Deep autoencoders for physics-constrained data-driven nonlinear materials modeling
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97 MATHEMATICS AND COMPUTING↗
SEARCH · Engineering Papers
Results for “biological material”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Scattering-type Scanning Near-Field Optical Microscopy of Polymer-Coated Gold Nanoparticles
Scattering-type scanning near-field optical microscopy (s-SNOM) has emerged over the past years as a powerful characterization tool that can probe important properties of advanced materials and biological samples in a label-free manner, with spatial resolutions lying in the nanoscale realm. In this work, we explore such usefulness in relationship with an interesting class of materials: polymer-coated gold nanoparticles (NPs). As thoroughly discussed in recent works, the interplay between the Au core and the polymeric shell has been found to be important in many applications devoted to biomedicine. We investigate bare Au NPs next to polystyrenesulfonate (PSS) and poly(diallyldimethylammonium chloride) (PDDA) coated ones under 532 nm laser excitation, an wavelength matching the surface plasmon band of the custom-synthesized nanoparticles. We observe consistent s-SNOM phase signals in the case of bare and shallow-coated Au NPs, whereas for thicker shell instances, these signals fade. For all investigated samples, the s-SNOM amplitude signals were found to be very weak, which may be related to reduced scattering efficiency due to absorption of the incident beam. We consider these observations important, as they may facilitate studies and applications in nanomedicine and nanotechnology where the precise positioning of polymer-coated Au NPs with nanoscale resolution is needed besides their dielectric function and related intrinsic optical properties, which are also quantitatively available with s-SNOM.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Reactor Performance Improvement Options to Sustain High Flux Isotope Reactor Leadership into the Future
The mission of the Neutron Sciences Directorate (NScD) at the U.S. Department of Energy’s Oak Ridge National Laboratory (ORNL) is the undertaking of high-impact research into the structure and properties of materials across the spectrum of biology, chemistry, physics, materials science, and engineering. NScD operates two world-leading neutron scattering facilities including the High Flux Isotope Reactor (HFIR) and the Spallation Neutron Source. HFIR achieved full power in 1966, and over a half century later, it continues to serve a variety of national missions. HFIR provides one of the highest steady-state neutron fluxes of any research reactor in the world to support scientific missions including cold and thermal neutron scattering, isotope production, and materials irradiation research. To sustain leadership in neutron sciences into the future, ORNL is exploring areas in which HFIR can be improved to enhance its performance. Many improvement areas are being explored such as upgrading the cold source and neutron scattering facilities; however, the improvement areas focused on in this paper include replacing the reactor pressure vessel, upgrading the neutron reflector, and converting from high-enriched uranium to low-enriched uranium fuel.
Chandler, David↗
Interactions between fullerene derivatives and biological systems
Attention towards nanoparticles from the pharmaceutical and biomedical fields has significantly increased due to their attractive surface modification, high drug-loading, and improved pharmacokinetics. Fullerenes, an allotrope of carbon, stand out for their molecularly precise structure, potent radical-scavenging activity, photoactivatable reactive-oxygen species generation, and ability to definitively confine metal atoms and clusters. Accordingly, fullerene systems have been applied in various biological contexts, including increased and controlled drug delivery, antioxidative, anti-inflammatory, and photodynamic therapy, and magnetic resonance imaging. Ultimately, the pleiotropic activity of fullerenes, coupled with its precise structure and functionalization, can realize precise and tailorable medicines. Here, different from some excellent reviews focusing on the structure and chemistry of fullerene derivatives and their biomedical applications, this review highlights the interaction of fullerene materials with biological systems, with insights into their structural influence on their interactions with the cellular environment.
