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At least 217 records · Page 12

ChAdOx1 interacts with CAR and PF4 with implications for thrombosis with thrombocytopenia syndrome

Vaccines derived from chimpanzee adenovirus Y25 (ChAdOx1), human adenovirus type 26 (HAdV-D26), and human adenovirus type 5 (HAdV-C5) are critical in combatting the severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic. As part of the largest vaccination campaign in history, ultrarare side effects not seen in phase 3 trials, including thrombosis with thrombocytopenia syndrome (TTS), a rare condition resembling heparin-induced thrombocytopenia (HIT), have been observed. This study demonstrates that all three adenoviruses deployed as vaccination vectors versus SARS-CoV-2 bind to platelet factor 4 (PF4), a protein implicated in the pathogenesis of HIT. We have determined the structure of the ChAdOx1 viral vector and used it in state-of-the-art computational simulations to demonstrate an electrostatic interaction mechanism with PF4, which was confirmed experimentally by surface plasmon resonance. These data confirm that PF4 is capable of forming stable complexes with clinically relevant adenoviruses, an important step in unraveling the mechanisms underlying TTS.

60 APPLIED LIFE SCIENCES↗

Introduction to Finite Element Analysis: Abaqus Tutorial [Slides]

Abaqus is a suite of powerful engineering simulation programs, based on the finite element method, that can solve a variety of problems, ranging from simple to complex, including the fields of: Structural mechanics, Structural dynamics, Thermodynamics, Heat transfer, and more

42 ENGINEERING↗

Solutal-buoyancy-driven intertwining and rotation of patterned elastic sheets

Abstract The intertwining of strands into 3D spirals is ubiquitous in biology, enabling functions from information storage to maintenance of cell structure and directed locomotion. In synthetic systems, entwined fibers can provide superior mechanical properties and act as artificial muscle or structural reinforcements. Unlike structures in nature, the entwinement of synthetic materials typically requires application of an external stimulus, such as mechanical actuation, light, or a magnetic field. Herein, we use computational modeling to design microscale sheets that mimic biology by transducing chemical energy into mechanical action, and thereby self-organize and interlink into 3D spirals, which spontaneously rotate. These flexible sheets are immersed in a fluid-filled microchamber that encompasses an immobilized patch of catalysts on the bottom wall. The sheets themselves can be passive or active (coated with catalyst). Catalytic reactions in the solution generate products that occupy different volumes than the reactants. The resulting density variations exert a force on the fluid (solutal buoyancy force) that causes motion, which in turn drives the interlinking and collective swirling of the sheets. The individual sheets do not rotate; rotation only occurs when the sheets are interlinked. This level of autonomous, coordinated 3D structural organization, intertwining, and rotation is unexpected in synthetic materials systems operating without external controls. Using physical arguments, we identify dimensionless ratios that are useful in scaling these ideas to other systems. These findings are valuable for creating materials that act as “machines”, and directing soft matter to undergo self-sustained, multistep assembly that is governed by intrinsic chemical reactions.

Manna, Raj Kumar (ORCID:0000000322729487)↗

First Principle Investigation of Electronic, Transport, and Bulk Properties of Zinc-Blende Magnesium Sulfide

We have studied electronic, structural, and transport properties of zinc-blende magnesium sulfide (zb-MgS). We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO) method. Our computational method is able to reach the ground state of a material, as dictated by the second theorem of density functional theory (DFT). Consequently, our findings have the physical content of DFT and agree with available, corresponding experimental ones. The calculated band gap of zb-MgS, a direct gap equal to 4.43 eV, obtained at the experimental lattice constant of 5.620 Å, completely agrees with the experimental band gap of 4.45 ± 0.2 eV. We also report total (DOS) and partial (pDOS) densities of states, electron and hole effective masses, the equilibrium lattice constant, and the bulk modulus. The calculated pDOS also agree with the experiment for the description of the states at the top and the bottom of the valence and conduction bands, respectively.

