Understanding Silicon Nitride Crystallization from Amorphous Deposited Layers with Molecular Dynamics
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Lane, James Matthew Doyle↗
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Atomic forces between noble gas atoms, alkali ions, and halogen ions for surface interactions
The components of the physical forces between noble gas atoms, alkali ions, and halogen ions are analyzed and a data base developed from analysis of the two-body potential data, the alkali-halide molecular data, and the noble gas crystal and salt crystal data. A satisfactory global fit to this molecular and crystal data is then reproduced by the model to within several percent. Surface potentials are evaluated for noble gas atoms on noble gas surfaces and salt crystal surfaces with surface tension neglected. Within this context, the noble gas surface potentials on noble gas and salt crystals are considered to be accurate to within several percent.
Wilson, J. W.↗
Real Time In-situ Monitoring of Molecular Processes during Growth of Protein Crystals
No abstract available
Vekilov, Peter G.↗
Protein Crystallization Processes at Three Length Scales: Molecular, Capilary and Transport
No abstract available
Vekilov, Peter G.↗
Protein Crystallization Processes at Three Length Scales: Molecular, Capillary and Transport
No abstract available
Vekilov, Peter G.↗
Influence of Carboxymethyl Cellulose as a Thickening Agent for Glauber’s Salt-Based Low Temperature PCM
This work is focused on a novel, promising low temperature phase change material (PCM), based on the eutectic Glauber’s salt composition. To allow phase transition within the refrigeration range of temperatures of +5 °C to +12 °C, combined with a high repeatability of melting–freezing processes, and minimized subcooling, the application of three variants of sodium carboxymethyl cellulose (Na-CMC) with distinct molecular weights (700,000, 250,000, and 90,000) is considered. The primary objective is to optimize the stabilization of this eutectic PCM formulation, while maintaining the desired enthalpy level. Preparation methods are refined to ensure repeatability in mixing components, thereby optimizing performance and stability. Additionally, the influence of Na-CMC molecular weight on stabilization is examined through differential scanning calorimetry (DSC), T-history, and rheology tests. The PCM formulation of interest builds upon prior research in which borax, ammonium chloride, and potassium chloride were used as additives to sodium sulfate decahydrate (Glauber’s salt), prioritizing environmentally responsible materials. The results reveal that CMC with molecular weights of 250 kg/mol and 90 kg/mol effectively stabilize the PCM without phase separation issues, slowing crystallization kinetics. Conversely, CMC of 700 kg/mol proved ineffective due to the disruption of gel formation at its low gel point, hindering higher concentrations. Calculations of ionic concentration indicate higher Na ion content in PCM stabilized with 90 kg/mol CMC, suggesting increased ionic interactions and gel strength. A tradeoff is discovered between the faster crystallization in lower molecular weight CMC and the higher concentration required, which increases the amount of inert material that does not participate in the phase transition. After thermal cycling, the best formulation had a latent heat of 130 J/g with no supercooling, demonstrating excellent performance. This work advances PCM’s reliability as a thermal energy storage solution for diverse applications and highlights the complex relationship between Na-CMC molecular weight and PCM stabilization.
25 ENERGY STORAGE↗
Can Solution Supersaturation Affect Protein Crystal Quality?
The formation of large protein crystals of "high quality" is considered a characteristic manifestation of microgravity. The physical processes that predict the formation of large, high quality protein crystals in the microgravity environment of space are considered rooted in the existence of a "depletion zone" in the vicinity of crystal. Namely, it is considered reasonable that crystal quality suffers in earth-grown crystals as a result of the incorporation of large aggregates, micro-crystals and/or large molecular weight "impurities", processes which are aided by density driven convective flow or mixing at the crystal-liquid interface. Sedimentation and density driven convection produce unfavorable solution conditions in the vicinity of the crystal surface, which promotes rapid crystal growth to the detriment of crystal size and quality. In this effort, we shall further present the hypothesis that the solution supersaturatoin at the crystal surface determines the growth mechanism, or mode, by which protein crystals grow. It is further hypothesized that protein crystal quality is affected by the mechanism or mode of crystal growth. Hence the formation of a depletion zone in microgravity environment is beneficial due to inhibition of impurity incorporatoin as well as preventing a kinetic roughening transition. It should be noted that for many proteins the magnitude of neither protein crystal growth rates nor solution supersaturation are predictors of a kinetic roughening transition. That is, the kinetic roughening transition supersaturation must be dtermined for each individual protein.