36 MATERIALS SCIENCE↗
Resolution-enhanced X-ray fluorescence microscopy via deep residual networks
Abstract Multimodal hard X-ray scanning probe microscopy has been extensively used to study functional materials providing multiple contrast mechanisms. For instance, combining ptychography with X-ray fluorescence (XRF) microscopy reveals structural and chemical properties simultaneously. While ptychography can achieve diffraction-limited spatial resolution, the resolution of XRF is limited by the X-ray probe size. Here, we develop a machine learning (ML) model to overcome this problem by decoupling the impact of the X-ray probe from the XRF signal. The enhanced spatial resolution was observed for both simulated and experimental XRF data, showing superior performance over the state-of-the-art scanning XRF method with different nano-sized X-ray probes. Enhanced spatial resolutions were also observed for the accompanying XRF tomography reconstructions. Using this probe profile deconvolution with the proposed ML solution to enhance the spatial resolution of XRF microscopy will be broadly applicable across both functional materials and biological imaging with XRF and other related application areas.
36 MATERIALS SCIENCE↗
Bifurcation Analysis Reveals Solution Structures of Phase Field Models
The phase field method is playing an increasingly important role in understanding and predicting morphological evolution in materials and biological systems. Here, in this study, we develop a new analytical approach based on the bifurcation analysis to explore the mathematical solution structure of phase field models. Revealing such solution structures not only is of great mathematical interest but also may provide guidance to experimentally or computationally uncover new morphological evolution phenomena in materials undergoing electronic and structural phase transitions. To elucidate the idea, we apply this analytical approach to three representative phase field equations: the Allen-Cahn equation, the Cahn-Hilliard equation, and the Allen-Cahn-Ohta-Kawasaki system. The solution structures of these three phase field equations are also verified numerically by the homotopy continuation method.
97 MATHEMATICS AND COMPUTING↗
33 Unresolved Questions in Nanoscience and Nanotechnology
Significant advances in science and engineering often emerge at the intersections of disciplines. Nanoscience and nanotechnology are inherently interdisciplinary, uniting researchers from chemistry, physics, biology, medicine, materials science, and engineering. This convergence has fostered novel ways of thinking and enabled the development of materials, tools, and technologies that have transformed both basic and applied research, as well as how we address critical societal challenges. In this Nano Focus, we pose and explore 33 questions whose answers could profoundly impact fields such as energy, electronics, the environment, optics, and medicine. These questions highlight the need for deeper foundational understanding, improved tools and techniques, and innovative applications─each with significant societal relevance. Together, they represent a global call-to-action for the scientific community.
77 NANOSCIENCE AND NANOTECHNOLOGY↗
A subdivision-stabilized B-spline mixed material point method
Subjected to external loadings, polymeric materials, e.g., biological tissues, hydrogels, and elastomers, may undergo extreme, nearly incompressible, (self-)contact deformations. For numerical modeling employing mesh-based techniques such as the finite element method (FEM), these deformations pose significant challenges due to large distortions in the deformed geometry, accuracy issues stemming from volumetric locking effects, and increased computational cost from complex contact searches. As an alternative to mesh-based methods, the material point method (MPM), a continuum-based particle technique, is gaining attention for its ability to handle extreme distortions and capture no-slip contact without added cost. For nearly incompressible material behaviors, while mixed formulations can address locking effects by treating displacements and pressure as independent fields, they can suffer from numerical instabilities close to the incompressibility limit due to the violation of the inf-sup condition, leading to inaccurate nodal pressure solutions. Here we propose an efficient and stable mixed B-spline material point method with highest achievable regularity for quasi-compressible polymeric materials. Using the two-scale relation of B-splines, we introduce a subdivision-stabilization for the two-field mixed MPM and obtain numerically stable, oscillation-free nodal solutions with equal-order interpolations with optimal regularity. Building on the Eulerian-Lagrangian nature of MPM, a previously-converged solution framework is adopted to mitigate issues related to cell-crossing and numerical fracture artifact present in standard MPM. We assess the stability and accuracy of the developed mixed MPM at large deformations for soft materials through the benchmark Cook’s membrane problem. Additionally, we test the robustness of the proposed MPM by modeling several examples, including the compression and indentation of a circular block into a quasi-compressible substrate and the twisting deformation of a rectangular block. The findings demonstrate the MPM’s capabilities for modeling practical soft material applications.
