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At least 163 records · Page 9

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

Computationally designed multi-subunit assemblies have shown considerable promise for a variety of applications, including a new generation of potent vaccines. One of the major routes to such materials is rigid body sequence-independent docking of cyclic oligomers into architectures with point group or lattice symmetries. Current methods for docking and designing such assemblies are tailored to specific classes of symmetry and are difficult to modify for novel applications. Here we describe RPXDock, a fast, flexible, and modular software package for sequence-independent rigid-body protein docking across a wide range of symmetric architectures that is easily customizable for further development. RPXDock uses an efficient hierarchical search and a residue-pair transform ( RPX ) scoring method to rapidly search through multidimensional docking space. We describe the structure of the software, provide practical guidelines for its use, and describe the available functionalities including a variety of score functions and filtering tools that can be used to guide and refine docking results towards desired configurations.

59 BASIC BIOLOGICAL SCIENCES↗

X-ray beam method for displacement measurement in hostile environments

A new method of extensometry using an X-ray beam was devised, and the results of current testing reveal it to be highly feasible. This technique has been shown to provide a non-contacting system that is immune to problems associated with density variations in gaseous environments, that plague currently available optical methods. This advantage is a result of the non-refracting penetrating nature of X-rays. The method is based on X-ray-induced X-ray fluorescence of targets, which subsequently serve as fudicial markers. Some target materials have melting points over 1600 degrees C which will facilitate measurement at extremely high temperatures. A highly focused intense X-ray beam, which is produced using a Johansen 'bent crystal', is then scanned across the target, which responds by fluorescing X-rays when stimulated by the incident beam. This secondary radiation is monitored using a detector. By carefully measuring beam orientation, change in target edge position can be determined. Many variations on this basic theme are now possible such as two targets demarcating a gage length, or a beam shadowing method using opaque targets.

Jordan, Eric H.↗

On the Onset of Plasticity: Determination of Strength and Ductility

The analysis of the work hardening variation with stress reveals insight to operative stress-strain mechanisms in material systems. The onset of plasticity can be assessed and related to ensuing plastic deformation up to the structural instability using one constitutive relationship that incorporates both behaviors of rapid work hardening (Stage 3) and the asymptotic leveling of stress (Stage 4). Results are presented for the mechanical behavior analysis of Ti-6Al-4V wherein the work hardening variation of Stages 3 and 4 are found to: be dependent through a constitutive relationship; be useful in a Hall-Petch formulation of yield strength; and provide the basis for a two point-slope fit method to model the experimental work hardening and stress-strain behavior.

36 MATERIALS SCIENCE↗

Rapid simulations of hyperspectral near-field images of three-dimensional heterogeneous surfaces

The scattering-type scanning near-field optical microscope (s-SNOM) has emerged as a powerful tool for resolving nanoscale inhomogeneities in laterally heterogeneous samples. However, most analytical models used to predict the scattering near-field signals are assuming homogenous landscapes (bulk materials), resulting in inconsistencies when applied to samples with more complex configurations. In this work, we combine the point-dipole model (PDM) to the finite-element method (FEM) to account for the lateral and vertical heterogeneities while keeping the computation time manageable. Full images, spectra, or hyperspectral line profiles can be simulated by calculating the self-consistent dipole radiation demodulated at higher harmonics of the tip oscillation, mimicking real experimental procedures. Using this formalism, we clarify several important yet puzzling experimental observations in near-field images on samples with rich typography and complex material compositions, heterostructures of two-dimensional material flakes, and plasmonic antennas. The developed method serves as a basis for future investigations of nano-systems with nontrivial topography.

36 MATERIALS SCIENCE↗

The Defects Genome of Janus Transition Metal Dichalcogenides

2D Janus Transition Metal Dichalcogenides (TMDs) have attracted much interest due to their exciting quantum properties arising from their unique two-faced structure, broken-mirror symmetry, and consequent colossal polarization field within the monolayer. While efforts are made to achieve high-quality Janus monolayers, the existing methods rely on highly energetic processes that introduce unwanted grain-boundary and point defects with still unexplored effects on the material's structural and excitonic properties Through high-resolution scanning transmission electron microscopy (HRSTEM), density functional theory (DFT), and optical spectroscopy measurements; this work introduces the most encountered and energetically stable point defects. It establishes their impact on the material's optical properties. HRSTEM studies show that the most energetically stable point defects are single (V S and V Se ) and double chalcogen vacancy (V S −V Se ), interstitial defects (Mi), and metal impurities (MW) and establish their structural characteristics. DFT further establishes their formation energies and related localized bands within the forbidden band. Cryogenic excitonic studies on h-BN-encapsulated Janus monolayers offer a clear correlation between these structural defects and observed emission features, which closely align with the results of the theory. Finally, the overall results introduce the defect genome of Janus TMDs as an essential guideline for assessing their structural quality and device properties.

