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At least 271 records · Page 15

Atomic Oxygen Effects on Spacecraft Materials

Low Earth orbital (LEO) atomic oxygen cannot only erode the external surfaces of polymers on spacecraft, but can cause degradation of surfaces internal to components on the spacecraft where openings to the space environment exist. Although atomic oxygen attack on internal or interior surfaces may not have direct exposure to the LEO atomic oxygen flux, scattered impingement can have can have serious degradation effects where sensitive interior surfaces are present. The effects of atomic oxygen erosion of polymers interior to an aperture on a spacecraft is simulated using Monte Carlo computational techniques. A 2-dimensional model is used to provide quantitative indications of the attenuation of atomic oxygen flux as a function of distance into a parallel walled cavity. The degree of erosion relative is compared between the various interior locations and the external surface of an LEO spacecraft.

Banks, Bruce A.↗

Scattered Atomic Oxygen Effects on Spacecraft Materials

Low Earth orbital (LEO) atomic oxygen cannot only erode the external surfaces of polymers on spacecraft, but can cause degradation of surfaces internal to components on the spacecraft where openings to the space environment exist. Although atomic oxygen attack on internal or interior surfaces may not have direct exposure to the LEO atomic oxygen flux scattered impingement can have serious degradation effects where sensitive interior surfaces are present. The effects of atomic oxygen erosion of polymer interior to an aperture on a spacecraft is simulated using Monte Carlo computational techniques. A 2-dimensional model is used to provide quantitative indications of the attenuation of atomic oxygen flux as a function of distance into a parallel walled cavity. The degree of erosion re1ative is compared between the various interior locations and the external surface of a LEO spacecraft.

Banks, Bruce A.↗

Sputtering Erosion in the Ion Thruster

During the first phase of this research, the sputtering yields of molybdenum by low energy (100 eV and higher) xenon ions were measured by using the methods of secondary neutral mass spectrometry (SNMS) and Rutherford backscattering spectrometry (RBS). However, the measured sputtering yields were found to be far too low to explain the sputtering erosions observed in the long-duration tests of ion thrusters. The only difference between the sputtering yield measurement experiments and the ion thruster tests was that the later are conducted at high ion fluences. Hence, a study was initiated to investigate if any linkage exists between high ion fluence and an enhanced sputtering yield. The objective of this research is to gain an understanding of the causes of the discrepancies between the sputtering rates of molybdenum grids in an ion thruster and those measured from our experiments. We are developing a molecular dynamics simulation technique for studying low-energy xenon ion interactions with molybdenum. It is difficult to determine collision sequences analytically for primary ions below the 200 eV energy range where the ion energy is too low to be able to employ a random cascade model with confidence and it is too high to have to consider only single collision at or near the surface. At these low energies, the range of primary ions is about 1 to 2 nm from the surface and it takes less than 4 collisions on the average to get an ion to degrade to such an energy that it can no longer migrate. The fine details of atomic motion during the sputtering process are revealed through computer simulation schemes. By using an appropriate interatomic potential, the positions and velocities of the incident ion together with a sufficient number of target atoms are determined in small time steps. Hence, it allows one to study the evolution of damages in the target and its effect on the sputtering yield. We are at the preliminary stages of setting up the simulation program.

Ray, Pradosh K.↗

Protective coatings for composite tubes in space applications

Protective coatings for graphite/epoxy (Gr/Ep) tubular structures for a Manned Space Station truss structure were evaluated. The success of the composite tube truss structure depends on its stability to long-term exposure to the Low Earth Orbit (LEO) environment with particular emphasis placed on atomic oxygen. Concepts for protectively coating Gr/Ep tubes include use of inorganic coated metal foils and electroplating. These coatings were applied to Gr/Ep tubes and then subjected to simulated LEO environmnet to evaluate survivability of coatings and coated tubes. Evaluation included: atomic oxygen resistance, changes in optical properties and adhesion, abrasion resistancem surface preparation required, coating uniformity, and formation of microcracks in the Gr/Ep tubes caused by thermal cycling. Program results demonstrated that both phosphoric and chromic acid anodized Al foil provided excellent adhesion to Gr/Ep tubes and exhibited stable optical properties when subjected to simulated LEO environment. The SiO2/Al coatings speuttered onto Al foils also resulted in an excellent protective coating. Electroplated Ni exhibited unaccepatble adhesion loss to Gr/Ep tubes during atomic oxygen exposure.

