Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Systems biology”

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 1,009 records · Page 56
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Rhythm of the Night (and Day): Predictive Metabolic Modeling of Diurnal Growth in Chlamydomonas

We have developed the first transient metabolic model for diurnal growth of algae based on experimental data and capable of predicting phenotype from genotype. This model enables us to evaluate the impact of genetic and environmental changes on the growth, biomass composition and intracellular fluxes of the model green alga, Chlamydomonas reinhardtii . The availability of this model will enable faster and more efficient design of cells for production of fuels, chemicals, and pharmaceuticals.

09 BIOMASS FUELS↗
NASA NTRS2016

A Mission Concept to Study Multigenerational Mammalian Reproduction in Partial Gravity

A team at NASA Langley Research Center conducted a study during which a conceptual space mission was designed. In this study, rodents are used as human analogs to gather biological and systems data in a relevant environment applicable to future settlements on Mars. The mission concept uniquely addresses the combined effects of long-durations (one-year or greater), autonomous and robotic operations, and biological responses to partial gravity with an emphasis on reproduction. The objectives of this study were to 1) understand challenges associated with designing an artificial gravity habitat that supports the reproduction and maturation of a large animal colony, 2) identify mission architectures and operational concepts to transport and maintain such a facility, and 3) identify fundamental science considerations for mammalian reproduction studies to inform vehicle design. A model demonstration unit was developed to visualize and test certain design concepts that resulted from these considerations. Three versions of this demonstration unit were built over the course of the study, each taking into account lessons learned from the previous version. This paper presents the updated baseline mission and spacecraft design concepts to achieve these objectives, with a specific emphasis on updates since publication in previous works. Analyses of the integrated system trades among the elements which make up the conceptual vehicle are described to address overall feasibility and identify potential integrated design opportunities. The latest iteration of the habitat robotics design and a conceptual design example for autonomous care of crew and systems are also presented. Finally, the conclusion of this conceptual design study, necessary future analyses to enable such a facility, and comments upon other applications of a similar exploration-focused research facilities are addressed.

Rodgers, Erica M.↗
DOE OSTI2020

Bayesian inference of Stochastic reaction networks using Multifidelity Sequential Tempered Markov Chain Monte Carlo

Stochastic reaction network models are often used to explain and predict the dynamics of gene regulation in single cells.These models usually involve several parameters, such as the kinetic rates of chemical reactions, that are not directly measurable and must be inferred from experimental data. Bayesian inference provides a rigorous probabilistic frame-work for identifying these parameters by finding a posterior parameter distribution that captures their uncertainty.Traditional computational methods for solving inference problems such as Markov Chain Monte Carlo methods based on classical Metropolis-Hastings algorithm involve numerous serial evaluations of the likelihood function, which in turn requires expensive forward solutions of the chemical master equation (CME). We propose an alternate approach based on a multifidelity extension of the Sequential Tempered Markov Chain Monte Carlo (ST-MCMC) sampler. This algorithm is built upon Sequential Monte Carlo and solves the Bayesian inference problem by decomposing it into a sequence of efficiently solved subproblems that gradually increase both model fidelity and the influence of the observed data. We reformulate the finite state projection (FSP) algorithm, a well-known method for solving the CME, to produce a hierarchy of surrogate master equations to be used in this multifidelity scheme. To determine the appropriate fidelity, we introduce a novel information-theoretic criteria that seeks to extract the most information about the ultimate Bayesian posterior from each model in the hierarchy without inducing significant bias. This novel sampling scheme is tested with high performance computing resources using biologically relevant problems.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1999

Multifractality in human heartbeat dynamics

There is evidence that physiological signals under healthy conditions may have a fractal temporal structure. Here we investigate the possibility that time series generated by certain physiological control systems may be members of a special class of complex processes, termed multifractal, which require a large number of exponents to characterize their scaling properties. We report on evidence for multifractality in a biological dynamical system, the healthy human heartbeat, and show that the multifractal character and nonlinear properties of the healthy heart rate are encoded in the Fourier phases. We uncover a loss of multifractality for a life-threatening condition, congestive heart failure.