2D materials↗

A Special Investigation to Develop a General Method for Three-dimensional Photoelastic Stress Analysis

The method of strain measurement after annealing is reviewed and found to be satisfactory for the materials available in this country. A new general method is described for the photoelastic determination of the principal stresses at any point of a general body subjected to arbitrary load. The method has been applied to a sphere subjected to diametrical compressive loads. The results show possibilities of high accuracy.

Frocht, M M↗

X-Ray Moire Techniques For Measuring Strain

X-ray moire method provides for measurement of strains throughout relatively large regions and in locations invisible or inaccessible to measurement by other techniques. For example, used to measure strains between layers of material in rubber tires. Method exploits body of knowledge already developed for optical moire measurement of strains. Offers advantages over optical methods of measuring strains within depths of objects, in that x-ray imaging not restricted to optically transparent materials. Also offers advantages over strain-gauge method that gauge wires not needed and measurements not limited to discrete gauge points.

Madaras, Eric Irvine↗

A Framework for Performing Multiscale Stochastic Progressive Failure Analysis of Composite Structures

A framework is presented that enables coupled multiscale analysis of composite structures. The recently developed, free, Finite Element Analysis - Micromechanics Analysis Code (FEAMAC) software couples the Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) with ABAQUS to perform micromechanics based FEA such that the nonlinear composite material response at each integration point is modeled at each increment by MAC/GMC. As a result, the stochastic nature of fiber breakage in composites can be simulated through incorporation of an appropriate damage and failure model that operates within MAC/GMC on the level of the fiber. Results are presented for the progressive failure analysis of a titanium matrix composite tensile specimen that illustrate the power and utility of the framework and address the techniques needed to model the statistical nature of the problem properly. In particular, it is shown that incorporating fiber strength randomness on multiple scales improves the quality of the simulation by enabling failure at locations other than those associated with structural level stress risers.

Bednarcyk, Brett A.↗

A Framework for Performing Multiscale Stochastic Progressive Failure Analysis of Composite Structures

A framework is presented that enables coupled multiscale analysis of composite structures. The recently developed, free, Finite Element Analysis-Micromechanics Analysis Code (FEAMAC) software couples the Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) with ABAQUS to perform micromechanics based FEA such that the nonlinear composite material response at each integration point is modeled at each increment by MAC/GMC. As a result, the stochastic nature of fiber breakage in composites can be simulated through incorporation of an appropriate damage and failure model that operates within MAC/GMC on the level of the fiber. Results are presented for the progressive failure analysis of a titanium matrix composite tensile specimen that illustrate the power and utility of the framework and address the techniques needed to model the statistical nature of the problem properly. In particular, it is shown that incorporating fiber strength randomness on multiple scales improves the quality of the simulation by enabling failure at locations other than those associated with structural level stress risers.

Bednarcyk, Brett A.↗

Integrating Manned Aircraft and UAVs for the Prediction, Tracking, and Eradication of Desert Locust Swarms

Desert locusts (Schistocerca gregaria) present an acute threat to the agriculture of certain regions, capable of annihilating vast expanses of farmland and destabilizing food security. In this paper, an aviation-based framework concept is introduced that integrates both manned aircraft and Unmanned Aerial Vehicles (UAVs) to preemptively forecast, localize, and eliminate locust swarms efficiently. The framework begins by leveraging predictive modeling methods to refine search areas and pinpoint high-value Points of Interest (POIs) where locust swarms are most likely to materialize. From there, the proposed two-step model uses optical, infrared, and hyperspectral sensors onboard manned aircraft to conduct long-range surveying of probable swarm locations. Upon detection of a swarm, UAVs equipped with sophisticated sensors, including pheromone detectors, thermal and optical imaging systems, are deployed directly from the aircraft to carry out targeted biopesticide applications. This approach, which capitalizes on the combined strengths of both vehicles, provides the rapid response and large-scale intervention necessary to control locust outbreaks. By targeting locust swarms during their most destructive phase, this paper aims to disrupt the locust life cycle and mitigate their severe agricultural impact, offering a scalable and sustainable solution for food security in afflicted regions.