42 ENGINEERING↗

CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials

In this paper, we present CTRAMER (Charge-Transfer RAtes from Molecular dynamics, Electronic structure, and Rate theory)—an opensource software package for calculating interfacial charge-transfer (CT) rate constants in organic photovoltaic (OPV) materials based on ab initio calculations and molecular dynamics simulations. The software is based on identifying representative donor/acceptor geometries within interfacial structures obtained from molecular dynamics simulation of donor/acceptor blends and calculating the corresponding Fermi’s golden rule CT rate constants within the framework of the linearized-semiclassical approximation. While the methods used are well established, the integration of these state-of-the-art tools originating from different disciplines to study photoinduced CT processes with explicit treatment of the environment, in our opinion, makes this package unique and innovative. The software also provides tools for investigating other observables of interest. After outlining the features and implementation details, the usage and performance of the software are demonstrated with results from an example OPV system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Identification of mechanisms driving heterogeneous void growth in ductile aluminum

Void growth plays a central role in ductile fracture, yet the specific mechanisms that control this remain obscure. Classical models, such as those proposed by Rice and Tracey in 1969, are able to capture average rates of void growth, but cannot capture the heterogeneity of individual void growth. Building on recent work, the present study employs laboratory-based diffraction contrast tomography and in-situ x-ray computed tomography to investigate the effect of grain structure and other microstructural factors on void growth in an Al-2219 alloy. Crystal plasticity finite element (CP-FE) modeling is used alongside experimental data to evaluate the contributions of local mechanical states, grain orientation, grain size, and neighboring microstructural features. No strong linear relationships are found with any of the considered descriptors and void growth rate. Potential complex nonlinear relationships are explored with the use of a random forest regression model, which identifies initial void volume, void aspect ratio, local normal stress state, local shear stress state, and local equivalent plastic strain (EQPS) as features that most improve void growth rate predictions. The combination of these analyses suggests that these features should be prioritized to improve models of void growth.

Diffraction contrast tomography (DCT)↗

A dynamic volumetric heat source model for laser additive manufacturing

Melt pool scale models of laser powder bed fusion (LPBF) offer insights into the process-structure-property relationships in additive manufacturing (AM). These models often neglect physical phenomena such as vapor cavity formation and fluid mechanics to reduce computational demands. Instead, volumetric heat source models are used to represent the effects that these phenomena have on the predicted melt pool dimensions. Generally, the dimensions and effective absorption of the volumetric heat source are calibrated to reproduce melt pool dimensions observed in metallographic cross sections taken from single-track experiments on bare plate. However, the transient nature of LPBF often deviates the melt pool dimensions from the assumed steady-state conditions of single-track experiments, motivating the need for a volumetric heat source model that more generally considers the dynamic relationship between melt pool shape and laser-material interactions. Here, we introduce a two-parameter volumetric heat source model that integrates several existing models into a generalized mathematical expression, providing independent control over the radial heat distribution via the parameter k and the volumetric shape of the heat source via the parameter m. This parameterization enables the calibration of melt pool shape predictions through simultaneous adjustment of these parameters, while keeping the radial heat source dimensions consistent with the experimental spot size (D4σ) and constraining the heat source depth and absorption to physically derived expressions for cavities. Consequently, the proposed volumetric heat source model adapts to changes in the local melt pool conditions due to scanning strategy and part geometry by dynamically adjusting the heat source depth and absorption. We demonstrate the capabilities of the proposed model through comparisons with a collection of experiments from the Additive Manufacturing Benchmark (AMBench).

36 MATERIALS SCIENCE↗

phosaa14SB and phosaa19SB: Updated Amber Force Field Parameters for Phosphorylated Amino Acids

Phosphorylated amino acids are involved in many cell regulatory networks; proteins containing these post-translational modifications are widely studied both experimentally and computationally. Simulations are used to investigate a wide range of structural and dynamic properties of biomolecules, such as ligand binding, enzyme-reaction mechanisms, and protein folding. However, the development of force field parameters for the simulation of proteins containing phosphorylated amino acids using the Amber program has not kept pace with the development of parameters for standard amino acids, and it is challenging to model these modified amino acids with accuracy comparable to proteins containing only standard amino acids. In particular, the popular ff14SB and ff19SB models do not contain parameters for phosphorylated amino acids. Here, the dihedral parameters for the side chains of the most common phosphorylated amino acids are trained against reference data from QM calculations adopting the ff14SB approach, followed by validation against experimental data. Finally, library files and corresponding parameter files are provided, with versions that are compatible with both ff14SB and ff19SB.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Influence of Pore Surface Structure and Contents on Shock-Induced Collapse and Energy Localization

