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All sourcesNASA NTRSDOE OSTI
NASA NTRS2015

Free-Energy Calculations. A Mathematical Perspective

Ion channels are pore-forming assemblies of transmembrane proteins that mediate and regulate ion transport through cell walls. They are ubiquitous to all life forms. In humans and other higher organisms they play the central role in conducting nerve impulses. They are also essential to cardiac processes, muscle contraction and epithelial transport. Ion channels from lower organisms can act as toxins or antimicrobial agents, and in a number of cases are involved in infectious diseases. Because of their important and diverse biological functions they are frequent targets of drug action. Also, simple natural or synthetic channels find numerous applications in biotechnology. For these reasons, studies of ion channels are at the forefront of biophysics, structural biology and cellular biology. In the last decade, the increased availability of X-ray structures has greatly advanced our understanding of ion channels. However, their mechanism of action remains elusive. This is because, in order to assist controlled ion transport, ion channels are dynamic by nature, but X-ray crystallography captures the channel in a single, sometimes non-native state. To explain how ion channels work, X-ray structures have to be supplemented with dynamic information. In principle, molecular dynamics (MD) simulations can aid in providing this information, as this is precisely what MD has been designed to do. However, MD simulations suffer from their own problems, such as inability to access sufficiently long time scales or limited accuracy of force fields. To assess the reliability of MD simulations it is only natural to turn to the main function of channels - conducting ions - and compare calculated ionic conductance with electrophysiological data, mainly single channel recordings, obtained under similar conditions. If this comparison is satisfactory it would greatly increase our confidence that both the structures and our computational methodologies are sufficiently accurate. Channel conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

free energy↗
NASA NTRS2003

Noninvasive, near infrared spectroscopic-measured muscle pH and PO2 indicate tissue perfusion for cardiac surgical patients undergoing cardiopulmonary bypass

OBJECTIVE: To determine whether near infrared spectroscopic measurement of tissue pH and Po2 has sufficient accuracy to assess variation in tissue perfusion resulting from changes in blood pressure and metabolic demand during cardiopulmonary bypass. DESIGN: Prospective clinical study. SETTING: Academic medical center. SUBJECTS: Eighteen elective cardiac surgical patients. INTERVENTION: Cardiac surgery under cardiopulmonary bypass. MEASUREMENTS AND MAIN RESULTS: A near infrared spectroscopic fiber optic probe was placed over the hypothenar eminence. Reference Po2 and pH sensors were inserted in the abductor digiti minimi (V). Data were collected every 30 secs during surgery and for 6 hrs following cardiopulmonary bypass. Calibration equations developed from one third of the data were used with the remaining data to investigate sensitivity of the near infrared spectroscopic measurement to physiologic changes resulting from cardiopulmonary bypass. Near infrared spectroscopic and reference pH and Po2 measurements were compared for each subject using standard error of prediction. Near infrared spectroscopic pH and Po2 at baseline were compared with values during cardiopulmonary bypass just before rewarming commenced (hypotensive, hypothermic), after rewarming (hypotensive, normothermic) just before discontinuation of cardiopulmonary bypass, and at 6 hrs following cardiopulmonary bypass (normotensive, normothermic) using mixed-model analysis of variance. Near infrared spectroscopic pH and Po2 were well correlated with the invasive measurement of pH (R2 =.84) and Po2 (R 2 =.66) with an average standard error of prediction of 0.022 +/- 0.008 pH units and 6 +/- 3 mm Hg, respectively. The average difference between the invasive and near infrared spectroscopic measurement was near zero for both the pH and Po2 measurements. Near infrared spectroscopic Po2 significantly decreased 50% on initiation of cardiopulmonary bypass and remained depressed throughout the bypass and monitored intensive care period. Near infrared spectroscopic pH decreased significantly during cardiopulmonary bypass, decreased significantly during rewarming, and remained depressed 6 hrs after cardiopulmonary bypass. Diabetic patients responded differently than nondiabetic subjects to cardiopulmonary bypass, with lower muscle pH values (p =.02). CONCLUSIONS: Near infrared spectroscopic-measured muscle pH and Po2 are sensitive to changes in tissue perfusion during cardiopulmonary bypass.