locust monitoring systems↗

Considerations to achieve directionality for gamma ray lasers

A method of alignment of nuclei for a gamma ray laser and a means of achieving preferential emission of radiation along the crystal axis are studied. Atomic alignment was achieved by materials researchers who made composite structures composed of needle-like single crystals all with the same orientation and all pointing in the same direction contained in a matrix of cobalt or nickel. The proposed method of preferential emission of radiation along the aligned needles is to have a symmetric field gradient at the nucleus and a sequence of excited levels of spin and parity 2(+) and 0(+). The proposed scheme reduces the density of excited states required for lasing and reduces the linewidth due to inhomogenous broadening. Mossbauer absorption experiments intended to test these ideas are outlined.

Jha, S.↗

Microstructural Influence on Deformation and Fatigue Life of Composites Using the Generalized Method of Cells

A fully coupled deformation and damage approach to modeling the response of composite materials and composite laminates is presented. It is based on the semi-­‐analytical generalized method of cells (GMC) micromechanics model as well as its higher fidelity counterpart, HFGMC, both of which provide closed-form constitutive equations for composite materials as well as the micro scale stress and strain fields in the composite phases. The provided constitutive equations allow GMC and HFGMC to function within a higher scale structural analysis (e.g., finite element analysis or lamination theory) to represent a composite material point, while the availability of the micro fields allow the incorporation of lower scale sub­‐models to represent local phenomena in the fiber and matrix. Further, GMC's formulation performs averaging when applying certain governing equations such that some degree of microscale field accuracy is surrendered in favor of extreme computational efficiency, rendering the method quite attractive as the centerpiece in a integrated computational material engineering (ICME) structural analysis; whereas HFGMC retains this microscale field accuracy, but at the price of significantly slower computational speed. Herein, the sensitivity of deformation and the fatigue life of graphite/epoxy PMC composites, with both ordered and disordered microstructures, has been investigated using this coupled deformation and damage micromechanics based approach. The local effects of fiber breakage and fatigue damage are included as sub‐models that operate on the microscale for the individual composite phases. For analysis of laminates, classical lamination theory is employed as the global or structural scale model, while GMC/HFGMC is embedded to operate on the microscale to simulate the behavior of the composite material within each laminate layer. A key outcome of this study is the statistical influence of microstructure and micromechanics idealization (GMC or HFGMC) on the overall accuracy of unidirectional and laminated composite deformation and fatigue response.

Microscale Models↗

Methods for manufacturing electrochemical sensors, and related electrochemical sensors

Methods for manufacturing an electrochemical sensor include forming at least one electrode by printing at least one conductive ink on a surface of at least one substrate. The conductive ink may comprise, e.g., a platinum-group metal, another transition-group metal with a high-temperature melting point, a conductive ceramic material, glass-like carbon, or a combination thereof. The electrochemical sensor may be free of another material over the at least one electrode. An electrochemical sensor, formed according to such methods, may be configured for use in harsh environments (e.g., a molten salt environment). Electrodes of the electrochemical sensor comprise conductive material formed from a printed, conductive ink. In some embodiments, at least a portion of the electrochemical sensor is free of silver, gold, copper, silicon, and polymer materials, such portion being that which is to be exposed to the harsh environment during use of the electrochemical sensor.

Shaltry, Michael R.↗

A Comprehensive Review on Finite Element Analysis of Laser Shock Peening

Laser shock peening (LSP) is a formidable cold working surface treatment that provides high-energy precision to enhance the mechanical properties of materials. This paper delves into the intricacies of the LSP process, offering insights into its methodology and the simulation thereof through the finite element method. This review critically examines various points, such as laser energy, overlapping of shots, effect of LSP on residual stress, effect of LSP on grain refinement, and algorithms for simulation extrapolated from finite element analyses conducted by researchers, shedding light on the nuanced considerations integral to this technique. As the significance of LSP continues to grow, the collective findings underscore its potential as a transformative technology for fortifying materials against mechanical stress and improving their overall performance and longevity. The discourse encapsulates the evolving landscape of the LSP, emphasizing the pivotal role played by finite element analysis in advancing our understanding and application of this innovative surface treatment.

