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NASA NTRS2013

Calculating Conductance of Ion Channels

We have simulated two small ion channels in a water/membrane system, which consists of 71,000-72,000 atoms, and have estimated the conductance by way of counting ions crossing these channels in applied field. The calculated values of conductance have been compared with predictions of the electrodiffusion model. In a recently developed theoretical framework, all commonly used assumptions of the model can be tested. If they are satisfied, which is often the case, the approach provides a rigorous way to extrapolate conductance calculated at one voltage to other voltages. This, in turn, allows for efficient estimations of current-voltage dependence, examining rectifying behavior of channels and calculating the reversal potential. Furthermore, the consistency of the results can be precisely tested. Simulations at microsecond time scales are required to sufficiently reduce statistical errors and separate them from possible systematic errors. Only then the accuracy of the proposed approach can be properly tested. Linking simulations with electrophysiology provides a stringent, highly relevant test for the correctness of computer simulations of ion channels. Considering biological, medical and pharmaceutical importance of these proteins, results of the proposed study might motivate the development of improved hardware and software that would enable applying a similar strategy to more complex channels at longer times.

Ion↗

NASA NTRSDate not supplied

NASA’s Advance Information Systems Technology (AIST) Program

NASA’s Earth Science Technology Office (ESTO) develops early-stage technologies to enhance scientific understanding. ESTO’s technologies can be reliably and confidently applied to a broad range of science measurements and missions, as well as facilitate practical applications to benefit society at large. As the lead technology office within the Earth Science Division of the NASA Science Mission Directorate, ESTO is focused on the technological challenges inherent to space-based investigations of our planet's dynamic, interrelated systems. Through flexible, science-driven technology strategies and a competitive selection process, ESTO-funded technologies have supported numerous Earth science missions as well as commercial applications. From next generation sensors and instruments to communication and information systems, ESTO technologies enable many NASA missions and data services. The Advanced Information Systems Technology (AIST) Program is one focal area of ESTO. AIST innovates information system technologies that enable the development of new observing systems as well as agile science investigations through data analytics and artificial intelligence tools and algorithms. AIST utilizes an end-to-end development approach with the goal of infusing mature technologies into future missions, measurements, and analysis. One thrust of AIST is data exploitation and analysis using an analytic center framework to make observational data and model output more accessible and usable to scientists conducting specific investigations as well as to extract higher-level science content and information from the data. The framework accelerates scientific discovery by harmonizing the data, tools, and computational resources. NASA’s upcoming Surface, Biology and Geology (SBG) mission is one such mission whose data architecture will leverage many of the technologies developed through the AIST program. This talk will highlight current and future program development goals.

Laura Rogers↗

NASA NTRS2005

Artificial Immune System for Recognizing Patterns

A method of recognizing or classifying patterns is based on an artificial immune system (AIS), which includes an algorithm and a computational model of nonlinear dynamics inspired by the behavior of a biological immune system. The method has been proposed as the theoretical basis of the computational portion of a star-tracking system aboard a spacecraft. In that system, a newly acquired star image would be treated as an antigen that would be matched by an appropriate antibody (an entry in a star catalog). The method would enable rapid convergence, would afford robustness in the face of noise in the star sensors, would enable recognition of star images acquired in any sensor or spacecraft orientation, and would not make an excessive demand on the computational resources of a typical spacecraft. Going beyond the star-tracking application, the AIS-based pattern-recognition method is potentially applicable to pattern- recognition and -classification processes for diverse purposes -- for example, reconnaissance, detecting intruders, and mining data.

Huntsberger, Terrance↗

NASA NTRS2010

GUI to Facilitate Research on Biological Damage from Radiation

A graphical-user-interface (GUI) computer program has been developed to facilitate research on the damage caused by highly energetic particles and photons impinging on living organisms. The program brings together, into one computational workspace, computer codes that have been developed over the years, plus codes that will be developed during the foreseeable future, to address diverse aspects of radiation damage. These include codes that implement radiation-track models, codes for biophysical models of breakage of deoxyribonucleic acid (DNA) by radiation, pattern-recognition programs for extracting quantitative information from biological assays, and image-processing programs that aid visualization of DNA breaks. The radiation-track models are based on transport models of interactions of radiation with matter and solution of the Boltzmann transport equation by use of both theoretical and numerical models. The biophysical models of breakage of DNA by radiation include biopolymer coarse-grained and atomistic models of DNA, stochastic- process models of deposition of energy, and Markov-based probabilistic models of placement of double-strand breaks in DNA. The program is designed for use in the NT, 95, 98, 2000, ME, and XP variants of the Windows operating system.

