potential, however, the underlying science base must be improved to facilitate effective process optimization and implementation of on-line process control. The National Institute of Standards and Technology (NIST) has a major program in LM that includes materials characterization, process simulation models, on-line process monitoring and control, and the fabrication of test specimens. The results of this program are applied to real parts through cooperative projects with industry. The key feature in the effort is a comprehensive and integrated approach to the processing science aspects of LM. This paper briefly outlines the NIST program and uses several examples to illustrate the work.

Hunston, D.↗

Impact of Water Extraction on Malonamide Aggregation: A Molecular Dynamics and Graph Theoretic Approach

Solution structure in liquid-liquid extraction affects the efficacy of separation; however, even for simplified organic phases, structural characterization and attribution of aggregation to intermolecular interactions are fundamental challenges. We investigate water uptake into organic phases for two malonamides commonly applied to actinide and lanthanide separations. Extracted water induces reorganization of the amphiphilic extractant molecules, although we find this rearrangement is not strongly manifested in small-angle X-ray scattering making it challenging to probe without methods such as atomistic simulation. Using a graph theoretic approach to define hydrogen bonded water/malonamide aggregates from molecular dynamics simulations, we find evidence of a characteristic aggregate size by water number that results from geometric accommodation of the surrounding malonamide molecules. Furthermore, this implies a degree of size selectivity inherent to these water-in-oil aggregates. Conversely, we find no evidence of a characteristic size of the aggregates with respect to their malonamide number. By defining a separate graphical representation of self-association of the amphiphilic malonamides, we quantify how water affects the local and nonlocal topology of the malonamide network, providing a basis for characterization of the structure and impact of polar solutes in increasingly complex organic phases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A blueprint for biomolecular condensation driven by bacterial microcompartment encapsulation peptides

Bacterial microcompartments are protein organelles with diverse metabolic capabilities. Their functional diversity is determined by an enzymatic core that is sequestered within a structurally conserved protein shell architecture. Segregation of protein cargo into the bacterial microcompartment is enabled by encapsulation peptides, which are short helical domains fused to core proteins through a disordered linker. Here, we investigate how encapsulation peptides drive multicomponent cargo assembly into biomolecular condensates. In vitro experiments supported by molecular dynamics simulations demonstrate the importance of both conserved hydrophobic packing and electrostatic interactions in stabilizing trimeric encapsulation peptide bundles. Topological rearrangements of encapsulation peptide domains can drive programmable liquid- or gel-like partitioning in vitro and in vivo. This partitioning is found to be encapsulation peptide-specific, modular, and can co-assemble at least three fluorescent reporters. In summary, we describe the molecular features necessary to drive biomolecular condensation using a widespread peptide tag. This work can serve as a blueprint for implementing encapsulation peptide biotechnology across diverse applications.

59 BASIC BIOLOGICAL SCIENCES↗

Measuring the structure and equation of state of polyethylene terephthalate at megabar pressures

Abstract We present structure and equation of state (EOS) measurements of biaxially orientated polyethylene terephthalate (PET, $$({\hbox {C}}_{10} {\hbox {H}}_8 {\hbox {O}}_4)_n$$ ( C 10 H 8 O 4 ) n , also called mylar) shock-compressed to ( $$155 \pm 20$$ 155 ± 20 ) GPa and ( $$6000 \pm 1000$$ 6000 ± 1000 ) K using in situ X-ray diffraction, Doppler velocimetry, and optical pyrometry. Comparing to density functional theory molecular dynamics (DFT-MD) simulations, we find a highly correlated liquid at conditions differing from predictions by some equations of state tables, which underlines the influence of complex chemical interactions in this regime. EOS calculations from ab initio DFT-MD simulations and shock Hugoniot measurements of density, pressure and temperature confirm the discrepancy to these tables and present an experimentally benchmarked correction to the description of PET as an exemplary material to represent the mixture of light elements at planetary interior conditions.