Dursch, Harry W.↗

Protective coatings for composite tubes in space applications

Protective coatings for graphite/epoxy (Gr/Ep) tubular structures for a manned Space Station truss structure were evaluated. The success of the composite tube truss structure depends on its stability to long-term exposure to the low earth orbit (LEO) environment, with particular emphasis placed on atomic oxygen. Concepts for protectively coating Gr/Ep tubes include use of inorganic coated metal foils and electroplating. These coatings were applied to Gr/Ep tubes and then subjected to simulated LEO environment to evaluate survivability of coatings and coated tubes. Evaluation included: atomic oxygen resistance, changes in optical properties and adhesion, abrasion resistance, surface preparation required, coating uniformity, and formation of microcracks in the Gr/Ep tubes caused by thermal cycling. Program results demonstrated that both phosphoric and chromic acid anodized Al foil provided excellent adhesion to Gr/Ep tubes and exhibited stable optical properties when subjected to simulated LEO environment. The SiO2/Al coatings sputtered onto Al foils also resulted in an excellent protective coating. Electroplated Ni exhibited unacceptable adhesion loss to Gr/Ep tubes during atomic oxygen exposure.

Dursch, Harry W.↗

Molecular Dynamics Simulation of a Multi-Walled Carbon Nanotube Based Gear

We used molecular dynamics to investigate the properties of a multi-walled carbon nanotube based gear. Previous work computationally suggested that molecular gears fashioned from (14,0) single-walled carbon nanotubes operate well at 50-100 gigahertz. The gears were formed from nanotubes with teeth added via a benzyne reaction known to occur with C60. A modified, parallelized version of Brenner's potential was used to model interatomic forces within each molecule. A Leonard-Jones 6-12 potential was used for forces between molecules. The gear in this study was based on the smallest multi-walled nanotube supported by some experimental evidence. Each gear was a (52,0) nanotube surrounding a (37,10) nanotube with approximate 20.4 and 16,8 A radii respectively. These sizes were chosen to be consistent with inter-tube spacing observed by and were slightly larger than graphite inter-layer spacings. The benzyne teeth were attached via 2+4 cycloaddition to exterior of the (52,0) tube. 2+4 bonds were used rather than the 2+2 bonds observed by Hoke since 2+4 bonds are preferred by naphthalene and quantum calculations by Jaffe suggest that 2+4 bonds are preferred on carbon nanotubes of sufficient diameter. One gear was 'powered' by forcing the atoms near the end of the outside buckytube to rotate to simulate a motor. A second gear was allowed to rotate by keeping the atoms near the end of its outside buckytube on a cylinder. The ends of both gears were constrained to stay in an approximately constant position relative to each other, simulating a casing, to insure that the gear teeth meshed. The stiff meshing aromatic gear teeth transferred angular momentum from the powered gear to the driven gear. The simulation was performed in a vacuum and with a software thermostat. Preliminary results suggest that the powered gear had trouble turning the driven gear without slip. The larger radius and greater mass of these gears relative to the (14,0) gears previously studied requires a smaller rotation rate and multiple rows of teeth to avoid excessive force on the gear teeth resulting, in slip and failure of the driven gear to turn. We hope that studies such as these will eventually lead to synthesis of components that can be assembled into atomically precise fullerene machines. These machines, in turn, may someday be used in machine-phase fullerene materials with remarkable properties.

Han, Jie↗

Hyperthermal-Atomic-Oxygen Generator

Small hyperthermal-atomic-oxygen generator (HAOG) compatible with ultrahigh vacuum (UHV) developed. Provides pure flux of ground-state oxygen atoms with mean kinetic energy of approximately 5 eV, accurately simulating conditions in low orbit around Earth, and mounted on any existing UHV processing or analysis system. HAOG clean and compatible with other UHV processing or diagnostic systems and relatively inexpensive and simple to operate. Valuable in studies involving atomic oxygen because added easily to existing systems.