The majority of computational efforts in the shockwave driven collapse of porosity focus on idealized pore geometries and structures. These give significant insight into the physical mechanisms in play, but omit some potentially important effects of real energetic materials. Here, to address this, we simulate pore collapse in 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) for four types of pore surfaces and fillings: an idealized cylindrical pore, a pore surface coated with polymer, a melted/amorphous pore surface, and a pore filled with gas molecules. We find that these perturbations to the pore structure result in only minor changes to the highly complex collapse mechanisms. However, significant differences in hotspot temperature are observed, with peak temperatures ranging over several hundred Kelvin. The polymer-coated system has the most effect, lowering the hotspot temperature by 300 K, and also limiting the manifestation of intramolecular strain energy that is known to induce mechanochemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Coupled Multiphysics Simulations of Heat Pipe Microreactors Using DireWolf

DireWolf is a multiphysics software driver application designed to simulate heat pipe–cooled nuclear microreactors. Developed under the U.S. Department of Energy, Office of Nuclear Energy Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, the DireWolf software application’s objective is to provide the nuclear community with a design and safety analysis simulation capability. Based upon the NEAMS program Multiphysics Object-Oriented Simulation Environment (MOOSE) computational framework, DireWolf tightly couples nuclear microreactor physics, reactor physics, radiation transport, nuclear fuel performance, heat pipe thermal hydraulics, power generation, and structural mechanics to resolve the interdependent nonlinearities. DireWolf is capable of simulating both steady and transient normal reactor operation and several postulated failure scenarios. We will present the fundamental physics of heat pipe–cooled nuclear microreactors and the MOOSE-based software employed in DireWolf. Both steady and transient results for coupled reactor physics, radiation transport, and nuclear fuel performance are demonstrated.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

MEUMAPPS (Microstructure Evolution Using Massively Parallel Phase-field Simulations)

The software “MEUMAPPS” is a h high-performance computing code used to simulate microstructure evolution associated with diffusional solid-state transformations in structural alloys. Understanding microstructure evolution during thermo-mechanical processing of structural alloys is the first step towards designing and processing alloys for specific applications by meeting property requirements demanded by the application. In this instance, the code is an important component in predicting processing-structure linkages during additive manufacturing of structural alloys as a function of processing parameters and alloy composition used in an additive manufacturing process. The code provides a detailed three-dimensional distribution of different types of phases / constituents and their morphologies, as well as the compositions of these phases that make up the microstructure. The microstructure is simulated by solving the governing partial differential equations using a Fourier Spectral Method.

Radhakrishnan, Balasubram↗

Four-Stage Multi-Physics Simulations to Assist Temperature Sensor Design for Industrial-Scale Coal-Fired Boiler

The growth of renewable energy sources presents a pressing challenge to the operation and maintenance of existing fossil fuel power plants, given that fossil fuel remains the predominant fuel source, responsible for over 60% of electricity generation in the United States. One of the main concerns within these fossil fuel power plants is the unpredictable failure of boiler tubes, resulting in emergency maintenance with significant economic and societal consequences. A reliable high-temperature sensor is necessary for in situ monitoring of boiler tubes and the safety of fossil fuel power plants. In this study, a comprehensive four-stage multi-physics computational framework is developed to assist the design, optimization installation, and operation of the high-temperature stainless-steel and quartz coaxial cable sensor (SSQ-CCS) for coal-fired boiler applications. With the consideration of various operation conditions, we predict the distributions of flue gas temperatures within coal-fired boilers, the temperature correlation between the boiler tube and SSQ-CCS, and the safety of SSQ-CCS. With the simulation-guided sensor installation plan, the newly designed SSQ-CCSs have been employed for field testing for more than 430 days. The computational framework developed in this work can guide the future operation of coal-fired plants and other power plants for the safety prediction of boiler operations.

42 ENGINEERING↗

Studying light–matter interactions and energy transfer at the nanoscale with a trapped–ion quantum computer

A grand challenge in materials sciences is to control energy transduction, transfer and dissipation at the nanoscale. Meeting this challenge requires progress in nanoscale fabrication and synthesis, but equally importantly, also progress in our understanding of how nanoscale structure influences these phenomena. Although detailed quantum mechanical models exist that capture the structure and physics of materials and molecular species, solving these models to calculate the relevant emergent phenomena, which often occur over vastly different time and energy scales, has so far proven difficult. In this project, we studied how to model energy transfer and light-matter interactions using trapped-ion quantum computers. Our studies focused on emulation of critical processes in natural systems, such as the well-known photosynthetic pigment-protein complexes responsible for capturing and transducing light to electrons. In addition, we implemented proof-of-principle experiments demonstrating that such calculations are possible on trapped-ion quantum computing hardware. These studies and experiments pave the way to investigate energy transport and transduction in a detail not accessible with classical computing technologies. We expect that our studies will allow to extract important guiding principles on how to improve the efficiency of nano-scale light-harvesting and transduction devices.