Gorti, Sridhar↗
Intergranular Hotspots: A Molecular Dynamics Study on the Influence of Compressive and Shear Work
Numerous crystal- and microstructural-level mechanisms are at play in the formation of hotspots, which are known to govern high explosives initiation behavior. Most of these mechanisms, including pore collapse, interfacial friction, and shear banding, involve both compressive and shear work done within the material and have thus far remained difficult to separate. Here, we assess hotspots formed at shocked crystal–crystal interfaces using quasi-1D molecular dynamics simulations that isolate effects due to compression and shear. Two high explosive materials are considered (TATB and PETN) that exhibit distinctly different levels of molecular conformational flexibility and crystal packing anisotropy. Temperature and intramolecular strain energy localization in the hotspot are assessed through parametric variation of the crystal orientation and two velocity components that respectively modulate compression and shear work. The resulting hotspots are found to be highly localized to a region within 5–20 nm of the crystal–crystal interface. Compressive work plays a considerably larger role in localizing temperature and intramolecular strain energy for both materials and all crystal orientations considered. Shear induces a moderate increase in energy localization relative to unsheared cases only for relatively weak compressive shock pressures of approximately 10 GPa. These results help isolate and rank the relative importance of hotspot generation mechanisms and are anticipated to guide the treatment of crystal–crystal interfaces in coarse-grained models of polycrystalline high-explosive materials.
36 MATERIALS SCIENCE↗
Polyoxometalate-Assisted Crystallization: A General Strategy Enabling Structural Characterization of Molecular Radium Complexes
A fundamental understanding of radium (Ra) coordination chemistry has been hindered by the scarcity and radiological hazards of 226 Ra, leaving the structural characterization of molecular Ra complexes almost entirely unexplored. Here, we introduce a polyoxometalate (POM)-assisted crystallization strategy that enables single-crystal X-ray diffraction analysis of Ra–chelator complexes from microgram-scale samples. Employing the plenary Keggin anion [SiW 12 O 40 ] 4– , we isolated and structurally characterized Ra 2+ complexes of 18-crown-6 and the bis-picolinate macrocycle macropa, together with their Sr 2+ and Ba 2+ analogues. The resulting structures reveal systematic, size-dependent trends in coordination number and metal-donor distances across the alkaline earth series and provide the first direct experimental measurements of Ra–N and Ra–OCOO bond distances. Together, these results establish POM-assisted crystallization as a robust approach for obtaining solid-state structural information on Ra 2+ complexes of organic chelators, opening new opportunities to advance the coordination chemistry needed to fully realize radium’s potential in isotope production and targeted radiotherapy. More broadly, this approach expands the experimental toolkit available for studying scarce, highly radioactive elements accessible only in microgram quantities.
Anions↗
The strength of a calcified tissue depends in part on the molecular structure and organization of its constituent mineral crystals in their organic matrix
High-voltage electron-microscopic tomographic (3D) studies of the ultrastructural interaction between mineral and organic matrix in a variety of calcified tissues reveal different crystal structural and organizational features in association with their respective organic matrices. In brittle or weak pathologic or ectopic calcifications, including examples of osteogenesis imperfecta, calciphylaxis, calcergy, and dermatomyositis, hydroxyapatite crystals occur in various sizes and shapes and are oriented and aligned with respect to collagen in a manner which is distinct from that found in normal calcified tissues. A model of collagen-mineral interaction is proposed which may account for the observed crystal structures and organization. The results indicate that the ultimate strength, support, and other mechanical properties provided by a calcified tissue are dependent in part upon the molecular structure and arrangement of its constituent mineral crystals within their organic matrix.
