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At least 271 records · Page 15

Thermodynamic precursors, liquid-liquid transitions, dynamic and topological anomalies in densified liquid germania

The thermodynamic, dynamic, structural, and rigidity properties of densified liquid germania (GeO{sub 2}) have been investigated using classical molecular dynamics simulation. We construct from a thermodynamic framework an analytical equation of state for the liquid allowing the possible detection of thermodynamic precursors (extrema of the derivatives of the free energy), which usually indicate the possibility of a liquid-liquid transition. It is found that for the present germania system, such precursors and the possible underlying liquid-liquid transition are hidden by the slowing down of the dynamics with decreasing temperature. In this respect, germania behaves quite differently when compared to parent tetrahedral systems such as silica or water. We then detect a diffusivity anomaly (a maximum of diffusion with changing density/volume) that is strongly correlated with changes in coordinated species, and the softening of bond-bending (BB) topological constraints that decrease the liquid rigidity and enhance transport. The diffusivity anomaly is finally substantiated from a Rosenfeld-type scaling law linked to the pair correlation entropy, and to structural relaxation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Algorithms for Determining Physical Responses of Structures Under Load

Ultra-efficient real-time structural monitoring algorithms have been developed to provide extensive information about the physical response of structures under load. These algorithms are driven by actual strain data to measure accurately local strains at multiple locations on the surface of a structure. Through a single point load calibration test, these structural strains are then used to calculate key physical properties of the structure at each measurement location. Such properties include the structure s flexural rigidity (the product of the structure's modulus of elasticity, and its moment of inertia) and the section modulus (the moment of inertia divided by the structure s half-depth). The resulting structural properties at each location can be used to determine the structure s bending moment, shear, and structural loads in real time while the structure is in service. The amount of structural information can be maximized through the use of highly multiplexed fiber Bragg grating technology using optical time domain reflectometry and optical frequency domain reflectometry, which can provide a local strain measurement every 10 mm on a single hair-sized optical fiber. Since local strain is used as input to the algorithms, this system serves multiple purposes of measuring strains and displacements, as well as determining structural bending moment, shear, and loads for assessing real-time structural health. The first step is to install a series of strain sensors on the structure s surface in such a way as to measure bending strains at desired locations. The next step is to perform a simple ground test calibration. For a beam of length l (see example), discretized into n sections and subjected to a tip load of P that places the beam in bending, the flexural rigidity of the beam can be experimentally determined at each measurement location x. The bending moment at each station can then be determined for any general set of loads applied during operation.

Richards, W. Lance↗

Structural and dynamical characteristics of tropomyosin epitopes as the major allergens in shrimp

Highlights: • The epitope region in tropomyosin was more stable than the non-epitope region. • The difference between epitope and non-epitope regions was largest at low pHs. • Lower content of Ala cluster is involved in higher stability of the epitope region. Ingestion of marine invertebrates often causes food allergy, where the major allergens have been reported to be derived from tropomyosin (TM). Intact or the digestive fragments of food allergens generally show resistance to digestion, which is usually attributable to the structural stability (or rigidity). The difference in the structural and dynamical characteristics between the epitope and the non-epitope regions in TM has not yet been well understood. In the present study, molecular dynamics simulation was performed at constant pHs for shrimp TM. By analyzing the main-chain dihedral angle fluctuations and local α-helix contents, we found that the epitope regions are more stable than the non-epitope counterparts, providing a possible physical reason for the resistance to digestion in the epitopes regions. The difference of the structural stability between the epitope and the non-epitope regions was largest at low pHs, even though pH dependence of the structural stability in itself was not significant in both regions. The lower content of the Ala cluster in the epitope region is considered to cause the higher stability of the epitope region.

60 APPLIED LIFE SCIENCES↗

Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators

T-box riboregulators are a class of cis-regulatory RNAs that govern the bacterial response to amino acid starvation by binding, decoding and reading the aminoacylation status of specific transfer RNAs. In this work, we provide a high-resolution crystal structure of a full-length T-box from Mycobacterium tuberculosis that explains tRNA decoding and aminoacylation sensing by this riboregulator. Overall, the T-box consists of decoding and aminoacylation sensing modules bridged by a rigid pseudoknot structure formed by the mid-region domains. Stem-I and the Stem-II S-turn assemble a claw-like decoding module, while the antiterminator, Stem-III, and the adjacent linker form a tightly interwoven aminoacylation sensing module. The uncharged tRNA is selectively recognized by an unexpected set of favorable contacts from the linker region in the aminoacylation sensing module. A complex structure with a charged tRNA mimic shows that the extra moiety dislodges the linker, which is indicative of the possible chain of events that lead to alternative base-pairing and altered expression output.