Non-NASA Center↗
NASA NTRS2003

An Examination of Issues Related to a Europa Subsurface Component for the JIMO Mission

The Galileo Europa data set served to revolutionize our view of Europa. In particular the strong evidence of a large, cold, salty Ocean beneath 5-30 km of ice has profoundly altered the significance of Europa in our thinking, especially of context of habitability in the solar system. While much remains to be learned from spacecraft observations of several sorts, there are significant questions answerable only by in-situ techniques; these relate to the formation of Europa, the nature of its ocean, and the prospects for life in its ocean, sediments, and ice. We feel that wide-ranging discussion of an in-situ subsurface mission to Europa, as part of JIMO, should proceed. The science objective of the mission is to characterize the icy shell of Europa to resolve its provenance, estimate the composition of brine of the Europa ocean, and search for evidence of Earth-like life. Probably anyone would agree that an in-situ mission to Europa would be of great value, but he or she would also immediately take the position that such a mission is utterly impractical. We take the position here of defining the least complex mission that can nonetheless justify its cost and to argue that such a mission is realistic enough that it should be seriously considered. Our mission thinking has been: 1) Soft landing. A soft lander is required on a site sufficiently flat to offer a stable platform; no further site selectivity is required. 2) Subsurface exploration. The Europa subsurface must be examined. Surficial processes on Europa arguably have exposed the upper 200 m of shell to chemical effects from the Jovian radiation belts as well as cometary infall, etc; to examine native ice we must descend below that point to, for discussion, 300 m. At that depth we argue that the ice is characteristic of ice at depth and possibly is effectively sea ice. 3) Science data. A few simple measurements at various depths and at 300 m constitute a scientifically successful mission. Measurements would include analysis of meltwater for a few inorganic ions and amino acids and an optical examination of the borehole wall. 4) Communication. Transmission of data to an orbiter is essential, but we will constrain the landed mission to a daily communication over a few days. 5) Subsurface access. Drilling to 300 m is a significant challenge; it can be addressed by several means: Thermal Probe (Cryobot) which permits water to refreeze above the vehicle. This is our tentative choice with plutonium as the fuel to generate thermal energy for drilling and electrical power for operations. Open Hole Drill, a thermal system in which the meltwater is removed for greater thermal efficiency. Meltwater removal on Europa is both a complexity and a risk, but analysis is improved. Mechanical Drilling in which cutting or grinding generates ice chips which are removed. This is too complex at Europa temperatures. The measurement objectives for the mission will be: Obj. 1: Determine the concentration of simple inorganic salts in the Europa Ice Shell and, by extrapolation, of the ocean. These data will also validate spaceborne sensors. Obj. 2: Determine the nature and abundance of amino acids in the ice such that cometary infall material in the upper ice can be compared to material at depth. Obj. 3: Optically examine the ice to resolve inclusion structure, particulate content, and stratification. Access to 300 m depth is a significant if not audacious plan; we are aware that this has not been done on any planetary body. Our approach is the use of a plutonium heat source; to overcome Europa's surface temperature and to melt ice a significant amount of plutonium is needed, and significant shielding and other protective steps will be required. The quantity of plutonium is a key concern. The mission will require subsurface collection and processing of samples for in situ analysis, calling for a miniature, high pressure micro-sampling system designed to meet needs of instruments that require low presses for operation. The inlet system itself collects a micro-sample in the external high pressure environment, then transfers it into a protected low pressure environment for analysis.

Carsey, F. D.↗
NASA NTRS1999

Origin and Reactivity of the Martian Soil: A 2003 Micromission

The role of water in the development of the martian surface remains a fundamental scientific question. Did Mars have one or more "warm and wet" climatic episodes where liquid water was stable at the surface? If so, the mineral phases present in the soils should be consistent with a history of aqueous weathering. More generally, the formation of hydrated mineral phases on Mars is a strong indicator of past habitable surface environments. The primary purpose of this investigation is to help resolve the question of whether such aqueous indicators are present on Mars by probing the upper meter for diagnostic mineral species. According to Burns [1993], the formation of the ferric oxides responsible for the visible color of Mars are the result of dissolution of Fe (+2) phases from basalts followed by aqueous oxidation and precipitation of Fe" mineral assemblages. These precipitates likely included iron oxyhydroxides such as goethite (a-FeOOH) and lepidocrocite (g-FeOOH), but convincing evidence for these phases at the surface is still absent. The stability of these minerals is enhanced beneath the surface, and thus we propose a subsurface search for hydroxylated iron species as a test for a large-scale chemical weathering process based on interactions with liquid water. It is also possible that the ferric minerals on Mars are not aqueous alteration products of the rocks. A chemical study of the Pathfinder landing site concluded that the soils are not directly derived from the surrounding rocks and are enhanced in Mg and Fe. The additional source of these elements might be from other regions of Mars and transported by winds, or alternatively, from exogenic sources. Gibson [1970] proposed that the spectral reflectivity of Mars is consistent with oxidized meteoritic material. Yen and Murray [1998] further extend Gibson's idea and show, in the laboratory, that metallic iron can be readily oxidized to maghemite and hematite under present-day martian surface conditions (in the absence of liquid water). A test for a meteoritic component of the soil can be conducted, as described below, by searching for the presence of Ni at the martian surface. The average abundance of nickel in an Fe-Ni meteorite is about 7% and, if present at measurable levels in the soil, would be indicative of an exogenic contribution. In addition, it may be possible to directly search for mineral phases common in meteorites. An understanding of the formation and evolution of the martian soil would not be complete without addressing the unusual reactivity discovered by the Viking Landers The presence of an inorganic oxidant, possibly one produced as a results of photochemical processes, is the most widely accepted explanation of the Viking results. Are these chemical species simply adsorbed on soil grains, or have they reacted with the metal oxide substrates and altered the mineral structures? Could a completely different (non-photochemical) process be responsible for the soil reactivity? The various ideas for the nature of this putative oxidant could be constrained by a measurement of the change in reactivity with depth. Different compositions will have different lifetimes and mobilities and thus will have different vertical profiles. Because the oxidizing compounds are believed to actively destroy organic molecules, determination of the reactivity gradient also has significant implications for the search for life on Mars. A DS2-based microprobe system can be instrumented for a 2003 micromission to investigate the origin and reactivity of the martian soil. These measurements would provide invaluable information regarding the climate history and exobiological potential of the planet. The NMR, X ray and chemiresistor measurement approach described embodies a highly synergistic and general set of soil interrogation methods for elements, compounds, and crystal structures and can also be applied to other geologic questions of interest. For example, if the capability for precise targeting of the probes is available, then in-situ investigations of suspected evaporite and hydrothermal deposits would be possible with the same set of instruments. Additional information is contained in the original.