Non-NASA Center↗
DOE OSTI2023

Photothermally Activated Artificial Neuromorphic Synapses

Biological nervous systems rely on the coordination of billions of neurons with complex, dynamic connectivity to enable the ability to process information and form memories. In turn, artificial intelligence and neuromorphic computing platforms have sought to mimic biological cognition through software-based neural networks and hardware demonstrations utilizing memristive circuitry with fixed dynamics. Here, to incorporate the advantages of tunable dynamic software implementations of neural networks into hardware, we develop a proof-of-concept artificial synapse with adaptable resistivity. This synapse leverages the photothermally induced local phase transition of VO 2 thin films by temporally modulated laser pulses. Such a process quickly modifies the conductivity of the film site-selectively by a factor of 500 to “activate” these neurons and store “memory” by applying varying bias voltages to induce self-sustained Joule heating between electrodes after activation with a laser. These synapses are demonstrated to undergo a complete heating and cooling cycle in less than 120 ns.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2022

Nonlinear model of infection wavy oscillation of COVID-19 in Japan based on diffusion kinetics

The infectious propagation of SARS-CoV-2 is continuing worldwide, and specifically, Japan is facing severe circumstances. Medical resource maintenance and action limitations remain the central measures. An analysis of long-term follow-up reports in Japan shows that the infection number follows a unique wavy oscillation, increasing and decreasing over time. However, only a few studies explain the infection wavy oscillation. This study introduces a novel nonlinear mathematical model of the new infection wavy oscillation by applying the macromolecule diffusion theory. In this model, the diffusion coefficient that depends on population density gives nonlinearity in infection propagation. As a result, our model accurately simulated infection wavy oscillations, and the infection wavy oscillation frequency and amplitude were closely linked with the recovery rate of infected individuals. In conclusion, our model provides a novel nonlinear contact infection analysis framework.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2003

The Effects of Spaceflight on the Rat Circadian Timing System

Two fundamental environmental influences that have shaped the evolution of life on Earth are gravity and the cyclic changes occurring over the 24-hour day. Light levels, temperature, and humidity fluctuate over the course of a day, and organisms have adapted to cope with these variations. The primary adaptation has been the evolution of a biological timing system. Previous studies have suggested that this system, named the circadian (circa - about; dies - a day) timing system (CTS), may be sensitive to changes in gravity. The NASA Neurolab spaceflight provided a unique opportunity to evaluate the effects of microgravity on the mammalian CTS. Our experiment tested the hypotheses that microgravity would affect the period, phasing, and light sensitivity of the CTS. Twenty-four Fisher 344 rats were exposed to 16 days of microgravity on the Neurolab STS-90 mission, and 24 Fisher 344 rats were also studied on Earth as one-G controls. Rats were equipped with biotelemetry transmitters to record body temperature (T(sub b)) and heart rate (HR) continuously while the rats moved freely. In each group, 18 rats were exposed to a 24-hour light-dark (LD 12:12) cycle, and six rats were exposed to constant dim red-light (LL). The ability of light to induce a neuronal activity marker (c-fos) in the circadian pacemaker of the brain, the suprachiasmatic nucleus (SCN), was examined in rats studied on flight days two (FD2) and 14 (FD14), and postflight days two (R+1) and 14 (R+13). The flight rats in LD remained synchronized with the LD cycle. However, their T(sub b), rhythm was markedly phase-delayed relative to the LD cycle. The LD flight rats also had a decreased T(sub b) and a change in the waveform of the T(sub b) rhythm compared to controls. Rats in LL exhibited free-running rhythms of T(sub b), and HR; however, the periods were longer in microgravity. Circadian period returned to preflight values after landing. The internal phase angle between rhythms was different in flight than in one-G. Compared with control rats, the flight rats exhibited no change in HR. Finally, the LD FD2 flight rats demonstrated a reduced sensitivity to light as shown by significantly reduced c-fos expression in the SCN in comparison with controls. These findings constitute the first demonstration that microgravity affects the fundamental properties of the mammalian circadian timing system, specifically by influencing the clock's period, and its ability to maintain temporal organization and phase angle of synchronization to an external LD cycle.