Outlaw, R. A.↗

Characterization of a 5-eV neutral atomic oxygen beam facility

An experimental effort to characterize an existing 5-eV neutral atomic oxygen beam facility being developed at Princeton Plasma Physics Laboratory is described. This characterization effort includes atomic oxygen flux and flux distribution measurements using a catalytic probe, energy determination using a commercially designed quadrupole mass spectrometer (QMS), and the exposure of oxygen-sensitive materials in this beam facility. Also, comparisons were drawn between the reaction efficiencies of materials exposed in plasma ashers, and the reaction efficiencies previously estimated from space flight experiments. The results of this study show that the beam facility is capable of producing a directional beam of neutral atomic oxygen atoms with the needed flux and energy to simulate low Earth orbit (LEO) conditions for real time accelerated testing. The flux distribution in this facility is uniform to +/- 6 percent of the peak flux over a beam diameter of 6 cm.

Vaughn, J. A.↗

Flow Characteristics of UHV Nitrogen Arcjet

Flow characteristics in the nozzle of a nitrogen arcjet have been simulated by a model. Electrons, ions, and neutral atoms and molecules are represented as separate species. Dissociation, ionization, and recombination are treated as separate reactions. Thermal non-equilibrium is represented by a two-temperature model. Energy input to plasma from the arc is modeled as a source determined by local current and electrical conductivity. Momentum and energy losses and recombinations at the nozzle wall are included as source/sink determined by fluxes to the wall. The results show essentially frozen gas-phase reactions and thermal nonequilibrium due to Joule heating of electrons and in the expansion part of the nozzle. Wall interactions have strong effects on the results, indicating that they play important roles in the flow due to very high surface area relative to the volume of the plasma. For example, plasma velocity decreases from 6000 m per s without wall interactions to 3000 m per s with modest amount of wall interactions. These results also show reasonable agreement with optical emission measurements, which confirms that the arcjet plasma is far from LTE. The spectra suggest nitrogen dissociation levels of 0.3% - 9%, depending on nitrogen flow rate and arc plasma current, which also determine the relative amounts of excited atomic and molecular nitrogen. Langmuir probe studies of the source show that electron and ion fluxes increase with increasing power, and that the ion energy distribution shifts to lower energies. Typical ion fluxes were on the order of 4E-9 A/cm**2 with a maximum ion kinetic energy of 3.5eV. The median electron energy was 1eV, with a maximum of less than 4eV.

Chang, C. H.↗

Empirical Modeling of the Storm Time Innermost Magnetosphere Using Van Allen Probes and THEMIS Data: Eastward and Banana Currents

The structure of storm time currents in the inner magnetosphere, including its innermost region inside 4R(sub E), is studied for the first time using a modification of the empirical geomagnetic field model TS07D and new data from Van Allen Probes and Time History of Events and Macroscale Interactions during Substorms missions. It is shown that the model, which uses basis-function expansions instead of ad hoc current modules to approximate the magnetic field, consistently improves its resolution and magnetic field reconstruction with the increase of the number of basis functions and resolves the spatial structure and evolution of the innermost eastward current. This includes a connection between the westward ring current flowing largely at R > or approx. 3R(sub E) and the eastward ring current concentrated at R < or approx. 3R(sub E) resulting in a vortex current pattern. A similar pattern coined 'banana current' was previously inferred from the pressure distributions based on the energetic neutral atom imaging and first-principles ring current simulations. The morphology of the equatorial currents is dependent on storm phase. During the main phase, it is complex, with several asymmetries forming banana currents. Near SYM-H minimum, the banana current is strongest, is localized in the evening-midnight sector, and is more structured compared to the main phase. It then weakens during the recovery phase resulting in the equatorial currents to become mostly azimuthally symmetric.

