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At least 1,045 records · Page 58

Rational Enzyme Design for Controlled Functionalization of Acetylated Xylan for Cell-Free Polymer Biosynthesis

Xylan O-acetyltransferase 1 (XOAT1) is involved in O-acetylating the backbone of hemicellulose xylan. Recent structural analysis of XOAT1 showed two unequal lobes forming a cleft that is predicted to accommodate and position xylan acceptors into proximity with the catalytic triad. Here, we used docking and molecular dynamics simulations to investigate the optimal orientation of xylan in the binding cleft of XOAT1 and identify putative key residues (Gln445 and Arg444 on Minor lobe & Asn312, Met311 and Asp403 on Major lobe) involved in substrate interactions. Site-directed mutagenesis coupled with biochemical analyses revealed the major lobe of XOAT1 is important for xylan binding. Mutation of single key residues yielded XOAT1 variants with various enzymatic efficiencies that are applicable to one-pot synthesis of xylan polymers with different degrees of O-acetylation. Taken together, our results demonstrate the effectiveness of computational modeling in guiding enzyme engineering aimed at modulating xylan and redesigning plant cell walls.

93 SC - Biological and Environmental Research (BER↗

Renewable Epoxy Thermosets from Fully Lignin-Derived Triphenols

A series of fully renewable triphenols (TPs) with various number of methoxy group substituents (n = 0–6) were synthesized using lignin-derived phenols (guaiacol and 2,6-dimethoxyphenol) and aldehydes (4-hydroxybenzaldehyde, vanillin, and syringaldehyde). The structural evolution from TPs to epoxy thermosets was followed by nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopy. Thermomechanical properties of the resulting epoxy thermosets were investigated by dynamic mechanical analysis (DMA), tensile analysis (TA), and thermogravimetric analysis (TGA). Increasing the content of methoxy groups decreased the glass transition temperature (132–118 °C) and glassy modulus (2.7–2.2 GPa). Thermal stability of high-methoxy-content thermosets was reduced due to electron-donating effects and higher oxygen content. Conversions and isolated yields of TPs significantly decreased as the number of methoxy substituents increased, which markedly determined the feasibility of TPs as precursors for polymers. This work widens the synthesis route of fully lignin-derived polyphenols, yielding polymers with thermomechanical properties comparable to bisphenol A (BPA) based materials. Finally, evaluation of methoxy substitution provides insight for the selection of lignin-derived monomers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Capturing dynamical correlations using implicit neural representations

Abstract Understanding the nature and origin of collective excitations in materials is of fundamental importance for unraveling the underlying physics of a many-body system. Excitation spectra are usually obtained by measuring the dynamical structure factor, S ( Q , ω ), using inelastic neutron or x-ray scattering techniques and are analyzed by comparing the experimental results against calculated predictions. We introduce a data-driven analysis tool which leverages ‘neural implicit representations’ that are specifically tailored for handling spectrographic measurements and are able to efficiently obtain unknown parameters from experimental data via automatic differentiation. In this work, we employ linear spin wave theory simulations to train a machine learning platform, enabling precise exchange parameter extraction from inelastic neutron scattering data on the square-lattice spin-1 antiferromagnet La 2 NiO 4 , showcasing a viable pathway towards automatic refinement of advanced models for ordered magnetic systems.

36 MATERIALS SCIENCE↗

Induced polarization restricts the conformational distribution of a light-harvesting molecular triad in the ground state

The light-harvesting molecular triad consisting of carotenoid polyene (C), diaryl-porphyrin (P) and pyrrole-fullerene (C60) is a donor–acceptor molecule capable of absorbing incident light in the visible range. Its ability to convert solar energy to electrical excitation and charge separation energy suggests a great potential in real-world applications. The ensemble of its conformations under ambient conditions varies widely according to its electronic state. In previous work, we applied a non-polarizable model to study the conformational distribution of the molecular triad in the ground and charge separated states. However, due to the lack of polarization, which imparts subtle changes in the charge distribution on atoms, molecular simulations fail to produce accurate average dipole moments. We developed the first polarizable model for a molecular triad to investigate the structural and dynamic properties of a molecular triad in the ground state in an explicit organic solvent, tetrahydrofuran (THF). We performed first-principles electronic structure calculations of the individual components in the triad as well as THF and then fit the partial atomic charges to the electrostatic potential using the i-RESP methodology. We validated these force field parameters by comparing the thermodynamic and dynamic properties obtained from molecular dynamics simulations with those from experiments. We enhanced the sampling of the triad conformations with replica exchange molecular dynamics simulations. We characterized the effects of induced polarization on the structural stability of the triad by analyzing the free energy landscapes constructed with polarizable force fields. Furthermore, by using principal component analysis, we found that the molecular triad conformations adopted a small range of torsional angles with induced polarization. The triad conformation solvated in polar solvent with a polarizable force field qualitatively agrees with that obtained from nuclear magnetic resonance spectroscopy.