Yen, Albert S.↗
NASA NTRS2020

Encealdus Orbilander: A Flagship Mission Concept for Astrobiology

"Whether life exists beyond Earth remains a fundamental question driving our exploration of the Solar System. At Saturn’s moon Enceladus, plumes of oceanic material vented into space allow the investigation of the astrobiological potential of an ocean world, hinted at by Cassini, without the necessity of drilling through kilometers of ice crust. The Enceladus Orbilander is a flagship ($2.56B in fiscal year 2025 dollars) mission concept created for the 2023–2033 Planetary Science Decadal Survey. Orbilander takes full advantage of the opportunity provided by Enceladus’ plumes to search for signs of life. A single spacecraft both orbits and lands, capturing samples from four distinct reservoirs offered by the plumes. These samples, both particulate and vapor, are then analyzed by the Life Detection Suite (LDS), a set of five instruments conducting complementary and orthogonal biosignature-seeking measurements. To provide the context that specifically enhances interpretation of LDS measurements, geochemical and geophysical investigations are conducted both in orbit and on the surface. These reveal the physio-chemical state of the ocean and core as well as the processes involved in ejection of plume material and how these affect the ocean material analyzed by the LDS. The Orbilander can be delivered to the Saturn system via several launch vehicle and trajectory options, including a direct trajectory (7-year cruise), a ∆V-EGA trajectory (9-year cruise) and several options using an inner cruise with Venus and Earth flybys (10-year cruise). Upon Saturn Orbit Insertion, a 4-year moon tour pumps down the Orbilander’s orbit to intercept Enceladus. The most optimal arrival times balance the Jupiter flyby opportunities of the late 2030s and solar illumination at the Enceladus high southern latitudes where plume material is most abundant. This mission concept therefore targets project start in 2030. Upon Enceladus Orbit Insertion, the Orbilander begins a 1.5-year-long campaign of landing site reconnaissance, remote sensing science, and collecting sufficient plume sample to run all but one of the LDS measurements. After successful landing, the Orbilander spends 2 years on the surface conducting multiple LDS measurements with all five instruments on actively and passively collected plume material, as well as seismic investigations. The schedule laid out here is well-defined, but the mission also has operational and resource flexibility should additional reconnaissance be needed. As part of the design study, mission and development risks were identified and mitigation strategies proposed. Technologies key to achieving the life detection science objectives include instrumentation matured under programs like COLDTech and ICEE-2, such as aspects of the sampling system and microfluidic devices, as well as well-known techniques like high-resolution and separation-capable mass spectrometers. Autonomous onboard navigation is planned to maintain a halo orbit around Enceladus to enable passive sampling from orbit as well as reconnaissance measurements for use in site selection and landing. Terrain relative navigation is included to ensure safe landing, given that targeted areas may contain landing hazards. Continued development of radioisotope thermoelectric generator (RTG) technology and long-life batteries is essential for this long duration mission. The Enceladus Orbilander represents an optimal point in the trade space of science value versus cost, taking advantage of the extensive knowledge of Enceladus provided by Cassini, how well Enceladus lends itself to a search for life in material from its ocean, and the flexibility afforded by the innovative design developed by the APL team. By taking full advantage of Enceladus’ plumes both in orbit and on the surface, Orbilander represents a robust search for life with complementary and orthogonal biosignatures as well as contextual geophysical and geochemical measurements, determining not only whether Enceladus is inhabited (at levels up to 500,000× scarcer than in Earth’s oceans) but also why. "

