Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “biological processing”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,675 records · Page 93
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Downregulated long non-coding RNA MEG3 in breast cancer regulates proliferation, migration and invasion by depending on p53’s transcriptional activity

Long non-coding RNAs (lncRNAs) was found to play critical roles in tumorigenesis, hence, screen of tumor-related lncRNAs, identification of their biological roles is important for understanding the processes of tumorigenesis. In this study, we identified the expressing difference of several tumor-related lncRNAs in breast cancer samples and found that, MEG3, which is downregulated in non-small cell lung cancer (NSCLC) tumor tissues, is also downregulated in breast cancer samples compared with adjacent tissues. For figuring out the effect of MEG3 in breast cancer cells MCF7 and MB231, we overexpressed MEG3 in these cells, and found that it resulted the inhibition of proliferation, colony formation, migration and invasion capacities by enhancing p53’s transcriptional activity on its target genes, including p21, Maspin and KAI1. MEG3 presented similar effects in MB157, which is a p53-null breast cancer cell line, when functional p53 but not p53R273H mutant, which lacks transcriptional activity, was introduced. Surprisingly, overexpression of MEG3 activates p53’s transcriptional activity by decreasing MDM2’s transcription level, and thus stabilizes and accumulates P53. Taken together, our findings indicate that MEG3 is downregulated in breast cancer tissues and affects breast cancer cells’ malignant behaviors, which indicate MEG3 a potential therapeutic target for breast cancer. - Highlights: • MEG3 RNA is widely downregulated in breast tumor tissue. • MEG3 regulates P53 indirectly through transcriptional regulation of MDM2. • Under unstressed condition, MEG3-related P53 accumulation transcriptionally activates p53’s target genes. • MEG3 expression level tightly regulates proliferation, colony formation, migration and invasion in breast tumor cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Sphingolipidomics analysis of large clinical cohorts. Part 1: Technical notes and practical considerations

Highlights: • Sphingolipids have remarkable structural diversity. • This diversity has complicated attempts to understand specific molecular functions. • Recent advances in mass spectrometry now allow high-throughput lipidomics analyses. • This review discusses practical aspects of this technology. Lipids comprise an exceptionally diverse class of bioactive macromolecules. While quantitatively abundant lipid species serve fundamental roles in cell structure and energy metabolism, thousands of structurally-distinct, quantitatively minor species may serve as important regulators of cellular processes. Historically, a complete understanding of the biological roles of these lipids has been limited by a lack of sensitive, discriminating analytical techniques. The class of sphingolipids alone, for example, is known to consist of over 600 different confirmed species, but is likely to include tens of thousands of metabolites with potential biological significance. Advances in mass spectrometry (MS) have improved the throughput and discrimination of lipid analysis, allowing for the determination of detailed lipid profiles in large cohorts of clinical samples. Databases emerging from these studies will provide a rich resource for the identification of novel biomarkers and for the discovery of potential drug targets, analogous to that of existing genomics databases. In this review, we will provide an overview of the field of sphingolipidomics, and will discuss some of the challenges and considerations facing the generation of robust lipidomics databases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Modulation of oxidative phosphorylation (OXPHOS) by radiation- induced biophotons

Highlights: • This paper provides evidence that the biophoton signals known to be emitted by irradiated cells, interfere with the processes of oxidative phosphorylation (OXPHOS) in cells receiving the signals. • The paper demonstrates that Complex 1 activity is completely supressed by these biophotons resulting in downstream compromise of ATP production. • The mechanism may help explain fatigue and immune compromise effects of low dose exposure to ionising radiation. Radiation-induced biophotons are an electromagnetic form of bystander signalling. In human cells, biophoton signalling is capable of eliciting effects in non-irradiated bystander cells. However, the mechanisms by which the biophotons interact and act upon the bystander cells are not clearly understood. Mitochondrial energy production and ROS are known to be involved but the precise interactions are not known. To address this question, we have investigated the effect of biophoton emission upon the function of the complexes of oxidative phosphorylation (OXPHOS). The exposure of bystander HCT116 p53 +/+ cells to biophoton signals emitted from β-irradiated HCT116 p53 +/+ cells induced significant modifications in the activity of Complex I (NADH dehydrogenase or NADH:ubiquinone oxidoreductase) such that the activity was severely diminished compared to non-irradiated controls. The enzymatic assay showed that the efficiency of NADH oxidation to NAD+ was severely compromised. It is suspected that this impairment may be linked to the photoabsorption of biophotons in the blue wavelength range (492–455 nm). The photobiomodulation to Complex I was suspected to contribute greatly to the inefficiency of ATP synthase function since it resulted in a lower quantity of H{sup +} ions to be available for use in the process of chemiosmosis. Other reactions of the ETC were not significantly impacted. Overall, these results provide evidence for a link between biophoton emission and biomodulation of the mitochondrial ATP synthesis process. However, there are many aspects of biological modulation by radiation-induced biophotons which will require further elucidation.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2020