Starovoytov, Oleg N.↗

Dynamics and density distributions in a capillary-discharge waveguide with an embedded supersonic jet

We present an analysis of the gas dynamics and density distributions within a capillary-discharge waveguide with an embedded supersonic jet. This device provides a target for a laser plasma accelerator which uses longitudinal structuring of the gas-density profile to enable control of electron trapping and acceleration. The functionality of the device depends sensitively on the details of the density profile, which are determined by the interaction between the pulsed gas in the jet and the continuously-flowing gas in the capillary. These dynamics are captured by spatially resolving recombination light from several emission lines of the plasma as a function of the delay between the jet and the discharge. We provide a phenomenological description of the gas dynamics as well as a quantitative evaluation of the density evolution. In particular, we show that the pressure difference between the jet and the capillary defines three regimes of operation with qualitatively different longitudinal density profiles and show that jet timing provides a sensitive method for tuning between these regimes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Jet charge with global event shapes: Probing quark flavor dynamics

We propose measuring the jet electric charge of jet regions, defined within the framework of global event shapes, as a probe of quark flavor dynamics within the nucleon and the hadronization process. In particular, we consider a measurement of the jet region charge while simultaneously keeping track of the energy flow throughout the event, as characterized by the global event shape. As a concrete example, we focus on the measurement of the (Q), the jet charge of the jet region (𝐽) defined within the framework of the 1-Jettiness global event shape (𝜏 1 ) for the Deep Inelastic Scattering (DIS) process, 𝑒 − +𝑝→𝑒 − +𝐽+𝑋, with unpolarized or longitudinally polarized protons. The 1-Jettiness distribution, binned according to jet charge, allows for enhanced quark flavor separation of the initial state unpolarized or polarized PDFs. On the other hand, the jet charge distribution binned by 1-Jettiness can serve as a probe of quark flavor dynamics in the final state hadronization process. We derive a factorization theorem for simultaneous measurements of 𝜏 1 and Q in the resummation region, 𝜏 1 ≪𝑃 𝐽 𝑇 , where 𝑃 𝐽 𝑇 denotes the transverse momentum of the jet region. The correlation between the jet region charge and the charge of the struck quark is expected to be the strongest in the resummation region. The factorization theorem contains a new universal , generalizing the standard jet function to include a jet charge measurement. Therefore these universal functions can be extracted from a global analysis of N-jettiness and thrust at 𝑒 + ⁢𝑒 − colliders. We provide simulation studies to demonstrate the sensitivity of the 1-Jettiness jet charge observable to quark flavor dynamics in nucleon structure and explore the possibility of probing the final state hadronization process. This observable is well-suited for applications with existing HERA data and the future Electron-Ion Collider (EIC).

Mantry, Sonny [University of North Georgia, Dahlon↗

Effects of γ-Radiation and Addition of Silicone Dioxide on the Properties of Polytetrafluoroethylene

We perform a comparative study of melting of polytetrafluoroethylene (PTFE) in its unmodified form, after irradiation, and after adding plant-derived silicon dioxide as an additive (content, 1%). Calculation of peak shapes on thermal capacity profiles within the theory of smeared phase transitions enable us to identify the structural changes and their features resulting from irradiation of PTFE and incorporation of the additive in it. α-relaxation at the glass transition in our samples is studied by dynamic mechanical analysis.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Computational Tools and Techniques for Modeling of Heterogeneous Materials

The specific goal of this CRADA was the development of computational tools and techniques for meso-to-macroscale modeling of transport processes to predict bulk properties of particulate and composite-based heterogeneous materials. These computational tools are particularly useful in exploring the relationship between a product's constituent materials, manufacturing process, resulting microstructure and bulk properties. The specific results of this project are: (i) advancements to the granular package and rigid body capability of the particle dynamics software, LAMMPS, for simulating fine cohesive particles and non-spherical granular particles; (ii) a software tool kit, documentation, and tutorials for statistical characterization, artificial reconstruction, and property-structure model analysis of material microstructure.