Exobiology↗
NASA NTRS2011

Why Atens Enjoy Enhanced Accessibility For Human Space Flight

In the context of human space flight (HSF), the concept of near-Earth object (NEO) accessibility is highly subjective. Whether or not a particular NEO is accessible critically depends on mass, performance, and reliability of interplanetary HSF systems yet to be designed. Such systems would certainly include propulsion and crew life support with adequate shielding from both solar flares and galactic cosmic radiation. Equally critical architecture options are relevant to NEO accessibility. These options are also far from being determined and include the number of launches supporting an HSF mission, together with whether or not consumables are to be pre-emplaced at the destination. Until the unknowns of HSF to NEOs come into clearer focus, the notion of relative accessibility is of great utility. Imagine a group of NEOs, each with nearly equal HSF merit determined from their individual characteristics relating to crew safety, scientific return, resource utilization, and planetary defense. The more accessible members of this group are more likely to be explored first. A highly accessible NEO could conceivably be deferred in favor of a less accessible HSF destination because the latter is more accessible during a programmatically desirable launch compliant mission trajectory solutions detected in association with a specific NEO. The known NEO population is then surveyed to illustrate in which regions of heliocentric semi-major axis, eccentricity, and inclination (a, e, i) space NEOs with large n values are mapped. The (a, e, i) mapping is also formatted such that membership in each of four NEO orbit classifications, as defined below, is evident. Amors have orbits everywhere superior to (outside of) Earth's. An Amor is therefore defined to have perihelion between 1.017 astronomical units (AU) and the maximum NEO value of 1.3 AU. As of 0 hrs Universal Time on 1 January 2011 (UT epoch 2011.0), Amors numbered 2855 in the Jet Propulsion Laboratory (JPL) Small-Body Database (SBDB), comprising 37.7% of known NEOs. Apollos have orbits crossing Earth's with periods greater than Earth's. An Apollo is therefore defined to have perihelion less than 1.017 AU and a greater than 1.0 AU. As of 2011.0 UT, Apollos numbered 4080 in the SBDB, comprising 53.9% of known NEOs. Atens have orbits crossing Earth's with periods less than Earth's. An Aten is therefore defined to have aphelion greater than 0.983 AU and a less than 1.0 AU. As of 2011.0 UT, Atens numbered 618 in the SBDB, comprising 8.2% of known NEOs. Atiras have orbits everywhere inferior to (inside of) Earth's. An Atira is therefore defined to have aphelion less than 0.983 AU. As of 2011.0 UT, Atiras numbered 11 in the SBDB, comprising 0.1% of known NEOs. It is no surprise that the largest n values are chiefly associated with Apollos and Atens. Because these orbits cross Earth's, distance to be covered in a given round trip mission time delta-t can be far less than is possible for Amors or Atiras . This delta-t or the sum of mission propulsive impulse magnitudes delta-v can more frequently be minimized to enhance NHATS compliance for Apollos and Atens than is generally the case for Amors and Atiras. A less intuitive trend in NHATS results is that Atens nearly outnumber the more numerous Apollos among the most compliant NEOs as measured by n. This trend is completely out of proportion to the degree Atens are represented among the known NEO population. A theory based on geocentric NEO dynamics is presented by this paper to explain why Atens enjoy inherently greater accessibility than do Apollos. Another trend evident from mapping into (a, e, i) space is the dearth of known NEOs at low e when a < 1 AU. Underrepresentation of Atens and Atiras in the NEO catalog is at least in part attributable to observing exclusively from a perspective near Earth. Generally inferior Aten and Atira orbits are rarely, if ever, in Earth's night sky. Until a comprehensive NEO survey is conducted from an appropriateegion remote from Earth, the theory developed in this paper indicates a substantial fraction of the most accessible NEOs will remain unknown. season. Such a season is really yet another undetermined HSF architecture option. A launch season's duration will likely be measured in weeks, and it will be utilized at an indeterminate point almost certainly more than a decade in the future when HSF programmatic maturity is sufficient. Furthermore, current knowledge of the NEO population relevant to HSF is far from complete. In the 100-m-diameter class of greatest interest, only a few percent of the estimated NEO population is known [2, Figure 2.4]. Therefore, any known, lost, or fictitious NEO in a highly accessible orbit is a potential HSF destination of merit. Even if lost, fictitious, small, or hazardous, such a potential target (or another in a similar orbit) may ultimately prove to be an early HSF destination when the pertinent NEO population is more thoroughly catalogued and NEO orbits are more thoroughly maintained at high accuracy. This paper first reviews methodology and pertinent results from NASA-sponsored research performed in late 2010 and dubbed NEO HSF Accessible Targets Study (NHATS, pronounced as "gnats"). A useful accessibility metric developed during this study is n, the tally of NHATS-

Barbee, Brent↗