The nitrosoamphetamine metabolite is accommodated in the active site of human hemoglobin: Spectroscopy and crystal structure

Amphetamine-based (Amph) drugs are metabolized in humans to their hydroxylamine (AmphNHOH) and nitroso (AmphNO) derivatives. The latter metabolites are known to bind to the Fe centers of cytochrome P450 and other heme enzymes to inhibit their activities. Although these AmphNHOH/AmphNO metabolites are present in vivo, their interactions with the blood protein hemoglobin (Hb) and the muscle protein (Mb) have been largely discounted due to a perception that the relatively small heme active sites of Hb and Mb will not be able to accommodate the large AmphNO group. Here, we report the 2.15 Å resolution X-ray crystal structure of the AmphNO adduct of adult human hemoglobin as the Hb [ α -Fe III (H 2 O)][ β -Fe II (AmphNO)] derivative. We show that the binding of AmphNO to the β subunit is enabled by an E helix movement and stabilization of ligand binding by H-bonding with the distal His63 residue. We also observe an AmphNHOH group in the Xe2 pocket in close proximity to the α heme site in this derivative. Additionally, UV–vis spectroscopy was used to characterize this and related wt and mutant Mb adducts. Importantly, our X-ray crystal structure of this Hb-nitrosoamphetamine complex represents the first crystal structure of a wild-type heme protein adduct of any amphetamine metabolite. Our results provide a framework for further studies of AmphNHOH/AmphNO interactions with Hb and Mb as viable processes that potentially contribute to the overall biological inorganic chemistry of amphetamine drugs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

pH Regulates Ion Dynamics in Carboxylated Mixed Conductors

Coupled ionic and electronic transport underpins processes as diverse as electrochemical energy conversion, biological signaling, and soft adaptive electronics. Yet, how chemical environments such as pH modulate this coupling at the molecular scale remains poorly understood. Here, we show that the protonation state of carboxylated polythiophenes provides precise chemical control over ion dynamics, doping efficiency, solvent uptake, and mechanical response. Using a suite of multimodal operando techniques, supported by simulations, we reveal that pH dictates the balance of cation/anion uptake during electrochemical doping. Mapping across pH uncovers a quasi-nonswelling regime (≈pH 3–3.5) where charge compensation proceeds with minimal volumetric change yet pronounced stiffening. These findings establish molecular acidity as a general strategy to program ionic preference and mechanical stability, offering design principles for pH-responsive mixed conductors and soft electronic materials that couple ionic, electronic, and mechanical functionality.

PH↗
DOE OSTI2026

Accurate Prediction of pKb in Amines: Validation of the CAM-B3LYP/6-311+G(d,p)/SMD Model

Amines play several key roles in chemistry and biology and are involved in numerous industrial processes, often with significant economic impacts. Recently, amines are also garnering interest as catalysts for polymer synthesis and for CO 2 fixation, incentivizing the need to rapidly design and screen new amino compounds. Hence, developing reliable methods to predict their physicochemical properties, e.g., the base dissociation constant (pKb), is pivotal. Here, a density functional theory (DFT)-based approach was employed to compute the pKb of substituted amines, exploring the impact of several key parameters, including (i) the number of explicit water molecules at the reaction center, (ii) the van der Waals (vdW) surface, and (iii) solvent polarizability. In previous work, it was determined that including two explicit water molecules at the reaction center resulted in highly accurate pKb estimates for primary amines. Here, we find that including a third water molecule at the reaction center is essential for accurate pKb for secondary and tertiary amines. The revised methodology was then applied to a wider selection of amines, obtaining a minimum average error (MAE) < 0.4. In conclusion, this result represents an extension of our “easy-to-use method,” a simple and direct DFT approach exploiting CAM-B3LYP/SMD/6-311G+(d,p) to compute pKb without post facto modifications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