Fuller, Charles A.↗
NASA NTRS2012

Processes that Drove the Transition from Chemistry to Biology: Concepts and Evidence

Two properties are particularly germane to the transition from chemistry to biology. One is the emergence of complex molecules (polymers) capable of performing non-trivial functions, such as catalysis, energy transduction or transport across cell walls. The other is the ability of several functions to work in concert to provide reproductive advantage to systems hosting these functions. Biological systems exhibit these properties at remarkable levels of efficiency and accuracy in a way that appears effortless. However, dissection of these properties reveals great complexities that are involved. This opens a question: how a simple, ancestral system could have acquired the required properties? Other questions follow. What are the chances that a functional polymer emerges at random? What is the minimum structural complexity of a polymer to carry out a function at a reasonable level of efficiency? Can we identify concrete, protobiologically plausible mechanisms that yield advantageous coupling between different functions? These and similar questions are at the core of the main topic of this session: how soulless chemistry became life? Clearly, we do not have complete answers to any of these questions. However, in recent years a number of new and sometimes unexpected clues have been brought to light. Of particular interest are proteins because they are the main functional polymers in contemporary cells. The emergence of protein functions is a puzzle. It is widely accepted that a well ]defined, compact structure (fold) is a prerequisite for function. It is equally widely accepted that compact folds are rare among random amino acid polymers. Then, how did protein functionality start? According to one hypothesis well folded were preceded by their poorly folded, yet still functional ancestors. Only recently, however, experimental evidence supporting this hypothesis has been presented. In particular, a small enzyme capable of ligating two RNA fragments with the rate of 106 above background was evolved in vitro. This enzyme does not look like any contemporary protein. It is very flexible and its structure is kept together just by a single salt bridge between a charged residue and a coordinating zinc. A similar picture emerges from studies of simple transmembrane channels that mimic those in ancestral cells. Again, they are extremely flexible and do not form a conventional pore. Yet, they efficiently mediate ion transport. Studies on simple proteins that are on-going in several laboratories hold promise of revealing crucial links between chemical and biological catalysis and other ubiquitous cell functions. Interaction between composition, growth and division of protobiologically relevant vesicles and metabolic reactions that they encapsulate is an example of coupling between simple functions that promotes reproduction and evolution. Recent studies have demonstrated possible mechanisms by which vesicles might have evolved their composition from fatty acids to phospholipids, thus facilitating a number of new cellular functions. Conversely, it has been also demonstrated that an encapsulated metabolism might drive vesicle division. These are, again, examples of processes that might have driven the transition from chemistry to biology.

Pohorille, Andrew↗
DOE OSTI2020

An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics

Mass spectrometry (MS)-based proteomics has great potential for overcoming the limitations of antibody-based immunoassays for antibody-independent, comprehensive, and quantitative proteomic analysis of single cells. Indeed, recent advances in nanoscale sample preparation have enabled effective processing of single cells. In particular, the concept of using boosting/carrier channels in isobaric labeling to increase the sensitivity in MS detection has also been increasingly used for quantitative proteomic analysis of small-sized samples including single cells. However, the full potential of such boosting/carrier approaches has not been significantly explored, nor has the resulting quantitation quality been carefully evaluated. Herein, we have further evaluated and optimized our recent boosting to amplify signal with isobaric labeling (BASIL) approach, originally developed for quantifying phosphorylation in small number of cells, for highly effective analysis of proteins in single cells. This improved BASIL (iBASIL) approach enables reliable quantitative single-cell proteomics analysis with greater proteome coverage by carefully controlling the boosting-to-sample ratio (e.g. in general <100×) and optimizing MS automatic gain control (AGC) and ion injection time settings in MS/MS analysis (e.g. 5E5 and 300 ms, respectively, which is significantly higher than that used in typical bulk analysis). By coupling with a nanodroplet-based single cell preparation (nanoPOTS) platform, iBASIL enabled identification of ~2500 proteins and precise quantification of ~1500 proteins in the analysis of 104 FACS-isolated single cells, with the resulting protein profiles robustly clustering the cells from three different acute myeloid leukemia cell lines. This study highlights the importance of carefully evaluating and optimizing the boosting ratios and MS data acquisition conditions for achieving robust, comprehensive proteomic analysis of single cells.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