Non-NASA Center↗
Synthesis, Magnetic Properties, and Electronic Structure of Magnetic Topological Insulator MnBi 2 Se 4
The intrinsic magnetic topological insulators MnBi 2 Te 4 and MnBi 2 Se 4 support novel topological states related to symmetry breaking by magnetic order. Unlike MnBi 2 Te 4 , the study of MnBi 2 Se 4 has been inhibited by the lack of bulk crystals, as the van der Waals (vdW) crystal is not the thermodynamic equilibrium phase. In this study, we report the layer-by-layer synthesis of vdW MnBi 2 Se 4 crystals using nonequilibrium molecular beam epitaxy. Atomic-resolution scanning transmission electron microscopy and scanning tunneling microscopy identify a well-ordered vdW crystal with septuple-layer base units. The magnetic properties agree with the predicted layered antiferromagnetic ordering but disagree with its predicted out-of-plane orientation. Instead, our samples exhibit an easy-plane anisotropy, which is explained by including dipole–dipole interactions. Angle-resolved photoemission spectroscopy reveals the gapless Dirac-like surface state, which demonstrates that MnBi 2 Se 4 is a topological insulator above the magnetic-ordering temperature. These studies show that MnBi 2 Se 4 is a promising candidate for exploring rich topological phases of layered antiferromagnetic topological insulators.
36 MATERIALS SCIENCE↗
Relationship Between Equilibrium Forms of Lysozyme Crystals and Precipitant Anions
Molecular forces, such as electrostatic, hydrophobic, van der Waals and steric forces, are known to be important in determining protein interactions. These forces are affected by the solution conditions and changing the pH, temperature or the ionic strength of the solution can sharply affect protein interactions. Several investigations of protein crystallization have shown that this process is also strongly dependent on solution conditions. As the ionic strength of the solution is increased, the initially soluble protein may either crystallize or form an amorphous precipitate at high ionic strengths. Studies done on the model protein hen egg white lysozyme have shown that different crystal forms can be easily and reproducibly obtained, depending primarily on the anion used to desolubilize the protein. In this study we employ pyranine to probe the effect of various anions on the water structure. Additionally, lysozyme crystallization was carried out at these conditions and the crystal form was determined by X-ray crystallography. The goal of the study was to understand the physico-chemical basis for the effect of changing the anion concentration on the equilibrium form of lysozyme crystals. It will also verify the hypothesis that the anions, by altering the bulk water structure in the crystallizing solutions, alter the surface energy of the between the crystal faces and the solution and, consequently, the equilibrium form of the crystals.
Nadarajah, Arunan↗
3D Nanocrystallography and the Imperfect Molecular Lattice
Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Hydrogen-Bonded Organic Framework Enables Phase-Pure Layered Tin Perovskite Nanowires for Room-Temperature Lasing
Room-temperature lasing is a key milestone in the development of miniaturized optoelectronic and photonic devices. We present a simple approach to synthesize phase-pure quasi-2D layered tin perovskite nanowires with varying quantum well thicknesses (n = 1 to 4). By incorporating a new organic spacer capable of forming a hydrogen-bonded organic framework, this method promoted anisotropic crystal growth and enhanced lattice rigidity. Furthermore, introducing molecular intercalants enabled controlled crystallization into well-defined nanowires that function as Fabry−Pérot cavities. Cavities made from n = 2 to 4 perovskites support efficient and robust nearinfrared, room-temperature optically pumped lasing with the threshold as low as 75.8 μJ/cm 2 , cavity quality factor over 3000, and negligible degradation over 106 pulses. A cleaved coupled nanolaser was fabricated as a proof-of-concept device for photonic applications.