Stephens, G. K.↗

Cyber Resiliency and the Implementation of a Host-Based Intrusion Detection System in an Urban Air Mobility Environment

With the growth in Urban Air Mobility systems and the increasing reliance on interconnected technologies, ensuring the security of these complex components has become critical. As cities evolve into smart urban centers, the vulnerability to cyber threats escalates, possibly endangering citizens safety and the efficiency of transportation networks.In response to these challenges, this paper presents a study on the need for cyber resilient techniques within future air traffic environments. It will pay specific attention to the implementation of a Host-Based Intrusion Detection System (HIDS) utilizing Atomic OSSEC software, tailored specifically to a NASA simulation of an UrbanAirMobility environments’ unique demands. Further, this study seeks to outline the rational for NASA’s recommendation for a HIDS in such environments. It explores the design, development, and deployment of the proposed HIDS, focusing on its adaptability to monitor the hybrid nature of the Urban Air Mobility environment. Leveraging machine learning algorithms and anomaly detection techniques, the HIDS is equipped to continuously monitor and analyze the behavior of individual host systems, vehicles, and devices, thereby providing a proactive approach to threat detection. Implementing a HIDS is a pivotal strategy for enhancing cyber resiliency, as it gives an organization granular visibility into internal system activities, enables rapid detection and response to anomalous behavior and cyber threats, and fortifies the organizations overall cybersecurity posture. Finally, this study aims to provide recommendations and include learned takeaways that the Urban Air Mobility industry should consider. In brief, this paper highlights the significance of host-based intrusion detection in UrbanAirMobility environments and underscores the necessity of tailored security solutions to safeguard against emerging cyber threats.

UAM↗

Pre-Flight Testing of Spaceborne GPS Receivers Using a GPS Constellation Simulator

The NASA Goddard Space Flight Center (GSFC) Global Positioning System (GPS) test facility has been established within the GSFC Guidance Navigation and Control Center. The GPS test facility is currently housing the STR2760 GPS satellite 40-channel attitude simulator and an STR4760 12-channel navigation simulator. The facility also contains a few other Goddard resources such as an atomic time standard test bed, a rooftop antenna platform and a radome. It provides a new capability of high dynamics GPS simulations for space flight that is unique within the aerospace community. The GPS facility gives a significant advantage in the development and support of GPS based technologies for position, attitude and precise time determination on-board a spacecraft, sounding rocket or balloon. The GPS simulator system is configured in a transportable rack and is available for GPS applications' component development as well as for spacecraft subsystem and system level testing at spacecraft integration and test sites. The GPS facility has been operational since early 1996 and has been already utilized by a few successful flight projects carrying GPS experiments, such as USA Seastar satellite and the first Argentine satellite SAC-A. The experience in the SAC-A pre-flight testing using the STR2760 simulator is summarized as well as the comparison with preliminary analysis of the GPS data from SAC-A telemetry.