59 BASIC BIOLOGICAL SCIENCES↗

Electronically- and crystal-structure-driven magnetic structures and physical properties of RScSb (R = rare earth) compounds. A neutron diffraction, magnetization and heat capacity study

The synthesis of the new equiatomic RScSb ( R = La-Nd, Sm, Gd-Tm, Lu, Y) compounds has been recently reported. These rare earth compounds crystallize in two different crystal structures, adopting the CeScSi-type ( I 4/ mmm) for the lighter R (La-Nd, Sm) and the CeFeSi-type (P4 /nmm) structure for the heavier R ( R = Gd-Tm, Lu, Y). Here we report the results of neutron diffraction, magnetization and heat capacity measurements on some of these compounds ( R = Ce, Pr, Nd, Gd and Tb). Band structure calculations have also been performed on CeScSb and GdScGe (CeScSi-type), and on GdScSb and TbScSb (CeFeSi-type) to compare and understand the exchange interactions in CeScSi and CeFeSi structure types. The neutron diffraction investigation shows that all five compounds order magnetically, with the highest transition temperature of 66 K in TbScSb and the lowest of about 9 K in CeScSb. The magnetic ground state is simple ferromagnetic (τ = [0 0 0]) in CeScSb, as well in NdScSb for 32 >T > 22 K. Below 22 K a second magnetic transition, with propagation vector τ = [¼ ¼ 0], appears in NdScSb. PrScSb has a magnetic structure within, determined by mostly ferromagnetic interactions and antiferromagnetic alignment of the Pr-sites connected through the I-centering ( τ = [1 0 0]). A cycloidal spiral structure with a temperature dependent propagation vector τ = [δ δ ½] is found in TbScSb. The results of magnetization and heat capacity lend support to the main conclusions derived from neutron diffraction. As inferred from a sharp peak in magnetization, GdScSb orders antiferromagnetically at 56 K. First principles calculations show lateral shift of spin split bands towards lower energy from the Fermi level as the CeScSi-type structure changes to the CeFeSi-type structure. This rigid shift may force the system to transform from exchange split ferromagnetic state to the antiferromagnetic state in RScSb compounds (as seen for example in GdScSb and TbScSb) and is proposed to explain the change-over from a ferromagnetic structure as found in the CeScSi-type compounds CeScSb and NdScSb to the antiferromagnetic state as found in TbScSb and GdScSb.

36 MATERIALS SCIENCE↗

Chapter 1: A Brief Introduction to Lignin Structure

Lignin is an alkyl-aromatic polymer found in the cell walls of terrestrial plants. Lignin provides structure and rigidity to plants, is a natural, highly effective barrier against microbial attack, and enables water and nutrient transport through plant tissues. Depending on the plant species, the constituents of lignin can vary considerably, leading to substantial diversity in lignin chemistry and structure. Despite nearly a century of research and development attempting to convert lignin into valuable products, lignin in most current and planned biorefinery contexts remains underutilized, most often being burned to generate heat and power. However, the drive towards effective lignin valorization processes has witnessed a significant resurgence in the past decade, catalyzed by advances in improved understanding of lignin chemistry, structure, and plasticity in parallel with new catalytic and biological approaches to valorize this important, prevalent biopolymer. As a preface to the subsequent chapters in this book, this chapter briefly highlights the known aspects of lignin structure.

09 BIOMASS FUELS↗

Low thermal conductance rigidizer for reducing torsional oscillations in cryogenic Dewars

A rigidizer, which provides greater rigidity against torsional oscillations, is highly resistant to radial motions, and has low thermal conductivity, has been developed to decrease vibrational levels affecting infrared detectors operated in cryostats (e.g., HD-3L Dewar) in aircraft such as NASA's Kuiper Airborne Observatory. The rigidizer is composed of two triangular elements and an intermediate support structure which joins them at the centers of their sides. The reentrant design provides a long heat path, while the triangular truss structure provides high rigidity in the horizontal plane. The structure is relatively compliant in the vertical direction, a desirable feature since the internal structure of the Dewar contracts as it cools. Rigidity in the vertical direction is provided by the neck tube. The support structure is quite compact. Several variants of the rigidizer have been fabricated, using flat sheets of G-10 fiberglass epoxy in thicknesses between 0.75-1.5 mm for the upper and lower truss assemblies, and either G-10 or stainless steel for the intermediate structure.