36 MATERIALS SCIENCE↗

TDP-43 α-helical structure tunes liquid–liquid phase separation and function

Liquid–liquid phase separation (LLPS) is involved in the formation of membraneless organelles (MLOs) associated with RNA processing. The RNA-binding protein TDP-43 is present in several MLOs, undergoes LLPS, and has been linked to the pathogenesis of amyotrophic lateral sclerosis (ALS). While some ALS-associated mutations in TDP-43 disrupt self-interaction and function, here we show that designed single mutations can enhance TDP-43 assembly and function via modulating helical structure. Using molecular simulation and NMR spectroscopy, we observe large structural changes upon dimerization of TDP-43. Two conserved glycine residues (G335 and G338) are potent inhibitors of helical extension and helix–helix interaction, which are removed in part by variants at these positions, including the ALS-associated G335D. Substitution to helix-enhancing alanine at either of these positions dramatically enhances phase separation in vitro and decreases fluidity of phase-separated TDP-43 reporter compartments in cells. Furthermore, G335A increases TDP-43 splicing function in a minigene assay. Therefore, the TDP-43 helical region serves as a short but uniquely tunable module where application of biophysical principles can precisely control assembly and function in cellular and synthetic biology applications of LLPS.

60 APPLIED LIFE SCIENCES↗

High-density Boron Nitride Nanotube Composites via Surfactant-stabilized Lyotropic Liquid Crystals for Enhanced Space Radiation Shielding

Despite significant technological advancements in space exploration, human space travel and colonization remain limited by the health risks associated with space radiation. Boron nitride nanotubes (BNNTs) have been proposed as an advanced material for space applications due to their high specific strength and efficient radiation shielding capabilities. However, the practical implementation of BNNTs has been slow, primarily due to technological challenges in fabricating structural materials incorporating BNNTs. In this study, a method is presented for fabricating high-density BNNT films that are mechanically robust, exhibit high thermal conductivity, and effectively attenuate space radiation. The key advancement enabling high-density BNNT films is the successful preparation of BNNT liquid crystals (LCs), achieved through the strategic use of a commercial dodecylbenzenesulfonic acid surfactant. This surfactant ensures exceptional BNNT stability in aqueous dispersion, even at concentrations exceeding the LC phase transition threshold. Simulations, estimating the equivalent radiation dose to the human body in space, indicate that a high-density BNNT film with a surface density of 50 g cm−2 reduces the total dose equivalent rate by 56% compared to zero shielding. This enhancement would allow astronauts to extend their mission duration on the lunar surface by a factor of two.

Young-Kyeong Kim↗

Molecular simulation and artificial intelligence for the circular economy of bioenergy and bioproducts

The concept of the circular bioeconomy is a carbon neutral, sustainable system with zero waste. One vision for such an economy is based upon lignocellulosic biomass. This lignocellulosic circular bioeconomy requires CO 2 absorption from biomass growth and the efficient deconstruction of recalcitrant biomass into solubilized and fractionated biopolymers, which are then used as precursors for the sustainable production of high-quality liquid fuels, chemical bioproducts, and bio-based materials. Here, in this study, we summarize the roles that molecular dynamics (MD) simulations and machine learning (ML) are playing in overcoming several fundamental challenges hindering the adoption of a circular bioeconomy. Specifically, we discuss the role of MD and ML/AI in overcoming lignocellulose recalcitrance by designing biomass pretreatment methods to efficiently produce solubilized cellulose/lignin/hemicellulose and of that in improving energy-intensive manufacturing of biomass-based materials and their structural and mechanical properties. Quantum mechanical methods and MD simulations, in addition to offering a mechanistic understanding of biomass deconstruction and biomaterials design, can provide meaningful structural, energetics, and physiochemical properties as inputs to train AI/ML models. The ML models can guide the experimental prioritization of materials/solvents and process parameters that significantly accelerate the development of biofuel and biomaterial components of the circular bioeconomy.