Kizhner, Semion↗

Atomistic Method Applied to Computational Modeling of Surface Alloys

The formation of surface alloys is a growing research field that, in terms of the surface structure of multicomponent systems, defines the frontier both for experimental and theoretical techniques. Because of the impact that the formation of surface alloys has on surface properties, researchers need reliable methods to predict new surface alloys and to help interpret unknown structures. The structure of surface alloys and when, and even if, they form are largely unpredictable from the known properties of the participating elements. No unified theory or model to date can infer surface alloy structures from the constituents properties or their bulk alloy characteristics. In spite of these severe limitations, a growing catalogue of such systems has been developed during the last decade, and only recently are global theories being advanced to fully understand the phenomenon. None of the methods used in other areas of surface science can properly model even the already known cases. Aware of these limitations, the Computational Materials Group at the NASA Glenn Research Center at Lewis Field has developed a useful, computationally economical, and physically sound methodology to enable the systematic study of surface alloy formation in metals. This tool has been tested successfully on several known systems for which hard experimental evidence exists and has been used to predict ternary surface alloy formation (results to be published: Garces, J.E.; Bozzolo, G.; and Mosca, H.: Atomistic Modeling of Pd/Cu(100) Surface Alloy Formation. Surf. Sci., 2000 (in press); Mosca, H.; Garces J.E.; and Bozzolo, G.: Surface Ternary Alloys of (Cu,Au)/Ni(110). (Accepted for publication in Surf. Sci., 2000.); and Garces, J.E.; Bozzolo, G.; Mosca, H.; and Abel, P.: A New Approach for Atomistic Modeling of Pd/Cu(110) Surface Alloy Formation. (Submitted to Appl. Surf. Sci.)). Ternary alloy formation is a field yet to be fully explored experimentally. The computational tool, which is based on the BFS (Bozzolo, Ferrante, and Smith) method for the calculation of the energetics, consists of a small number of simple PCbased computer codes that deal with the different aspects of surface alloy formation. Two analysis modes are available within this package. The first mode provides an atom-by-atom description of real and virtual stages 1. during the process of surface alloying, based on the construction of catalogues of configurations where each configuration describes one possible atomic distribution. BFS analysis of this catalogue provides information on accessible states, possible ordering patterns, and details of island formation or film growth. More importantly, it provides insight into the evolution of the system. Software developed by the Computational Materials Group allows for the study of an arbitrary number of elements forming surface alloys, including an arbitrary number of surface atomic layers. The second mode involves large-scale temperature-dependent computer 2. simulations that use the BFS method for the energetics and provide information on the dynamic processes during surface alloying. These simulations require the implementation of Monte-Carlo-based codes with high efficiency within current workstation environments. This methodology capitalizes on the advantages of the BFS method: there are no restrictions on the number or type of elements or on the type of crystallographic structure considered. This removes any restrictions in the definition of the configuration catalogues used in the analytical calculations, thus allowing for the study of arbitrary ordering patterns, ultimately leading to the actual surface alloy structure. Moreover, the Monte Carlo numerical technique used for the large-scale simulations allows for a detailed visualization of the simulated process, the main advantage of this type of analysis being the ability to understand the underlying features that drive these processes. Because of the simplicity of the BFS method for e energetics used in these calculations, a detailed atom-by-atom analysis can be performed at any point in the simulation, providing necessary insight on the details of the process. The main objective of this research program is to develop a tool to guide experimenters in understanding and interpreting often unexpected results in alloy formation experiments. By reducing the computational effort without losing physical accuracy, we expect that powerful simulation tools will be developed in the immediate future, which will allow material scientists to easily visualize and analyze processes at a level not achievable experimentally.

Bozzolo, Guillermo H.↗

Building and Breaking Carbon Composites with REACTER

Carbon-based composites have become indispensable materials in aerospace and other high-performance applications, yet obtaining a detailed, nanoscale understanding of their morphology and failure mechanisms using only experimental methods remains a difficult challenge. REACTER is a versatile computational modeling tool for atomistic molecular dynamics simulations designed to model chemical reactions at the speed and length scales of classical force fields. In this work, several recent features of REACTER were applied to the creation and subsequent mechanical testing of two classes of carbon composites: carbon nanotube (CNT) composites and carbon fiber reinforced polymers (CFRP). A network of CNTs was grown dynamically using the new ‘create atoms’ feature of REACTER. The CNT filler was embedded into a polyarylacetylene (PAA) matrix by simulated in situ polymerization to obtain the final composite model. To generate the second class of carbon composite, fully carbonized (graphitic) carbon fiber morphologies were created by the method of Desai et al. [1], but using the advanced reaction constraints framework of REACTER. Two fiber models were created, representing a circular carbon fiber core and a flat surface, and similarly infiltrated with resin to obtain the final CFRP structure. Failure mechanisms were elucidated by simulating mechanically induced bond breaking, as characterized by third order DFT-based tight-binding simulations, via a reaction constraint on the total potential energy of the involved atoms.