Lechman, Jeremy↗

Investigation into the instantaneous centre of rotation for enhanced design of floating offshore wind turbines

The dynamic behaviour of floating offshore wind turbines (FOWTs) involves complex interactions of multivariate loads from wind, waves, and currents, which result in complex motion characteristics. Although methods for analysing global motion responses are well-established, the time- and location-dependent kinematics remain underexplored. This paper investigates the instantaneous centre of rotation (ICR), a point of zero velocity at a time instance of general plane motion. Understanding and strategically positioning the ICR can reduce the dynamic motion in critical structural locations, enhancing the performance and structural robustness of FOWTs. The paper presents a method for computing the ICR using time-domain simulation results and proposes a statistical analysis approach suitable for design studies. Building on prior research, it examines the sensitivity of the ICR to external loading and design features, providing insights into how these factors influence motion response and how the motion response influences the statistics of the ICR, structural loads, and other performance metrics of interest. The study explores two FOWT configurations, a spar and a semisubmersible, identifying design variables that most effectively control the ICR statistics and identifying the ICR statistics most correlated with the responses of interest. Finally, through two case studies, we demonstrate how to apply these new insights in a practical design scenario. By adjusting the design variables most correlated with the ICR (fairlead vertical position and centre of mass for the spar and mooring line length and offset column diameter for the semisubmersible), we successfully modified the designs of the floating support structures to reduce the loads in the mooring lines, tower base, and blade roots, improving the ultimate strength and fatigue characteristics compared to the original designs.

17 WIND ENERGY↗

Strengthening of the Coordination Shell by Counter Ions in Aqueous Th 4+ Solutions

The presence of counter ions in solutions containing highly charged metal cations can trigger processes such as ion-pair formation, hydrogen bond breakages and subsequent reformation, and ligand exchanges. In this work, it is shown how halide (Cl-, Br-) and perchlorate (ClO4-) anions affect the strength of the primary solvent coordination shells around Th4+ using explicit solvent and finite temperature ab initio molecular dynamics modeling methods. The 9-fold solvent geometry was found to be the most stable hydration structure in each aqueous solution. Relative to the dilute aqueous solution, the presence of the counter ions did not significantly alter the geometry of the primary hydration shell. However, the free energy analyses indicated that the 10-fold hydrated states were thermodynamically accessible in dilute and bromide aqueous solutions within 1 kcal/mol. Analysis of the results showed that the hydrogen bond lifetimes were longer and solvent exchange energy barriers were larger in solutions with counter ions in comparison with the solution with no counter ions. This implies that the presence of the counter ions induces a strengthening of the Th4+ hydration shell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Efficiency analysis of helium-cooled MAS DNP: case studies of surface-modified nanoparticles and homogeneous small-molecule solutions

Despite the growing number of successful applications of dynamic nuclear polarization (DNP)-enhanced magic-angle spinning (MAS) NMR in structural biology and materials science, the nuclear polarizations achieved by current MAS DNP instrumentation are still considerably lower than the theoretical maximum. Here, the method could be significantly strengthened if experiments were performed at temperatures much lower than those currently widely used (~100 K). Recently, the prospects of helium (He)-cooled MAS DNP have been increased with the instrumental developments in MAS technology that uses cold helium gas for sample cooling. Despite the additional gains in sensitivity that have been observed with He-cooled MAS DNP, the performance of the technique has not been evaluated in the case of surfaces and interfaces that benefit the most from DNP. Herein, we studied the efficiency of DNP at temperatures between ~30 K and ~100 K for organically functionalized silica material and a homogeneous solution of small organic molecules at a magnetic field B 0 = 16.4 T. We recorded the changes in signal enhancement, paramagnet-induced quenching and depolarization effects, DNP build-up rate, and Boltzmann polarization. For these samples, the increases in MAS-induced depolarization and DNP build-up times at around 30 K were not as severe as anticipated. In the case of the surface species, we determined that MAS DNP at 30 K provided ~10 times higher sensitivity than MAS DNP at 90 K, which corresponds to the acceleration of experiments by multiplicative factors of up to 100.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Decoding the Mechanisms of Phase Transitions from In Situ Microscopy Observations