36 MATERIALS SCIENCE↗
A scalable and tunable thermoreversible polymer for 3D human pluripotent stem cell biomanufacturing
Human pluripotent stem cells (hPSCs) are an exciting and promising source to enable cell replacement therapies for a variety of unmet medical needs. Though hPSCs can be successfully derived into numerous physiologically relevant cell types, effective translation to the clinic is limited by challenges in scalable production of high-quality cells, cellular immaturity following the differentiation process, and the use of animal-derived components in culture. To address these limitations, we have developed a fully defined, reproducible, and tunable thermoreversible polymer for high-quality, scalable 3D cell production. Our reproducible synthesis method enables precise control of gelation temperature (24°C–32°C), hydrogel stiffness (100–4000 Pa), and the prevention of any unintended covalent crosslinking. After material optimization, we demonstrated hPSC expansion, pluripotency maintenance, and differentiation into numerous lineages within the hydrogel. Overall, this 3D thermoreversible hydrogel platform has broad applications in scalable, high-quality cell production to overcome the biomanufacturing burden of stem cell therapy.
59 BASIC BIOLOGICAL SCIENCES↗
Biomanufacturing and bioprocessing of lunar regolith
Microbial biomanufacturing is important to accelerate lunar construction because it can leverage lunar material and waste streams as feedstocks to create a circular production system. In-space bio-mining and biomanufacturing using moon and asteroidal source material will enable the creation of infrastructure, produce industrial fuels and lubricants, and enable recovery of actinides and rare-earth elements (REEs) present in trace concentrations. Moreover, biomanufacturing in closed-loop systems (recycling and reuse of resources toward the establishment of a circular economy) will enable long-term lunar activities by recycling waste (CO 2 , gray water) and producing oxygen and biomaterials. Our response focuses on the use of lunar regolith and waste streams as feedstocks for protein and microbial-enabled biomining and bioprocessing to extract actinides and REEs, and to create biocomposites for lunar infrastructure. We envision an enclosed process that initiates with (1a) extracting actinides and REEs from lunar regolith using immobilized proteins, followed by (1b) creating biocomposites from the post-extracted lunar regolith for infrastructure, and (1c) cultivating diatoms and other microalgae on waste streams to harvest silica shells for incorporating into biocomposites and to generate O 2 for human respiration and/or producing refinable feedstocks. LLNL has significant expertise in all three processes and provides facilities, personnel, and expertise at the intersection of metal (lanthanide, actinide, transition) separations, purifications, biohydrometallurgy, radiobiochemistry, synthetic and systems biology, and materials science and engineering. Importantly, all three processes are relatively well-studied for Earth-based workflows and can be derisked for demonstration on the lunar surface by 2029.
59 BASIC BIOLOGICAL SCIENCES↗
Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi
Fungi exhibit behaviors distinct from other microbes. Filamentous fungi grow by extending complex networks of branched filaments collectively referred to as the mycelium. These networks can expand over large distances and traverse low-nutrient areas by translocating nutrients through the filament network. This spatial characteristic makes filamentous fungi crucial for soil ecosystems, supporting stable microbial communities and promoting plant growth. However, simulating these behaviors is complex. The elongated nature of fungal compartments results in different mechanical interactions compared to the commonly modeled spherical bacteria. These detailed hyphal mechanics require specialized consideration and are often excluded from conventional fungal simulation packages. Additionally, the extensive fungal networks in nature demand computationally intensive simulations, necessitating high-performance algorithms. Therefore, realistic fungi simulations require specialized software. Here, we introduce a fungal modeling expansion to the high-performance biological modelling and interface exchange (bmx) software suite. bmx leverages adaptive mesh refinement in AMReX for chemical diffusion and incorporates a full mechanical model for bacterial cells, accelerated by GPUs. By extending bmx to model filamentous particles, we demonstrate the formation of complex filament networks through interactions like hyphal branching and fusion (anastomosis). We show that the networks produced match real-world fungal structures through various metrics. This work supports computational studies of fungal growth dynamics and can be adapted to investigate the growth of other filamentous structures in biology or materials science. The expanded-BMX package is open-sourced and is available online.