Cucinotta, Frances A.↗

NASA NTRS1992

High level cognitive information processing in neural networks

Two related research efforts were addressed: (1) high-level connectionist cognitive modeling; and (2) local neural circuit modeling. The goals of the first effort were to develop connectionist models of high-level cognitive processes such as problem solving or natural language understanding, and to understand the computational requirements of such models. The goals of the second effort were to develop biologically-realistic model of local neural circuits, and to understand the computational behavior of such models. In keeping with the nature of NASA's Innovative Research Program, all the work conducted under the grant was highly innovative. For instance, the following ideas, all summarized, are contributions to the study of connectionist/neural networks: (1) the temporal-winner-take-all, relative-position encoding, and pattern-similarity association techniques; (2) the importation of logical combinators into connection; (3) the use of analogy-based reasoning as a bridge across the gap between the traditional symbolic paradigm and the connectionist paradigm; and (4) the application of connectionism to the domain of belief representation/reasoning. The work on local neural circuit modeling also departs significantly from the work of related researchers. In particular, its concentration on low-level neural phenomena that could support high-level cognitive processing is unusual within the area of biological local circuit modeling, and also serves to expand the horizons of the artificial neural net field.

Barnden, John A.↗

NASA NTRS1989

Preliminary analyses of space radiation protection for lunar base surface systems

Radiation shielding analyses are performed for candidate lunar base habitation modules. The study primarily addresses potential hazards due to contributions from the galactic cosmic rays. The NASA Langley Research Center's high energy nucleon and heavy ion transport codes are used to compute propagation of radiation through conventional and regolith shield materials. Computed values of linear energy transfer are converted to biological dose-equivalent using quality factors established by the International Commision of Radiological Protection. Special fluxes of heavy charged particles and corresponding dosimetric quantities are computed for a series of thicknesses in various shield media and are used as an input data base for algorithms pertaining to specific shielded geometries. Dosimetric results are presented as isodose contour maps of shielded configuration interiors. The dose predictions indicate that shielding requirements are substantial, and an abbreviated uncertainty analysis shows that better definition of the space radiation environment as well as improvement in nuclear interaction cross-section data can greatly increase the accuracy of shield requirement predictions.

Nealy, John E.↗

NASA NTRS1997

Linear and nonlinear ARMA model parameter estimation using an artificial neural network

This paper addresses parametric system identification of linear and nonlinear dynamic systems by analysis of the input and output signals. Specifically, we investigate the relationship between estimation of the system using a feedforward neural network model and estimation of the system by use of linear and nonlinear autoregressive moving-average (ARMA) models. By utilizing a neural network model incorporating a polynomial activation function, we show the equivalence of the artificial neural network to the linear and nonlinear ARMA models. We compare the parameterization of the estimated system using the neural network and ARMA approaches by utilizing data generated by means of computer simulations. Specifically, we show that the parameters of a simulated ARMA system can be obtained from the neural network analysis of the simulated data or by conventional least squares ARMA analysis. The feasibility of applying neural networks with polynomial activation functions to the analysis of experimental data is explored by application to measurements of heart rate (HR) and instantaneous lung volume (ILV) fluctuations.

NASA Discipline Regulatory Physiology↗

NASA NTRS2002

A genomic regulatory network for development

Development of the body plan is controlled by large networks of regulatory genes. A gene regulatory network that controls the specification of endoderm and mesoderm in the sea urchin embryo is summarized here. The network was derived from large-scale perturbation analyses, in combination with computational methodologies, genomic data, cis-regulatory analysis, and molecular embryology. The network contains over 40 genes at present, and each node can be directly verified at the DNA sequence level by cis-regulatory analysis. Its architecture reveals specific and general aspects of development, such as how given cells generate their ordained fates in the embryo and why the process moves inexorably forward in developmental time.

Non-NASA Center↗

NASA NTRS1993

Improved inhalation technology for setting safe exposure levels for workplace chemicals

Threshold Limit Values recommended as allowable air concentrations of a chemical in the workplace are often based upon a no-observable-effect-level (NOEL) determined by experimental inhalation studies using rodents. A 'safe level' for human exposure must then be estimated by the use of generalized safety factors in attempts to extrapolate from experimental rodents to man. The recent development of chemical-specific physiologically-based toxicokinetics makes use of measured physiological, biochemical, and metabolic parameters to construct a validated model that is able to 'scale-up' rodent response data to predict the behavior of the chemical in man. This procedure is made possible by recent advances in personal computer software and the emergence of appropriate biological data, and provides an analytical tool for much more reliable risk evaluation and airborne chemical exposure level setting for humans.