In Situ 3D Imaging of Catalysis Induced Strain in Gold Nanoparticles

Multielectron transfer processes are crucially important in energy and biological science but require favorable catalysts to achieve fast kinetics. Nanostructuring catalysts can dramatically improve their properties, which can be difficult to understand due to strain- and size-dependent thermodynamics, the influence of defects, and substrate-dependent activities. Here, we report three-dimensional (3D) imaging of single gold nanoparticles during catalysis of ascorbic acid decomposition using Bragg coherent diffractive imaging (BCDI). Local strains were measured in single nanoparticles and modeled using reactive molecular dynamics (RMD) simulations and finite element analysis (FEA) simulations. RMD reveals the pathway for local strain generation in the gold lattice: chemisorption of hydroxyl ions. FEA reveals that the RMD results are transferable to the nanocrystal sizes studied in the experiment. Our study probes the strain-activity connection and opens a powerful avenue for theoretical and experimental studies of nanocrystal catalysis.

Ulvestad, Andrew↗
DOE OSTI2021

Substrate Partitioning into Protein Macromolecular Frameworks for Enhanced Catalytic Turnover

Spatial partitioning of chemical processes is an important attribute of many biological systems, the effect of which is reflected in the high efficiency of enzymes found within otherwise chaotic cellular environments. Barriers, often provided through the formation of compartments or phase segregation, gate the access of macromolecules and small molecules within the cell and provide an added level of metabolic control. Taking inspiration from nature, we have designed virus-like particles (VLPs) as nanoreactor compartments that sequester enzyme catalysts and have used these as building blocks to construct 3D protein macromolecular framework (PMF) materials, which are structurally characterized using small-angle X-ray scattering (SAXS). Additionally, the highly charged PMFs form a separate phase in suspension, and by tuning the ionic strength, we show positively charged molecules preferentially partition into the PMF, while negatively charged molecules are excluded. This molecular partitioning was exploited to tune the catalytic activity of enzymes enclosed within the individual particles in the PMF, the results of which showed that positively charged substrates had turnover rates that were 8500× faster than their negatively charged counterparts. Moreover, the catalytic PMF led to cooperative behavior resulting in charge dependent trends opposite to those observed with individual P22 nanoreactor particles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Electronic origin of reorganization energy in interfacial electron transfer

Electron transfer (ET) reactions underpin energy conversion and chemical transformations in both biological and a biological systems. The efficiency of any ET process relies on achieving a desired ET rate within an optimal driving force range. Marcus theory provides a microscopic framework for understanding the activation free energy—and therefore the rate—of ET in terms of a key parameter: the reorganization energy. For electrified solid–liquid interfaces, it has long been conventionally understood that only factors in the electrolyte phase are responsible for determining the reorganization energy and that the electronic density of states (DOS) of the electrode only serves to dictate the number of thermally accessible channels for ET. Here we show instead that the electrode DOS plays a central role in governing the reorganization energy, far outweighing its conventionally assumed role. Using atomically layered heterostructures, we tune the DOS of graphene and measure outer-sphere ET kinetics. We find the ensuing variation in ET rate arises from strong modulation in a reorganization energy associated with image potential localization in the electrode. Here we redefine the traditional paradigm of heterogeneous ET kinetics, revealing a deeper role of the electrode electronic structure in interfacial reactivity.

Electrochemistry↗
DOE OSTI2016

Stochastic lag time in nucleated linear self-assembly

Protein aggregation is of great importance in biology, e.g., in amyloid fibrillation. The aggregation processes that occur at the cellular scale must be highly stochastic in nature because of the statistical number fluctuations that arise on account of the small system size at the cellular scale. We study the nucleated reversible self-assembly of monomeric building blocks into polymer-like aggregates using the method of kinetic Monte Carlo. Kinetic Monte Carlo, being inherently stochastic, allows us to study the impact of fluctuations on the polymerization reactions. One of the most important characteristic features in this kind of problem is the existence of a lag phase before self-assembly takes off, which is what we focus attention on. We study the associated lag time as a function of system size and kinetic pathway. We find that the leading order stochastic contribution to the lag time before polymerization commences is inversely proportional to the system volume for large-enough system size for all nine reaction pathways tested. Finite-size corrections to this do depend on the kinetic pathway.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Experimental and theoretical description of the process of contact laser surgery with a titanium-doped optothermal fibre converter