Cell mechanics↗
Microbial Design for a Developing Bioeconomy: Frontier Science for the Bioeconomy Workshop Series
The Microbial Design for a Developing Bioeconomy workshop report is one of a four-part Frontier Science for the Bioeconomy series hosted by the DOE Biological and Environmental Research program’s Biological Systems Science Division. The series defines frontiers of plant science, agriculture, synthetic biology, biobased materials, and environmental microbiome science that will unlock the promise of an innovative, resilient U.S. bioeconomy.
59 BASIC BIOLOGICAL SCIENCES↗
Bio-Optimized Technologies to Keep Thermoplastics out of Landfills and the Environment (BOTTLE)
Plastics have revolutionized modern life, but reliance on these fossil-based materials that persist for centuries is causing a pollution crisis and contributing to greenhouse gas (GHG) emissions. To develop new technologies to address this problem, the Bio-Optimized Technologies to keep Thermoplastics out of Landfills and the Environment (BOTTLE) Consortium will deliver selective, scalable technologies to enable cost-effective recycling, upcycling, and increased energy efficiency. BOTTLE is an interdisciplinary team of experts that aim to develop selective, scalable processes to deconstruct and upcycle today's plastics and thermosets, redesign tomorrow's plastics to be recyclable-by-design (RBD) and derived from both bio-based and plastic waste-based feedstocks, work with industrial partners across the value chain to catalyze the circular economy for plastics, and leverage AMO and BETO investments in analysis-guided R&D, integrated process development, chemical and biological catalysis, materials characterization, modeling, and data science. BOTTLE is guided by techno-economic analysis (TEA) and supply chain-based life-cycle assessment (LCA). BOTTLE comprises members from ten partner institutions. Primary outcomes to date include establishment of a full consortium, impactful, benchmarking analyses that will be important for the plastics recycling and upcycling community, and multiple impactful, high-impact publications across the breadth of our research portfolio.
bio-optimized↗
Real-time bioelectronic sensing of environmental contaminants
Real-time chemical sensing is crucial for applications in environmental and health monitoring. Biosensors can detect a variety of molecules through genetic circuits that use these chemicals to trigger the synthesis of a coloured protein, thereby producing an optical signal. However, the process of protein expression limits the speed of this sensing to approximately half an hour, and optical signals are often difficult to detect in situ. Here we combine synthetic biology and materials engineering to develop biosensors that produce electrical readouts and have detection times of minutes. Here we programmed Escherichia coli to produce an electrical current in response to specific chemicals using a modular, eight-component, synthetic electron transport chain. As designed, this strain produced current following exposure to thiosulfate, an anion that causes microbial blooms, within 2 min. This amperometric sensor was then modified to detect an endocrine disruptor. The incorporation of a protein switch into the synthetic pathway and encapsulation of the bacteria with conductive nanomaterials enabled the detection of the endocrine disruptor in urban waterway samples within 3 min. Our results provide design rules to sense various chemicals with mass-transport-limited detection times and a new platform for miniature, low-power bioelectronic sensors that safeguard ecological and human health.
59 BASIC BIOLOGICAL SCIENCES↗
Recent advances in nano-scale spatial resolution x-ray microscopy instrumentation at NSLS-II
X-ray microscopy is an invaluable and powerful characterization tool applied in many scientific fields, such as materials science, biology, environmental science, and energy research. In recent years it has been driven by rapid developments of novel technologies and systems resulting in imaging experiments elucidating structural inhomogeneities and chemical reactions at the nanometer scale. To obtain high spatial resolution comprehensive chemical and structural information, an X-ray microscope must be equipped with adequate capabilities and allow for simultaneous acquisition of multiple datasets. In recent years, a number of X-ray microscopes have been designed, constructed, and commissioned at NSLS-II. Here we provide an overview of the microscopy instrumentation development program at NSLS-II and specifically focus on the multilayer Laue lens-based hard X-ray nanoprobe optimized for ~10 nm spatial resolution imaging, its current status, and future upgrades along with recently constructed Kirkpatrick-Baez based scanning microscope designed for ~100 nm spatial resolution experiments.