Stuart, Bruce O.↗

NASA NTRS1995

Low Temperature Performance of High-Speed Neural Network Circuits

Artificial neural networks, derived from their biological counterparts, offer a new and enabling computing paradigm specially suitable for such tasks as image and signal processing with feature classification/object recognition, global optimization, and adaptive control. When implemented in fully parallel electronic hardware, it offers orders of magnitude speed advantage. Basic building blocks of the new architecture are the processing elements called neurons implemented as nonlinear operational amplifiers with sigmoidal transfer function, interconnected through weighted connections called synapses implemented using circuitry for weight storage and multiply functions either in an analog, digital, or hybrid scheme.

artificial neural networks image processing signal↗

NASA NTRS2012

Computing Radiative Transfer in a 3D Medium

A package of software computes the time-dependent propagation of a narrow laser beam in an arbitrary three- dimensional (3D) medium with absorption and scattering, using the transient-discrete-ordinates method and a direct integration method. Unlike prior software that utilizes a Monte Carlo method, this software enables simulation at very small signal-to-noise ratios. The ability to simulate propagation of a narrow laser beam in a 3D medium is an improvement over other discrete-ordinate software. Unlike other direct-integration software, this software is not limited to simulation of propagation of thermal radiation with broad angular spread in three dimensions or of a laser pulse with narrow angular spread in two dimensions. Uses for this software include (1) computing scattering of a pulsed laser beam on a material having given elastic scattering and absorption profiles, and (2) evaluating concepts for laser-based instruments for sensing oceanic turbulence and related measurements of oceanic mixed-layer depths. With suitable augmentation, this software could be used to compute radiative transfer in ultrasound imaging in biological tissues, radiative transfer in the upper Earth crust for oil exploration, and propagation of laser pulses in telecommunication applications.

Von Allmen, Paul↗

NASA NTRSDate not supplied

Pushing the Limits of Aquatic Remote Sensing: Synthetic Data and Deep Learning for Fast Inverse Emulation of A Coupled Ocean-Atmosphere Radiative Transfer Model

The inversion of electromagnetic information to physical and biological properties of the water column is a notoriously difficult problem, yet fundamental to our ability of understanding aquatic processes on large time and space scales. There is now a growing necessity to develop pragmatic approaches that allow timely and effective extrapolation of local processes, to spatially resolved global products, and to promote operational and sustainable resource policy management. This presentation will discuss research integrating advanced biological and radiative modeling, high-end computation, and machine learning to develop a portable global processor for simultaneous retrieval of atmosphere and water optics for diverse aquatic systems from the open and coastal ocean to optically extreme inland waters and harmful algal blooms. We will discuss some of the basic concepts behind the forward modeling approach including DEAP, the novel Distributed Equivalent Algal Populations model, for developing large spectral libraries of aquatic particle optics to aid in our ability to distinguish phytoplankton functional types (PFTs) and inorganic material, as well as other factors which enable comprehensive modeling from the benthos to top-of-atmosphere (TOA). This information is being used to understand how we can leverage next-generation deep learning methods for maximum information retrieval and rapid image processing, while also providing capabilities to identify minimum sensor spectral requirements necessary for certain aquatic applications. Further, I will touch on how we envision this research to enable the aquatic community for science discovery and how we are moving closer towards the capability for high-fidelity global analysis of aquatic ecosystems.

Jeremy Alan Kravitz↗

NASA NTRS2004

Biomimetic robots using EAP as artificial muscles - progress and challenges

Biology offers a great model for emulation in areas ranging from tools, computational algorithms, materials science, mechanisms and information technology. In recent years, the field of biomimetics, namely mimicking biology, has blossomed with significant advances enabling the reverse engineering of many animals' functions and implementation of some of these capabilities.

robotics↗

NASA NTRSDate not supplied

Graphical User Interface (GUI) Implementation for Agent-Based Microbial Radiobiology Model

Sending human life past the Low Earth Orbit (LEO) to explore the Moon and Mars will be challenging. The Earth’s magnetic field naturally protects life from deep-space particle radiation such as Galactic Cosmic Rays (GCR) and Solar Particle Events (SPE); these will pose health risks to humans in deep space. Research has been done to investigate these effects, like BioSentinel, the first biological CubeSat to fly beyond the LEO, designed to culture yeast in a microfluidic device and record optical measurements of growth and metabolism. However, experiments can only report cell damage as bulk growth curves, while deep-space radiation causes damage that is heterogeneous among individual cells. AMMPER is an open-source, agent-based, computational model coded in Python to simulate the effects of deep-space radiation on individual yeast cells (Saccharomyces cerevisiae) to facilitate interpretation of biological radiation experiments. Version 1.0 of the code ran in a command line interface (CLI), limiting use to those familiar with modularization, object-oriented programming, and computational models. Here we present a graphical user interface (GUI) for AMMPER to increase its accessibility. GUI development included converting input points and UI files, designing an application and logo, and expanding program packages. Additionally, we added optical assistance that corresponded with simulation parameters, which included simulation type, cell type, ROS model, and radiation dosage, as well as customizable display and file exportation features. Following a pilot testing period, its structure was updated further to enhance abilities, adding increased runs, video visualization, data plotting, and an educational/tutorial component. Future work will include creating a bit installer and runtime environment for AMMPER. Ultimately, the creation of the GUI has two main goals: to facilitate the integration of computational models into the work of researchers in microbial radiobiology, and to act as an interactive and visual resource for space biology education.