In an in vitro experiment simulating a surgeon’s actions in the process of contact laser surgery of soft biological tissue, the dependences of the temperature of a titanium-doped optothermal fibre converter (TOTFC) and the depths of coagulation and ablation of biological tissue on the average radiation power of a diode laser with a wavelength of 980 nm and on the speed of the converter movement along biological tissue are obtained. The structural, optical, and thermophysical models of TOTFC are discussed, as well as the thermophysical model of the interaction of a laser-heated converter with biological tissue, which takes into account the temperature dependences of the basic thermophysical parameters of the converter and biological tissue, as well as the contribution of the thickness h{sub int} of the water vapour layer between the converter and biotissue. It is shown that the proposed model allows describing the result of contact laser surgery of soft biotissue with TOTFC adequately to the experiment. (laser biophotonics)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Nonequilibrium statistical thermodynamics of multicomponent interfaces

Nonequilibrium interfacial thermodynamics has important implications for crucial biological, physical, and industrial-scale transport processes. Here, we discuss a theory of local equilibrium for multiphase multicomponent interfaces that builds upon the “sharp” interface concept first introduced by Gibbs, allowing for a description of nonequilibrium interfacial processes such as those arising in evaporation, condensation, adsorption, etc. By requiring that the thermodynamics be insensitive to the precise location of the dividing surface, one can identify conditions for local equilibrium and develop methods for measuring the values of intensive variables at the interface. We then use extensive, high-precision nonequilibrium molecular dynamics (NEMD) simulations to verify the theory and establish the validity of the local equilibrium hypothesis. In particular, we demonstrate that equilibrium equations of state are also valid out of equilibrium, and can be used to determine interfacial temperature and chemical potential(s) that are consistent with nonequilibrium generalizations of the Clapeyron and Gibbs adsorption equations. We also show, for example, that, far from equilibrium, temperature or chemical potential differences need not be uniform across an interface and may instead exhibit pronounced discontinuities. However, even in these circumstances, we demonstrate that the local equilibrium hypothesis and its implications remain valid. These results provide a thermodynamic foundation and computational tools for studying or revisiting a wide variety of interfacial transport phenomena.

36 MATERIALS SCIENCE↗
DOE OSTI2022

On the mechanisms of ion adsorption to aqueous interfaces: air-water vs. oil-water

The adsorption of ions to water-hydrophobe interfaces influences a wide range of phenomena, including chemical reaction rates, ion transport across biological membranes, and electrochemical and many catalytic processes; hence, developing a detailed understanding of the behavior of ions at water-hydrophobe interfaces is of central interest. Here, we characterize the adsorption of the chaotropic thiocyanate anion (SCN − ) to two prototypical liquid hydrophobic surfaces, water-toluene and water-decane, by surface-sensitive nonlinear spectroscopy and compare the results against our previous studies of SCN − adsorption to the air-water interface. For these systems, we observe no spectral shift in the charge transfer to solvent spectrum of SCN − , and the Gibb’s free energies of adsorption for these three different interfaces all agree within error. We employed molecular dynamics simulations to develop a molecular-level understanding of the adsorption mechanism and found that the adsorption for SCN − to both water-toluene and water-decane interfaces is driven by an increase in entropy, with very little enthalpic contribution. This is a qualitatively different mechanism than reported for SCN − adsorption to the air-water and graphene-water interfaces, wherein a favorable enthalpy change was the main driving force, against an unfavorable entropy change.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Towards nanoscale electrical measurements in liquid by advanced KPFM techniques: a review

Fundamental mechanisms of energy storage, corrosion, sensing, and multiple biological functionalities are directly coupled to electrical processes and ionic dynamics at solid–liquid interfaces. In many cases, these processes are spatially inhomogeneous taking place at grain boundaries, step edges, point defects, ion channels, etc and possess complex time and voltage dependent dynamics. This necessitates time-resolved and real-space probing of these phenomena. In this review, we discuss the applications of force-sensitive voltage modulated scanning probe microscopy (SPM) for probing electrical phenomena at solid–liquid interfaces. We first describe the working principles behind electrostatic and Kelvin probe force microscopies (EFM & KPFM) at the gas–solid interface, review the state of the art in advanced KPFM methods and developments to (i) overcome limitations of classical KPFM, (ii) expand the information accessible from KPFM, and (iii) extend KPFM operation to liquid environments. We briefly discuss the theoretical framework of electrical double layer (EDL) forces and dynamics, the implications and breakdown of classical EDL models for highly charged interfaces or under high ion concentrations, and describe recent modifications of the classical EDL theory relevant for understanding nanoscale electrical measurements at the solid–liquid interface. We further review the latest achievements in mapping surface charge, dielectric constants, and electrodynamic and electrochemical processes in liquids. Lastly, we outline the key challenges and opportunities that exist in the field of nanoscale electrical measurements in liquid as well as providing a roadmap for the future development of liquid KPFM.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Poplar: a phylogenomics pipeline