36 MATERIALS SCIENCE↗

Dielectric screening and vacancy formation for large neutral and charged Si n H m ( n > 1500 ) nanocrystals using real-space pseudopotentials

A commonly used procedure for computing the properties of defects in crystalline materials is to consider a large supercell that includes the defect of interest. This is a straightforward technique as standard energy band codes can be used for such computations. For neutral defects, the only impediment of such an approach is to avoid defect-defect interactions between adjoining cells. However, this procedure can be complex if the defect of interest is charged as the system at large contains Coulombic divergences. Moreover, some have recently argued that the conventional definition of formation energies for charged defects cannot be reconciled with statistical mechanics. Here, we focus on an alternative approach. We consider large nanocrystals wherein a charged defect can be placed. Since the system is confined, a charged defect within the nanocrystal does not result in a Coulombic divergence. The chief impediment is computational, i.e., while no defect-defect or Coulombic divergences are present, the nanocrystal must be sufficiently large to allow the system to properly replicate a bulklike configuration. With the development of new algorithms and hardware advances, computations for systems of sufficient size to address this issue are feasible. In particular, we solve the Kohn-Sham equation in real space using pseudopotential-density-functional theory for large silicon nanocrystals, which contain thousands of atoms. Further, we focus on (i) the screening of a point charge and (ii) the formation of a charged vacancy in hydrogen-terminated silicon nanocrystals. This approach allows us to examine the role of quantum confinement in addition to exploring the bulk limit. Comparisons to other methods confirm the viability of this approach.

36 MATERIALS SCIENCE↗

Surface analysis insight note: Differentiation methods applicable to noisy data for determination of sp2‐ versus sp3‐hybridization of carbon allotropes and AES signal strengths

The derivatives of the spectra are commonly used for quantification in Auger Electron Spectroscopy (AES) spectra, while the derivative of the KLL C Auger line has proven to be valuable in obtaining a measure of the relative proportions of sp 2 ‐ and sp 3 ‐hybridization using the D‐parameter in both AES and X‐ray Photoelectron Spectroscopy (XPS). Differentiation of X‐ray Photoelectron Spectroscopy (XPS) and Auger Electron Spectroscopy (AES) spectra by numerical means is presented and illustrated for polymeric, such as PEEK and Nylon, as well as for graphitic materials including highly ordered pyrolytic graphite and graphene oxide. The most commonly available Savitzky–Golay method is explained mathematically and developed through the case of constructing a 5‐point quadratic polynomial convolution kernel suitable for differentiating spectra of adequate signal to noise. The concept of differentiation of spectra where signal to noise is less than adequate is also developed. Two alternative strategies to Savitzky–Golay differentiation are presented, which fit curves to data that allow derivatives to be obtained where Savitzky–Golay would otherwise fail. These alternative methods involve constructing a parametric curve that fits data over the entire energy interval of interest. Derivatives of spectra are then obtained by differentiating these parametric curves directly. A comparison of results for different materials for which specific sp 2 ‐ vs sp 3 ‐hybridized carbon proportions are of interest is used to emphasize the importance of characterizing methods used to differentiate spectra and understanding the characteristics of instrumentation used to measure spectra. The case for using Principal Component Analysis noise reduction with C KLL spectra is made for spectra collected from a heterogeneous graphene oxide sample.

Fairley, Neal↗

Efficacy of the Method of Four Coefficients to Determine Charge-Carrier Scattering

The investigation of the electronic properties of semiconductors from transport measurements (i.e., resistivity, Hall, and Seebeck coefficient measurements) is challenging due to the averaging of charge-carrier dynamics inherent in such measurements. Here, we investigate the incorporation of a fourth measurement of electronic transport, the Nernst coefficient, into the analysis, termed the method of four coefficients. This approach yields the Fermi level, effective mass, scattering exponent, and relaxation time prefactor. We begin with a review of the underlying mathematics and investigate the mapping between the four-dimensional material property and transport coefficient spaces. We then investigate how the traditional single-parabolic band method yields a single, potentially incorrect point on the solution subspace. This uncertainty can be resolved through Nernst coefficient measurements and we map the span of the ensuing subspace. We conclude with an investigation of how sensitive the analysis of transport coefficients is to experimental error for different sample types.

charge carriers↗

Radiant Heating of Ampoule contents

Ampoule charge heating system exploits spectral properties of blackbody radiation and ampoule material transparency to heat charge to high temperature. Cooling gas prevents softening of outside wall of ampoule. Use of proposed method may be limited by tendency of silica (or any other viteous material) to devitrify on prolonged exposure to temperatures near softening point.

Holland, L. R.↗