36 MATERIALS SCIENCE↗
Less Is More: Oligomer Extraction and Hydrothermal Annealing Increase PDMS Adhesion Forces for Materials Studies and for Biology-Focused Microfluidic Applications
Cues in the micro-environment are key determinants in the emergence of complex cellular morphologies and functions. Primary among these is the presence of neighboring cells that form networks. For high-resolution analysis, it is crucial to develop micro-environments that permit exquisite control of network formation. This is especially true in cell science, tissue engineering, and clinical biology. We introduce a new approach for assembling polydimethylsiloxane (PDMS)-based microfluidic environments that enhances cell network formation and analyses. We report that the combined processes of PDMS solvent-extraction and hydrothermal annealing create unique conditions that produce high-strength bonds between solvent-extracted PDMS (E-PDMS) and glass—properties not associated with conventional PDMS. Extraction followed by hydrothermal annealing removes unbound oligomers, promotes polymer cross-linking, facilitates covalent bond formation with glass, and retains the highest biocompatibility. Herein, our extraction protocol accelerates oligomer removal from 5 to 2 days. Resulting microfluidic platforms are uniquely suited for cell-network studies owing to high adhesion forces, effectively corralling cellular extensions and eliminating harmful oligomers. We demonstrate the simple, simultaneous actuation of multiple microfluidic domains for invoking ATP- and glutamate-induced Ca 2+ signaling in glial-cell networks. These E-PDMS modifications and flow manipulations further enable microfluidic technologies for cell-signaling and network studies as well as novel applications.
36 MATERIALS SCIENCE↗
Sampling Rare Events in Aqueous Systems Using Molecular Simulations
Birth of a new distinct phase is a phenomenon encountered in a myriad of processes, and has wide ranging consequences in material processing, biological self-assembly, separations and several other processes. Several phase transitions are nucleation driven. The nucleation events occur over nanosecond timescales and involve hundreds to thousands of molecules. These length and timescales are difficult to access in experiments, thereby making experimental studies of nucleation challenging. On the other hand, molecular simulations sample the nanosecond and nanometer scales making them ideal to study nucleation. However, nucleation is a rare event, meaning that the waiting time to observe one nucleation event is significant. This makes simulation studies of rare events challenging. The project focused on a multi-pronged approach to address such challenges to develop the next generation rare event sampling methods for molecular simulations. The key outcomes of our work include developing more effective methods for sampling rare events, utilizing machine learning to better elucidate nucleation mechanisms, development of software for easy implementation of the methodologies, and applications of the methods to realistic systems to push the method applicability beyond model systems. Overall, this work has enabled pushing the frontiers of molecular simulations to study rare events with a focus on nucleation in aqueous solutions.
36 MATERIALS SCIENCE↗
Physical Models from Physical Templates Using Biocompatible Liquid Crystal Elastomers as Morphologically Programmable Inks For 3D Printing
Advanced manufacturing has received considerable attention as a tool for the fabrication of cell scaffolds however, finding ideal biocompatible and biodegradable materials that fit the correct parameters for 3D printing and guide cells to align remain a challenge. Herein, a photocrosslinkable smectic-A (Sm-A) liquid crystal elastomer (LCE) designed for 3D printing is presented, that promotes cell proliferation but most importantly induces cell anisotropy. The LCE-based bio-ink allows the 3D duplication of a highly complex brain structure generated from an animal model. Vascular tissue models are generated from fluorescently stained mouse tissue spatially imaged using confocal microscopy and subsequently processed to create a digital 3D model suitable for printing. The 3D structure is reproduced using a Digital Light Processing (DLP) stereolithography (SLA) desktop 3D printer. Synchrotron Small-Angle X-ray Diffraction (SAXD) data reveal a strong alignment of the LCE layering within the struts of the printed 3D scaffold. The resultant anisotropy of the LCE struts is then shown to direct cell growth. This study offers a simple approach to produce model tissues built within hours that promote cellular alignment.
3D cell culture↗