Smith, Jeremy C. [Oak Ridge National Laboratory (O↗

Computational study of the electrostatic potential and charges of multivalent ionic liquid molecules

The electrostatic interactions in ionic liquids (ILs) can be difficult to quantify, but this information is very valuable for improving intermolecular potentials for performing molecular-level simulations. Although polarizable forcefields can provide improved accuracy, the computational efficiency of fixed charge molecular models is often preferred for larger systems. Here, we propose a multi-scale screening approach for analyzing the charge scaling behavior and other electrostatic properties of ILs, which is more attainable than previous analysis methods that rely on the IL crystalline structures. Based on isolated molecules and small clusters, we study the electrostatic potential properties and charges of multivalent IL molecules using density-functional theory calculations and ab initio molecular dynamics simulations. The charges of the IL molecules are calculated and compared using several different charge estimation techniques. Although there are some differences among the estimated partial charges on the atoms, the total anion and cation charges are very similar. In conclusion, the charge scaling factors are substantial, and they are only slightly affected by the IL cluster size model.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Carbon-carbon interactions in warm dense titanium carbide

Encouraged by experimental reports of diamond precipitation in carbon-containing materials under warm dense matter conditions and in shock compression experiments, we examine the behavior of carbon in TiC using density functional theory-molecular dynamics simulations. Two polymorphs of TiC are considered, the ambient-pressure B1 ($Fm$$\overline{3}$$m$) structure in which C-C interactions are prevented by geometric constraints, and a high-pressure Cmcm structure in which C atoms condense into zigzag chains. Chemistry-inspired bonding analyses confirm the covalently bound nature of these chains and further illuminate important interatomic interactions in both structures. Upon melting of B1 TiC, new short-range C-C interactions develop in the liquid, while the pre-existing C-C interactions in Cmcm TiC persist in the liquid. Here, the resulting carbon networks in the melt provide a promising environment for eventual diamond nucleation.

Ab initio molecular dynamics↗

Multiple Environmental Influences on the Lightning of Cold-Based Continental Cumulonimbus Clouds. Part I: Description and Validation of Model

In this two-part paper, influences from environmental factors on lightning in a convective storm are assessed with a model. In Part I, an electrical component is described and applied in the Aerosol–Cloud model (AC). AC treats many types of secondary (e.g., breakup in ice–ice collisions, raindrop-freezing fragmentation, rime splintering) and primary (heterogeneous, homogeneous freezing) ice initiation. AC represents lightning flashes with a statistical treatment of branching from a fractal law constrained by video imagery. The storm simulated is from the Severe Thunderstorm Electrification and Precipitation Study (STEPS; 19/20 June 2000). The simulation was validated microphysically [e.g., ice/droplet concentrations and mean sizes, liquid water content (LWC), reflectivity, surface precipitation] and dynamically (e.g., ascent) in our 2017 paper. Predicted ice concentrations (~10 L -1 ) agreed—to within a factor of about 2—with aircraft data at flight levels (-10° to -15°C). Here, electrical statistics of the same simulation are compared with observations. Flash rates (to within a factor of 2), triggering altitudes and polarity of flashes, and electric fields, all agree with the coincident STEPS observations. The “normal” tripole of charge structure observed during an electrical balloon sounding is reproduced by AC. It is related to reversal of polarity of noninductive charging in ice–ice collisions seen in laboratory experiments when temperature or LWC are varied. Positively charged graupel and negatively charged snow at most midlevels, charged away from the fastest updrafts, is predicted to cause the normal tripole. Total charge separated in the simulated storm is dominated by collisions involving secondary ice from fragmentation in graupel–snow collisions.