Harper, D. A.↗

Design of a D-Strut and its application results in the JPL, MIT, and LaRC test beds

High damping at very low magnitudes of vibration is provided by an 'Arched Flexure' D-Strut. Five of these devices have been incorporated in JPL's CSI truss structure, and five more in MIT's interferometer test bed. Two were also temporarily installed in the LaRC CSI test structure. Damping factors in the 50 percent category are being provided at vibration motions as small as 50 nm. The 'Arched Flexure' used in the D-Strut maximizes the volumetric stiffness parameter relative to its axial stiffness. In turn, this enables high damping factors, even in a very rigid truss structure. This paper includes a presentation and discussion of both element and system test data taken at JPL, LaRC, and MIT. Also provided is a detailed description of the D-Strut, the dynamic model, and several graphs showing design parameter variations that will make it possible to evaluate the D-Strut for other applications.

Davis, L. P.↗

Predicting interface structure using the minima hopping method

Here, we adapt the minima hopping method (MHM) to the problem of interfacial structure prediction and apply it to study a canonical problem, the tilt grain boundaries in SrTiO 3 . Our method employs a hybrid approach by first exploring the potential energy surface (PES) of different grain boundary samplings with an empirical force field, among which the fifteen candidates with lower energies are then refined using ab initio density functional theory (DFT) calculations. During the exploratory stage, we bias the search using a local order parameter to primarily sample various reconstructions in the vicinity of the interface, while preserving the crystallinity of the bulk regions. We further enhance the search by incorporating initial structures with rigid body displacements to account for translational variations between bulk phases, enabling the MHM to effectively generate both stoichiometric and nonstoichiometric SrTiO 3 Σ⁢3(111)[110] and Σ⁢3(112)[110] grain boundaries. From an algorithmic standpoint, MHM outperforms earlier studies based on genetic algorithms (GA) by identifying more stable interfacial structures of several SrTiO 3 grain boundaries. The performance of the present implementation of the MHM approach is primarily limited by exploring an approximate description of the PES with a rather simple Buckingham potential. This limitation leads to variations in performance when compared to approaches utilizing more advanced surrogate PES models, such as direct DFT-PES sampling or GA with the embedded atom method (EAM). Despite the present limitations, the MHM approach is able to yield interfacial structures with comparable or lower interfacial energies in specific cases, such as Σ⁢3(111)[110] Γ=1, ±0.5 and Σ⁢3(112)[110] Γ= ±1, −2, underscoring the robustness of the MHM approach even with a simple approximation of the DFT PES. The MHM interfacial structure prediction method thus offers an efficient approach to understanding the grain boundaries and heterointerfaces at the atomic scale, providing an important prerequisite for effective materials design.

density functional theory↗

Inflatable Softgoods Testing Capability Development for Habitation

The Habitation Systems Development Office (HP40) at NASA Marshall Space Flight Center supports systems engineering, integration, and project management for next generation space habitats. The office is responsible for formulation activities for Lunar Surface Habitat and Mars Transit Habitat. HP40 also manages commercial partnerships for exploration habitat development. The Lunar Surface Habitat is intended to initially support a minimum of two crew on the lunar surface for an approximately 30-day mission, with the ability to accommodate four crew for short durations. The Mars Transit Habitat will transport four crew to and from Mars orbit on a potentially 1,200 day mission. Both concepts are envisioned to leverage inflatable softgoods as the primary structural material for the habitation portion of the architecture. Inflatable softgoods are a complex, multi-material system consisting of multiple layers which perform specific functions. A bladder layer (polymer) contains the habitat’s atmosphere. The bladder is indexed to a woven restraint layer, usually Kevlar or Vectran, which serves as the structural layer. The remaining outer layers are for micro-meteoroid orbital debris (MMOD) shielding, protection from atomic Oxygen (if the material system is to be deployed in low earth orbit), and thermal insulation. The primary advantage of inflatable softgoods is that they can offer a larger volume per unit mass relative to a rigid metal structure. Inflatable softgoods have a strong development heritage within NASA, beginning with work in the 1960s in partnership with Goodyear Aerospace and continuing with Johnson Space Center’s TransHab project in the 1990s . Some development efforts subsequently transitioned into the private sector to mature the material technology for flight applications, including human habitation. In August 2022, NASA published its guidelines for certification of crewed inflatable softgoods structures (JSC-67721). This document outlines a series of tests which will be needed to certify inflatable softgoods material systems for use in crewed mission applications. It includes burst testing at the subscale and full-scale to determine the ultimate burst pressure of the softgoods architecture. Creep (long term deformation of the material under stress) is a key failure mode which must be characterized. Creep testing at the component and module levels is also recommended to generate time to failure curves and verify that the inflatable system has a predicted operational life which exceeds mission parameters. ET (Test Engineering) at MSFC and HP40 have worked together to establish softgoods testing capabilities for the center. This includes the ability to conduct module level burst tests and creep tests. The poster will highlight these capabilities and provide examples of testing which has been performed to date by ET. NASA MSFC anticipates that these test capabilities will continue to offer critical support for companies pursuing inflatable softgoods for exploration applications (lunar surface habitation, Mars transit) as well as commercial low earth orbit platforms.