Cavities↗
The Building Blocks of Materials: Gathering Knowledge at the Molecular Level
Two start-up positions were created within SD46 to pursue developments in the rapidly expanding areas of biomineralization and nano-technology. As envisioned by Dr. Sandor Lehoczy, the new laboratories to be developed must have the capacity to investigate not only processes associated with the self-assembly of molecules but also the examination of self-assembled structures. For these purposes, laboratories capable of performing the intended function, particularly light scattering spectroscopy and atomic force microscopy were created. What follows then are recent advances arising from the development of these new laboratories. With the implementation of the Atomic Force Microscopy Facility, examples of investigations that determine a correlation between the molecular structure of materials and their macroscopic physical properties are provided. In addition, examples of investigations with particular emphasis on the physical properties of protein crystals, at the molecular level, and subsequent macroscopic characteristics are as provided. Finally, progress in fabrication of technology at the nano-scale levels at the developmental stage is also presented.
Source record↗
A riboswitch separated from its ribosome-binding site still regulates translation
Abstract Riboswitches regulate downstream gene expression by binding cellular metabolites. Regulation of translation initiation by riboswitches is posited to occur by metabolite-mediated sequestration of the Shine-Dalgarno sequence (SDS), causing bypass by the ribosome. Recently, we solved a co-crystal structure of a prequeuosine1-sensing riboswitch from Carnobacterium antarcticum that binds two metabolites in a single pocket. The structure revealed that the second nucleotide within the gene-regulatory SDS, G34, engages in a crystal contact, obscuring the molecular basis of gene regulation. Here, we report a co-crystal structure wherein C10 pairs with G34. However, molecular dynamics simulations reveal quick dissolution of the pair, which fails to reform. Functional and chemical probing assays inside live bacterial cells corroborate the dispensability of the C10–G34 pair in gene regulation, leading to the hypothesis that the compact pseudoknot fold is sufficient for translation attenuation. Remarkably, the C. antarcticum aptamer retained significant gene-regulatory activity when uncoupled from the SDS using unstructured spacers up to 10 nucleotides away from the riboswitch—akin to steric-blocking employed by sRNAs. Accordingly, our work reveals that the RNA fold regulates translation without SDS sequestration, expanding known riboswitch-mediated gene-regulatory mechanisms. The results infer that riboswitches exist wherein the SDS is not embedded inside a stable fold.
59 BASIC BIOLOGICAL SCIENCES↗
Protein Crystallization
Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.
Chernov, Alexander A.↗
Some Sources of Contaminants in the Shuttle Bay Measured with Temperature-Controlled Quartz Crystal Microbalances (TQCM)
The sources of molecular deposits on a Temperature-Controlled Quartz Crystal Microbalance (TQCM) attached to the shuttle bay wall at some distance from the payload and pointing out of the bay have been investigated. Explored as possible sources are: (1) the outgassing of the shuttle tiles treated with the water proofing di-methyl-ethoxy-silane (DMES) compound, scattered back by the ambient molecules into the bay; (2) The ambient scattered return flux of the outgassing, from the RTV 560 silicone which is used as the adhesive for the tiles; (3) the ambient scattered return flux of the payload outgassing; (4) the return C, flux from outgassing source originating near, below, or adjacent to the package containing the TQCM; and (5) the self-scattering of venting plumes and outgassing above the monitor package depositing on the TQCM. In all of these sources, the magnitudes of the outgassing, of the leakage rates, and venting had to be estimated in the absence of data. The resulting analyses which can be useful for similar investigations, indicates that the outgassin- from the tiles, the RTV, the payloads, or the shuttle may not have been the sources of the deposit (about 1 micro g/cm(sup 2) during a the period from bay door opening and payload release from the bay). It appears more probable that the origin is the self- and/or ambient-scattered return fluxes originating near, below, or internal to the monitor package.
Scialdone, John J.↗