54 ENVIRONMENTAL SCIENCES↗

Atomic Cluster Aggregates in Nucleation of Solid Alumina Inclusion in the Aluminum Deoxidation for Liquid Iron

Nucleation plays a decisive role in determining the structure and size distribution of a solid inclusion particle in liquid iron. The literature does not yet provide a clear picture about the pathway leading to solid alumina inclusion from liquid iron. The main confusion surrounds the little-known structures and thermodynamic properties of metastable alumina phase (MAP) that appear in the nucleation of alumina inclusion. In this work, it is suggested that MAP could appear in the Al-deoxidation reaction, based on the summaries and analysis in terms of various equilibrium experimental results and thermodynamic modeling of the Al deoxidation in liquid iron since the 1950s. The structures and thermodynamic properties of a species of MAP, alumina atomic cluster aggregates (AACAs), are calculated by density functional theory (DFT) methods. The thermodynamics on formation and transformation of AACAs shows that AACAs are in equilibrium with Al and O with various contents measured in the Al-deoxidation equilibrium experiments for liquid iron. It is suggested that the residual Al and O, which cannot nucleate, appear in the form of AACAs in Al-deoxidized liquid iron. It can be concluded that AACAs are the metastable intermediates and structural units for alumina inclusion nucleating from liquid iron. Thus, the behaviors of AACAs are important to the control of the nucleation rate of alumina inclusions in the Al deoxidation for liquid iron.

36 MATERIALS SCIENCE↗

How initial conditions-, structural-, and parameter-based model uncertainty interact and influence predictions in permafrost ecosystems: Modeling Archive

This dataset contains model output and input data, as well as source code examples for the Terrestrial Ecosystem Model with the Dynamic Vegetation Model and Dynamic Organic Soil (DVM-DOS-TEM) for the field sites Imnavait creek and the Bonanza creek Long Term Ecological Research Network (LTER). The data covers simulations from the last glacial maximum (LGM) until 2100 for a selection of paleo scenarios, setting the mean temperature of the LGM up to 10°C lower than pre-industrial conditions. The model structure was modulated to represent various model versions, and this dataset contains the relevant changes in the source code. The raw output data, the processed statistical data, the setup and processing scripts as well as parameter value distribution files from a parameter sensitivity analysis are included as well. Model outputs include active layer depth, organic soil carbon, soil layer depths, gross primary productivity (GPP) with and without nitrogen limitation, net primary productivity (NPP), soil liquid water content, heterotrophic, maintenance, and growth respiration, soil temperature, and vegetation carbon (*.nc files). The Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) project is a research effort to reduce uncertainty in the Department of Energy’s Energy Exascale Earth System Model (E3SM) by developing a predictive understanding of Arctic tundra ecosystems underlain by permafrost and to quantify feedbacks from the Arctic tundra to the Earth system. NGEE Arctic is supported by the Department of Energy's Office of Biological and Environmental Research.Over Phases 1–3, observations made by the NGEE Arctic team across a gradient of permafrost landscapes in Arctic Alaska improved the representation of tundra processes in the land surface component of E3SM (the E3SM Land Model, ELM). Model improvements emphasized unique aspects of permafrost environments and explored reductions in model complexity while retaining predictive power. The Arctic-informed ELM developed by NGEE Arctic has been used to make novel predictions on processes ranging from permafrost thaw to soil biogeochemical cycling to Earth system feedbacks associated with the unique characteristics of tundra plants. In Phase 4, the NGEE Arctic team is evaluating our new predictive understanding under novel conditions across the Arctic domain. In collaboration with partners at long-term pan-Arctic research sites we are examining whether an Arctic-informed ELM can faithfully simulate interactions among surface and subsurface processes at site, regional, and pan-Arctic scales. In turn, we are using variety of tools to dynamically extend and evaluate ELM inference, with an emphasis on data synthesis and pan-Arctic model evaluation, reintegration of code with an evolving E3SM, scaling across heterogeneous Arctic landscapes, and the appropriate representation of the impacts of increasingly frequent Arctic disturbances.

54 ENVIRONMENTAL SCIENCES↗