habitation↗

Compatibility of Fuel System Elastomers and Plastics with a Fast-Pyrolysis Oil (Bio-oil) at Room Temperature

Herein the compatibility of a fast-pyrolysis bio-oil with 17 elastomer and 21 plastic materials common to fuel storage, dispensing, and delivery systems was assessed by measuring volume and hardness. Diesel was used as the baseline for comparison. The elastomer and plastic specimens were exposed to the test fuels at 23 °C. The exposure times were 4 and 16 weeks for the elastomers and plastics, respectively. The elastomers (except for silicone and styrene butadiene) exhibited pronounced swelling in the bio-oil. This was especially true for the fluorocarbons and acrylonitrile rubbers. For the elastomers, a strong correlation between polarity and volume swell was observed. Compositional and structural analysis on one of the fluorocarbon materials showed that the bio-oil was less effective at extracting phthalate additives than the diesel. However, the crystallinity of a fluorocarbon was altered by the bio-oil. Unlike the elastomers, the plastic materials were less impacted by exposure to the bio-oil. This finding is attributed to their denser and more rigid molecular structures (compared to the elastomers). Notable swelling did occur in the nylons, but this swelling was attributed to water absorption rather than polarity. Comparison with previous studies showed that the observed swelling was lower for both the elastomers and the plastics. Solubility (and hence swell) increases with temperature, and because this study was conducted at 23 °C rather than 50 °C, the reduced temperature is responsible for the lower swell levels.

09 BIOMASS FUELS↗

Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

New interaction potentials for alkaline earth silicate and borate glasses

New interaction potentials were developed for molecular dynamics simulations to study the role of Mg and Ca in modifying the structure and properties of alkaline earth silicates and borates. Competition between the depolymerization of the silica network and the formation of new bonds between oxygen atoms and modifiers leads to the enhancement of the elastic moduli with increasing modifier content in alkaline earth silicate glasses. Compared with calcium silicate, the higher elastic moduli of magnesium silicate result from a higher connectivity of the overall glass network due to the incorporation of fourfold coordinated magnesium and a more rigid connection between oxygen atoms and modifiers. In contrast to the silicates, the effect of modifier on the elastic moduli of alkaline earth borates is dominated by the formation of fourfold coordinated boron (N 4 ). Calcium borate with higher N 4 shows a more rigid network structure and higher elastic moduli.

36 MATERIALS SCIENCE↗

Enhancement in Open-Circuit Voltage in Organic Solar Cells by Using Ladder-Type Nonfullerene Acceptors

The open-circuit voltage (V oc ) loss has always been a major factor in lowering power conversion efficiencies (PCEs) in bulk heterojunction organic photovoltaic cells (OPVs). A method to improve the V oc is indispensable to achieve high PCEs. Here in this paper, we investigated a series of perylene diimide-based ladder-type molecules as electron acceptors in nonfullerene OPVs. The D-A ladder-type structures described here lock our pi-systems into a planar structure and eliminate bond twisting associated with linear conjugated systems. This enlarges the interface energy gap (ΔE DA ), extends electronic delocalization, and hence improves the V oc . More importantly, these devices showed an increase in V oc without compromising either the J sc or the FF. C5r exhibited a strong intermolecular interaction and a PCE value of 6.1%. Moreover, grazing-incident wide-angle X-ray scattering analysis and atomic force microscopy images suggested that our fused-ring acceptors showed a suitable domain size and uniform blend films, which were not affected by their rigid molecular structures.

25 ENERGY STORAGE↗

Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.

59 BASIC BIOLOGICAL SCIENCES↗