Hybrid Modeling for Testing Intelligent Software for Lunar-Mars Closed Life Support

Intelligent software is being developed for closed life support systems with biological components, for human exploration of the Moon and Mars. The intelligent software functions include planning/scheduling, reactive discrete control and sequencing, management of continuous control, and fault detection, diagnosis, and management of failures and errors. Four types of modeling information have been essential to system modeling and simulation to develop and test the software and to provide operational model-based what-if analyses: discrete component operational and failure modes; continuous dynamic performance within component modes, modeled qualitatively or quantitatively; configuration of flows and power among components in the system; and operations activities and scenarios. CONFIG, a multi-purpose discrete event simulation tool that integrates all four types of models for use throughout the engineering and operations life cycle, has been used to model components and systems involved in the production and transfer of oxygen and carbon dioxide in a plant-growth chamber and between that chamber and a habitation chamber with physicochemical systems for gas processing.

Malin, Jane T.↗
NASA NTRSDate not supplied

The membrane bioreactor (MBR): A hybrid technology for bioregenerative wastewater treatment and resource recovery in space

Extraplanetary surface habitat life support systems (LSS) on the Moon and Mars, as well as long-duration space travel, will require novel capabilities to withstand anticipated unique, harsh conditions. In order to provide safe, habitable environments for the crew, water purification and waste processing systems will be required to treat all sources of water (condensate, Sabatier, urine, hygiene, fecal, food waste) in order to achieve the necessary levels of recovery needed to sustain life over the long-duration missions. The ability to recycle organic wastes creates an opportunity to recover critical elements (e.g., C, H, O, N, P) for subsequent food production, water purification, and atmospheric regeneration. Bioregenerative systems mimic functions of nature in engineered systems, or bioreactors, utilizing combination of prokaryotes, eukaryotes and archaea. While these systems are commonly used on Earth for wastewater treatment, bioreactors for space travel face additional challenges. Terrestrial bioreactors often rely on gravitational settling of dense flocs and granules for cell retention. For micro- or partial-gravity environments, density differential alone will not be adequate for cell retention; a gravity-independent means for cell retention is crucial. The membrane bioreactor represents the state of the art in wastewater treatment. This hybrid system combines biological processes with membrane filtration to achieve performance beyond what each can accomplish individually. The complete cell retention in an MBR allows for the decoupling of hydraulic retention time (HRT) and solids retention time (SRT), which result in a high-thruput, compact, treatment system. The Bioregenerative Water Technology Team at NASA Kennedy Space Center and the University of South Florida has developed a bioregenerative platform based on the hybrid MBR technology. The overall architecture is compact, modular, flexible, and adaptable to mission evolutions. The main subsystems of the bioregenerative architecture include: 1) Anaerobic membrane bioreactor (AnMBR): Also termed the Organic processor assembly (OPA), the function of the AnMBR is to treat organic wastes such as fecal and food wastes. These wastes are characterized by a concentration of suspended solids comprised of carbohydrates, proteins and lipids. The assigned function of the AnMBR is to break down and covert suspended solids to biogas (methane, hydrogen and carbon dioxide), reduce effluent chemical oxygen demand (COD), liberate organically-bound nutrients, and remove pathogenic organisms. 2) Phototrophic membrane bioreactor (PMBR): The PMBR is comprised of a co-culture of microalgae and bacteria. The assigned function of the PMBR is to polish the permeate of the AnMBR to further remove dissolved organic carbon, manage nutrients (nitrogen transformation, load dampening), and perform air revitalization. 3) Food processor assembly (FPA): The FPA is a food production platform (prokaryotic or eukaryotic), fueled by outputs from the AnMBR, or PMBR. For the presentation, we will describe each step of the bioregenerative architecture, and present performance data from extended trials treating analog and real metabolic wastes.