Abstract Analysis of the temperature‐ and stimulus‐dependent imaging data toward elucidation of the physical transformations is an ubiquitous problem in multiple fields. Here, temperature‐induced phase transition in BaTiO 3 is explored using the machine learning analysis of domain morphologies visualized via variable‐temperature scanning transmission electron microscopy (STEM) imaging data. This approach is based on the multivariate statistical analysis of the time or temperature dependence of the statistical descriptors of the system, derived in turn from the categorical classification of observed domain structures or projection on the continuous parameter space of the feature extraction‐dimensionality reduction transform. The proposed workflow offers a powerful tool for the exploration of the dynamic data based on the statistics of image representation as a function of the external control variable to visualize the transformation pathways during phase transitions and chemical reactions. This can include the mesoscopic STEM data as demonstrated here, but also optical, chemical imaging, etc., data. It can further be extended to the higher dimensional spaces, for example, analysis of the combinatorial libraries of materials compositions.

Valleti, Sai Mani Prudhvi↗

Numerical insight into the seismic behavior of eight masonry towers in Northern Italy: FE pushover vs non-linear dynamic analyses

This study presents some FE results regarding the behavior under horizontal loads of eight existing masonry towers located in the North-East of Italy. The towers, albeit unique for geometric and architectural features, show some affinities which justify a comparative analysis, as for instance the location and the similar masonry material. Their structural behavior under horizontal loads is therefore influenced by geometrical issues, such as slenderness, walls thickness, perforations, irregularities, presence of internal vaults, etc., all features which may be responsible for a peculiar output. The geometry of the towers is deduced from both existing available documentation and in-situ surveys. On the basis of such geometrical data, a detailed 3D realistic mesh is conceived, with a point by point characterization of each single geometric element. The FE models are analysed under seismic loads acting along geometric axes of the plan section, both under non-linear static (pushover) and non-linear dynamic excitation assumptions. A damage-plasticity material model exhibiting softening in both tension and compression, already available in the commercial code Abaqus, is used for masonry. Pushover analyses are performed with both G1 and G2 horizontal loads distribution, according to Italian code requirements, along X+/− and Y+/− directions. Non-linear dynamic analyses are performed along both X and Y directions with a real accelerogram scaled to different peak ground accelerations. Some few results are presented in this paper. It is found that the results obtained with pushover analyses reasonably well fit expensive non-linear dynamic simulations, with a slightly less conservative trend.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Computational Analysis of Hydraulic Efficiency of Michigan DOT Cover C

Drainage structures are used to capture stormwater runoff in streets and highways in urban environments. These drainage structures, which typically consist of catch basins with grates, inlets, or combination grates/inlets, collect stormwater runoff and discharge through buried conveyance systems. They are strategically placed for public safety in curb and gutter systems to provide efficient drainage of water from roadways and thus reduce the risk of hydroplaning. The performance of drainage structures is measured in terms of hydraulic efficiency, which is defined as the percentage of flow captured by the basin as compared to the total flow drainage to the structure. Understanding of the performance of these drainage structures helps designers properly space inlets to promote an economic design that ensures the safety of the traveling public. The current design methodology used to determine drainage structure follows guidelines established in the current Michigan Department of Transportation (MDOT) Drainage Manual (2006). The guidelines in the MDOT Drainage Manual were modeled after the Federal Highway Administration’s (FHWA) Hydraulic Engineering Circular 22 “Urban Drainage Design” (HEC-22). HEC-22 includes empirically derived equations to calculate the interception capacity of drainage structures for several commonly used grate configurations, such as the parallel bar, curved vane and tilt bar grates, which are based on a research study performed by Burgi et al. in the 1970s. MDOT uses several drainage structures to capture runoff that are detailed as Standard Plans. Many of these drainage structures utilize sinusoidal type grates that are not described in HEC-22. Physical modeling of these structures has been limited, posing the need to have them analyzed to verify their capture efficiency. Current MDOT practice is to assume a similar sized reticuline grate, as described in HEC-22, for capture efficiencies. Until recently, evaluating the hydraulic performance of drainage structures was limited to physical modeling in a hydraulics laboratory. With advances in engineering software and computing power, computational fluid dynamics (CFD) modeling has become a more cost-effective alternative. The Federal Highway Administration (FHWA) provides states the option to evaluate their drainage structures using CFD through the Transportation Pooled Fund Program. This study, “Computational Analysis of Hydraulic Efficiency of Michigan DOT Cover C,” was carried out using the pooled fund. MDOT’s Cover C was chosen as the first test candidate, given its similar sinusoidal pattern to other MDOT grates, but it is typically used for high-volume, higher speed applications. A similar version, Cover CX, is used on interstate highways but does not have traverse bars for bicycle safety. Additional grates may be considered for evaluation in the future.