Motivation Generating phylogenomic trees from the genomic data is essential in understanding biological systems. Each step of this complex process has received extensive attention and has been significantly streamlined over the years. Given the public availability of data, obtaining genomes for a wide selection of species is straightforward. However, analyzing that data to generate a phylogenomic tree is a multistep process with legitimate scientific and technical challenges, often requiring a significant input from a domain-area scientist. Results We present Poplar, a new, streamlined computational pipeline, to address the computational logistical issues that arise when constructing the phylogenomic trees. It provides a framework that runs state-of-the-art software for essential steps in the phylogenomic pipeline, beginning from a genome with or without an annotation, and resulting in a species tree. Running Poplar requires no external databases. In the execution, it enables parallelism for execution for clusters and cloud computing. The trees generated by Poplar match closely with state-of-the-art published trees. The usage and performance of Poplar is far simpler and quicker than manually running a phylogenomic pipeline. Availability and implementation Freely available on GitHub at https://github.com/sandialabs/poplar. Implemented using Python and supported on Linux.

Koning, Elizabeth [Sandia National Laboratories (S↗
DOE OSTI2015

Optical laser systems at the Linac Coherent Light Source

Ultrafast optical lasers play an essential role in exploiting the unique capabilities of recently commissioned X-ray free-electron laser facilities such as the Linac Coherent Light Source (LCLS). Pump–probe experimental techniques reveal ultrafast dynamics in atomic and molecular processes and reveal new insights in chemistry, biology, material science and high-energy-density physics. This manuscript describes the laser systems and experimental methods that enable cutting-edge optical laser/X-ray pump–probe experiments to be performed at LCLS.

42 ENGINEERING↗
DOE OSTI2019

Crystal Growth for Beginners. Fundamentals of Nucleation, Crystal Growth and Epitaxy , 3rd edition . Edited by Ivan V Markov. World Scientific, 2017. Pp. 632. Hardback. Price GBP 123.00. ISBN 978-981-3143-42-5

Crystal growth is a classical discipline lying at the interfaces of Physics, Chemistry, Materials Science and Medicine. The research field has enjoyed an increasing number of young investigators over the past couple of decades, largely due to the burgeoning fields of nanoscience and nanotechnology which aim to fabricate nano-devices and/or to deliver nano-medicines in a process that mimics the exquisite wisdom of biologically controlled crystals. The interdisciplinary nature of these fields has posed a request for introductory monographs on the fundamental concepts of crystallization that are suitable for the diverse scientific backgrounds of researchers new to the field. Among many of the introductory crystal growth books, the Crystal Growth for Beginners (3rd edition) by Ivan Markov is an excellent one that can serve the purpose and is worth reading.

36 MATERIALS SCIENCE↗
DOE OSTI2015

WE-EF-BRA-08: Cell Survival in Modulated Radiation Fields and Altered DNA-Repair at Field Edges

Purpose: Tissue damage prognoses in radiotherapy are based on clonogenic assays that provide dose dependent cell survival rates. However, recent work has shown that apart from dose, systemic reactions and cell-cell communication crucially influence the radiation response. These effects are probably a key in understanding treatment approaches such as microbeam radiation therapy (MRT). In this study we tried to quantify the effects on a cellular level in spatially modulated radiation fields. Methods: Pancreas carcinoma cells were cultured, plated and irradiated by spatially modulated radiation fields with an X-ray tube and at a synchrotron. During and after treatment cells were able to communicate via the intercellular medium. Afterwards we stained for DNA and DNA damage and imaged with a fluorescence microscope. Results: Intriguingly we found that DNA damage does not strictly increase with dose. Two cell entities appear that have either a high or a low amount of DNA lesions, indicating that DNA damage is also a cell stress reaction. Close to radiation boundaries damage-levels became alike; they were higher than expected at low and lower than expected at high doses. Neighbouring cells reacted similarly. 6 hours after exposure around 40% of the cells resembled in their reactions neighbouring cells more than randomly chosen cells that received the same dose. We also observed that close to radiation boundaries the radiation induced cell-cycle arrest disappeared and the size of DNA repair-centres increased. Conclusion: Cell communication plays an important role in the radiation response of tissues and may be both, protective and destructive. These effects may not only have the potential to affect conventional radiotherapy but may also be exploited to spare organs at risk by intelligently designing irradiation geometries. To that end intensive work is required to shed light on the still obscure processes in cell-signalling and radiation biology.

60 APPLIED LIFE SCIENCES↗