yeast↗

NASA NTRS2011

Evolutionary Computational Methods for Identifying Emergent Behavior in Autonomous Systems

A technique based on Evolutionary Computational Methods (ECMs) was developed that allows for the automated optimization of complex computationally modeled systems, such as autonomous systems. The primary technology, which enables the ECM to find optimal solutions in complex search spaces, derives from evolutionary algorithms such as the genetic algorithm and differential evolution. These methods are based on biological processes, particularly genetics, and define an iterative process that evolves parameter sets into an optimum. Evolutionary computation is a method that operates on a population of existing computational-based engineering models (or simulators) and competes them using biologically inspired genetic operators on large parallel cluster computers. The result is the ability to automatically find design optimizations and trades, and thereby greatly amplify the role of the system engineer.

Terrile, Richard J.↗

NASA NTRS2007

Microscopic Observation of Self-Propagation of Calcifying Nanoparticles (Nanobacteria)

Biologists typically define living organisms as carbon and water-based cellular forms with :self-replication" as the fundamental trait of the life process. However, this standard dictionary definition of life does not help scientists to categorize self-replicators like viruses, prions, proteons and artificial life. CNP also named nanobacteria were discovered in early 1990s as about 100 nanometer-sized bacteria-like particles with unique apatite mineral-shells around them, and found to be associated with pathological-calcification related diseases. Although CNP have been isolated and cultured from mammalian blood and diseased calcified tissues, and their biomineralizing properties well established, their biological nature and self-replicating capability have always been severely challenged. The terms "self-replication", "self-assembly" or "self-propagation" have been widely used for all systems including nanomachines, crystals, computer viruses and memes. In a simple taxonomy, all biological and non-biological "self replicators", have been classified into "living" or "nonliving" based on the properties of the systems and the amount of support they require to self-replicate. To enhance our understanding about self-replicating nature of CNP, we have investigated their growth in specific culture conditions using conventional inverted light microscope and BioStation IM, Nikon s latest time-lapse imaging system. Their morphological structure was examined using scanning (SEM) and transmission (TEM) electron microscopy. This present study, in conjunction with previous findings of metabolic activity, antibiotic sensitivity, antibody specificity, morphological aspects and infectivity, all concomitantly validate CNP as living self-replicators.

Mathew, Grace↗

NASA NTRS2000

The Biological Relevance of Artificial Life: Lessons from Artificial Intelligence

There is no fundamental reason why A-life couldn't simply be a branch of computer science that deals with algorithms that are inspired by, or emulate biological phenomena. However, if these are the limits we place on this field, we miss the opportunity to help advance Theoretical Biology and to contribute to a deeper understanding of the nature of life. The history of Artificial Intelligence provides a good example, in that early interest in the nature of cognition quickly was lost to the process of building tools, such as "expert systems" that, were certainly useful, but provided little insight in the nature of cognition. Based on this lesson, I will discuss criteria for increasing the biological relevance of A-life and the probability that this field may provide a theoretical foundation for Biology.

Colombano, Silvano↗

NASA NTRSDate not supplied

Biological Research and Space Health Enabled by Machine Learning to Support Deep Space Missions

A key science goal of the NASA “Moon to Mars” campaign is to understand how biology responds to the Lunar, Martian, and deep space environments in order to advance fundamental knowledge and support human space missions. Through artificial intelligence (AI) and machine learning (ML), a paradigm shift has begun in space biosciences and engineered astronaut health systems, to enable Earth-independence and mission operations autonomy. We describe current AI/ML methods to support 1) fundamental biology, 2) in situ analytics, 3) high performance computing, 4) automated science, 5) self-driving labs, 6) remote data management, 7) integrated mission biomonitoring, and 8) a Precision Space Health system. AI/ML approaches that can be integrated to support these domains include active learning, explainable AI, adaptive learning, causal inference, knowledge graphs, federated learning, transfer learning, and large language models. Finally, we present results from several current ML projects that are underway in the space biology field to address key challenges of small sample n, high feature count, heterogeneity, and sparse data. These include 1) connecting omics to phenotypic data using an ensemble model to infer causality of rodent liver health disruption, 2) usage of explainable ML to interrogate muscular underpinnings of muscle atrophy, 3) ML models analyzing and determining directed acyclic graphs of human health risk leveraging rodent bone datasets, 4) usage of large pre-trained models connecting biomedical knowledgebases with small spaceflight datasets to understand gene-to-gene interactions, and 5) a suite of benchmarked open science datasets enabling programmers to identify best algorithms to answer space biology questions.

space biology↗