36 MATERIALS SCIENCE↗

In situ visualization of multicomponents coevolution in a battery pouch cell

Lithium-ion battery (LIB) is a broadly adopted technology for energy storage. With increasing demands to improve the rate capability, cyclability, energy density, safety, and cost efficiency, it is crucial to establish an in-depth understanding of the detailed structural evolution and cell-degradation mechanisms during battery operation. Here, we present a laboratory-based high-resolution and high-throughput X-ray micro–computed laminography approach, which is capable of in situ visualizing of an industry-relevant lithium-ion (Li-ion) pouch cell with superior detection fidelity, resolution, and reliability. This technique enables imaging of the pouch cell at a spatial resolution of 0.5 μm in a laboratory system and permits the identification of submicron features within cathode and anode electrodes. We also demonstrate direct visualization of the lithium plating in the imaged pouch cell, which is an important phenomenon relevant to battery fast charging and low-temperature cycling. Our development presents an avenue toward a thorough understanding of the correlation among multiscale structures, chemomechanical degradation, and electrochemical behavior of industry-scale battery pouch cells.

25 ENERGY STORAGE↗

New Dimension in Ab Initio Electronic Structure Theory: Temperature, Pressure, and Chemical Potential

Ab initio electronic structure theory has transformed gas-phase molecular science with its predictive ability. In the attempt to bring such predictive ability to macroscopic systems and condensed matter, the theory must integrate quantum mechanics with statistical thermodynamics, so that thermodynamic functions such as free energy, internal energy, entropy, and chemical potentials are computed as functions of temperature in a systematically converging series of approximations. Here, a general, versatile strategy of elevating ab initio electronic structure theory to nonzero temperatures is introduced and discussed.

74 ATOMIC AND MOLECULAR PHYSICS↗

Confusion-Driven Machine Learning of Structural Phases of a Flexible, Magnetic Stockmayer Polymer

We use a semisupervised, neural-network-based machine learning technique, the confusion method, to investigate structural transitions in magnetic polymers, which we model as chains of magnetic colloidal nanoparticles characterized by dipole–dipole and Lennard-Jones interactions. As input for the neural network, we use the particle positions and magnetic dipole moments of equilibrium polymer configurations, which we generate via replica-exchange Wang–Landau simulations. We demonstrate that by measuring the classification accuracy of neural networks, we can effectively identify transition points between multiple structural phases without any prior knowledge of their existence or location. We corroborate our findings by investigating relevant conventional order parameters. Our study furthermore examines previously unexplored low-temperature regions of the phase diagram, where we find new structural transitions between highly ordered helicoidal polymer configurations.

36 MATERIALS SCIENCE↗

Progress and Challenges in Self-Healing Cementitious Materials

Concrete is the most used man-made material today consisting of a mixture of aggregates (sand, gravel, crashed rock) and paste. The paste component, made up of cement and water, cracks with time. Despite this shortcoming, research towards next-generation cement and concrete has only taken a boost in the past 10-15 years. In particular, self-healing cementitious materials is a research area that has attracted a great deal of attention. A number of reported novel formulations have demonstrated an increase in mechanical and chemical stability with respect to conventional Portland cement, through the addition of inorganic, organic, and even biological additives. This review reports on the latest advances in cement research related to the synthesis of self-healing cements applied in concrete structures. These include geopolymers, engineered cementitious materials (ECC), bacterial cement composites, microencapsulated self-healing materials, shape memory alloys (SMA), and polymer-cement composites. This work describes the performance of each cementitious material and the mechanism responsible for self-healing, including a section on the latest computational modeling studies towards this end. A detailed understanding of these various self-healing cement technologies, including their strengths and weaknesses, is critical at the time of determining the type of structures that these materials could be used for.

Fernandez, Carlos A.↗