Bioreactor↗
NASA NTRS2016

GeneLab: Multi-Omics Investigation of Rodent Research-1 Bio-Banked Tissues

NASAs Rodent Research (RR) project is playing a critical role in advancing biomedical research on the physiological effects of space environments. Due to the limited resources for conducting biological experiments aboard the International Space Station (ISS), it is imperative to use crew time efficiently while maximizing high-quality science return. NASAs GeneLab project has as its primary objectives to 1) further increase the value of these experiments using a multi-omics, systems biology-based approach, and 2) disseminate these data without restrictions to the scientific community. The current investigation assessed viability of RNA, DNA, and protein extracted from archived RR-1 tissue samples for epigenomic, transcriptomic, and proteomic assays. During the first RR spaceflight experiment, a variety of tissue types were harvested from subjects, snap-frozen or RNAlater-preserved, and then stored at least a year at -80OC after return to Earth. They were then prioritized for this investigation based on likelihood of significant scientific value for spaceflight research. All tissues were made available to GeneLab through the bio-specimen sharing program managed by the Ames Life Science Data Archive and included mouse adrenal glands, quadriceps, gastrocnemius, tibialis anterior, extensor digitorum longus, soleus, eye, and kidney. We report here protocols for and results of these tissue extractions, and thus, the feasibility and value of these kinds of omics analyses. In addition to providing additional opportunities for investigation of spaceflight effects on the mouse transcriptome and proteome in new kinds of tissues, our results may also be of value to program managers for the prioritization of ISS crew time for rodent research activities. Support from the NASA Space Life and Physical Sciences Division and the International Space Station Program is gratefully acknowledged.

GeneLab↗
DOE OSTI2025

A SynBio explosion: a whole new world for Rubisco engineering

The first Escherichia coli synthetic biology (SynBio) system to successfully heterologously assemble chloroplast Rubisco represented the culmination of decades of Rubisco biogenesis research (Aigner et al., 2017). This system for Arabidopsis Rubisco ushered in a new era of higher throughput Rubisco studies, and has since been adapted for a limited number of other Rubiscos, accelerating both fundamental and applied Rubisco research. Archer et al. (2025) have developed new SynBio systems to assemble a larger variety of C 3 Rubiscos and the first C 4 and monocot Rubiscos, greatly expanding crop Rubisco engineering capabilities. Their explorations of chaperone selectivity and versatility could enable rapid production of SynBio systems for additional species.

Rubisco↗
NASA NTRS2003

Micro-Detection System for Determination of the Biotic or Abiotic Origin of Amino Acids

The research carried out under this PIDDP involves the development of a breadboard version of a spacecraft-based system for the detection of amino acid chirality (molecular handedness) on solar system bodies. Chirality provides an unambiguous way of distinguishing between abiotic and biotic origins since only one mirror-image form is used in the functional molecules of life. Recent advances in a variety of nano-fabrication technologies have resulted in concepts for enabling miniaturized chemical and biological analytical systems. These are complete application-specific systems that integrate fluid micro handling systems for extracting and reacting target molecules, micro-separation technologies for enhanced sensitivity and resolution, and advanced detection technologies. This effort makes use of a relatively new technology that shows demonstrated promise for spacecraft-based amino acid analysis: microchip-based capillary electrophoresis (μCE). The μCE system is capable of analyzing the type of amino acids present as well as the relative amounts of their mirror image forms. The system we developed will be able to chirally resolve all of the major amino acids found in extraterrestrial material (Gly, Ala, Val, Pro, Asp, Glu, a-aminoisobutyric acid, and isovaline) at sub-part-per-billion levels. The -CE analysis requires that the amino acids be extracted from the sample and derivatized for either optical or electrochemical detection. In our implementation, the amino acids are released from the sample by sublimation and prepared for μCE analysis using a microfluidic circuit. In addition, we have investigated the use of a microfluidic circuit for the release of amino acids from samples in which sublimation has proven to be problematic.

Jeffrey L Bada↗