42 ENGINEERING↗

Data publication with the structural biology data grid supports live analysis

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

59 BASIC BIOLOGICAL SCIENCES↗

Direct numerical simulations of turbulent premixed cool flames: Global and local flame dynamics analysis

The cool flame dynamics, especially in turbulent flows, is of great interest for both practical application and fundamental research. Here, in this study, a series of direct numerical simulations of turbulent premixed n-C 7 H 16 /O 2 /O 3 /N 2 cool flames are performed, with the focus on the influence of turbulence intensity (u'/S L , where S L is the laminar flame speed) on the flame structure as well as the global and local cool flame dynamics. It is found that the cool flame front is considerably wrinkled by turbulence at high u'/S L , leading to significantly thickened turbulent cool flame brush and largely altered local reactivity compared with the reference laminar flame. However, the turbulent flame structure in the temperature space is found to be insensitive to u'/S L . Besides, with increasing u'/S L , the normalized turbulent cool flame speed (S L /S L ) is monotonically increased, attributed to substantial augmentation on the flame surface area (A T /A L ), while the stretching factor (I 0 ) remains almost constant and is smaller than 1. The underlying mechanisms for such variations are revealed through local flame dynamics analysis. Specifically, the local flame displacement speed S d is found to be strongly negatively correlated with flame curvature; meanwhile, such negative correlation and the probability distribution function (PDF) of flame curvature are barely influenced by u'/S L , leading to a weak dependence of I 0 on u'/S L . In contrast, the PDF of the tangential strain rate is found to span a much wider range and shift to the positive side as u'/S L increases, suggesting that the enhanced tangential strain rate is the main cause for the increase in surface area of the turbulent premixed cool flame. Finally, the influence of equivalence ratio on above findings is found to be insignificant, indicating that although the local reactivity of turbulent premixed cool flames is altered due to the differential diffusion, the resultant flame- stretch interaction is insensitive to the equivalence ratio. This study presents some unique cool flame dynamics that are distinct from hot flames, which can help improve the understanding and modeling of turbulent cool flames.

Cool flames↗

Air Flow Modeling in the Wind Tunnel of the FHWA Aerodynamics Laboratory at Turner-Fairbank Highway Research Center

Computational fluid dynamics (CFD) modeling is widely used in industry for design and in the research community to support, compliment, and extend the scope of experimental studies. Analysis of transportation infrastructure using high performance cluster computing with CFD and structural mechanics software is done at the Transportation Research and Analysis Computing Center (TRACC) at Argonne National Laboratory. These resources, available at TRACC, were used to perform advanced three-dimensional computational simulations of the wind tunnel laboratory at the Turner-Fairbank Highway Research Center (TFHRC). The goals were to verify the CFD model of the laboratory wind tunnel and then to use versions of the model to provide the capability to (1) perform larger parametric series of tests than can be easily done in the laboratory with available budget and time, (2) to extend testing to wind speeds that cannot be achieved in the laboratory, and (3) to run types of tests that are very difficult or impossible to run in the laboratory. Modern CFD software has many physics models and domain meshing options. Models, including the choice of turbulence and other physics models and settings, the computational mesh, and the solver settings, need to be validated against measurements to verify that the results are sufficiently accurate for use in engineering applications. The wind tunnel model was built and tested, by comparing to experimental measurements, to provide a valuable tool to perform these types of studies in the future as a complement and extension to TFHRC’s experimental capabilities. Wind tunnel testing at TFHRC is conducted in a subsonic open-jet wind tunnel with a 1.83 m (6 foot) by 1.83 m (6 foot) cross section. A three component dual force-balance system is used to measure forces acting on tested models, and a three degree of freedom suspension system is used for dynamic response tests. Pictures of the room are shown in Figure 1-1 to Figure 1-4. A detailed CAD geometry and CFD model of the wind tunnel laboratory at TFHRC was built and tested. Results were compared against experimental wind velocity measurements at a large number of locations around the room. This testing included an assessment of the air flow uniformity provided by the tunnel to the test zone and assessment of room geometry effects, such as influence of the proximity the room walls, the non-symmetrical position of the tunnel in the room, and the influence of the room setup on the air flow in the room. This information is useful both for simplifying the computational model and in deciding whether or not moving, or removing, some of the furniture or other movable objects in the room will change the flow in the test zone.

97 MATHEMATICS AND COMPUTING↗