Polymer↗

High-Performance Computing Optimization for Aladyn – Adaptive Neural Network Molecular Dynamics Mini-Application

This report provides a description and performance evaluation of the optimization techniques for high performance computing (HPC) implementation of the open source Computational Materials mini-application Aladyn (https://github.com/nasa/aladyn). Aladyn is a basic molecular dynamics code written in FORTRAN 2003, which is designed to demonstrate the use of adaptive neural networks (ANNs) in atomistic simulations. The role of ANNs is to efficiently reproduce the very complex energy landscape resulting from the atomic interactions in materials with the accuracy of the more expensive quantum mechanics-based calculations. The ANN is trained on a large set of atomic structures calculated using the density functional theory (DFT) method. While achieving orders of magnitude faster computational performance than DFT, the ANN-based approach was still very computationally demanding compared to the conventional approach of using empirically fitted energy functions. After its initial development, Aladyn was evaluated and optimized by experts at the NASA Advanced Supercomputing (NAS) division to exploit modern supercomputer architectures. The code has been optimized for execution on multicore central processing units (CPUs), including Intel® Skylake microarchitecture, and on graphic accelerators, such as Nvidia® V100 graphic processing units (GPUs), using Open Multi-Processing (OpenMP) and Open Accelerators (OpenACC) programming interfaces. The optimization achieved a speedup of 4.7 times the baseline version on CPU performance and an additional 2.4 times on CPU+GPU performance. Atomistic computer simulations are a fundamental tool in materials research to model material properties form physics-based first principles. Atomic interaction, governed by Quantum Mechanics (QM) require sophisticated and highly computationally demanding mathematical models to calculate [1]. Classical methods use approximate functional forms, empirically fitted through a set of variable parameters to emulate atomic energies as direct functions of atomic coordinates [2]. While empirical potentials are computationally much simpler, allowing simulations of large-scale systems of up to a trillion (1012) atoms [3], they are substantially less accurate compared to quantum calculations and applicable only to very specific atomic configurations or predefined crystallographic phases. A recently suggested approach is to use heuristic machine learning methods [4], such as those based on Adaptive Neural Networks (ANNs) to predict atomic energies, after being trained on a sufficiently large database of QM-calculated structures [5,6]. This approach reduces significantly the computational complexity, allowing for simulations of orders of magnitude larger systems compared to QM-based methods without compromising accuracy. Still, compared to classical methods using empirical energy functions, ANN methods remain two- to three orders of magnitude more computationally demanding. Hence, the computational cost of simulations, together with the need for extensive training of ANNs, still makes the practical implementation of ANN-based methods quite challenging. The purpose of the Aladyn mini-application software [7], available as open source at https://github.com/nasa/aladyn, is to be a testbed for exploring possible optimization strategies to develop highly scalable parallel algorithms for ANN-based atomistic simulations. Aladyn is aimed at utilizing the architecture of the high-end modern highperformance computing (HPC) hardware based on multicore central processing units (CPUs) equipped with graphic processing unit (GPU) accelerators. Specifically, the goal is to optimize the performance on a single HPC compute node, before implementing scaling to multi-node parallelization using message passing interface (MPI). At the same time, the open source code of Aladyn can serve as a training model for students and professors in academia.

Yamakov, Vesselin I.↗

MCNP Simulations of Measurement of Insulation Compaction in the Cryogenic Rocket Fuel Tanks at Kennedy Space Center by Fast/Thermal Neutron Techniques

MCNP simulations have been run to evaluate the feasibility of using a combination of fast and thermal neutrons as a nondestructive method to measure of the compaction of the perlite insulation in the liquid hydrogen and oxygen cryogenic storage tanks at John F. Kennedy Space Center (KSC). Perlite is a feldspathic volcanic rock made up of the major elements Si, AI, Na, K and 0 along with some water. When heated it expands from four to twenty times its original volume which makes it very useful for thermal insulation. The cryogenic tanks at Kennedy Space Center are spherical with outer diameters of 69-70 feet and lined with a layer of expanded perlite with thicknesses on the order of 120 cm. There is evidence that some of the perlite has compacted over time since the tanks were built 1965, affecting the thermal properties and possibly also the structural integrity of the tanks. With commercially available portable neutron generators it is possible to produce simultaneously fluxes of neutrons in two energy ranges: fast (14 Me V) and thermal (25 me V). The two energy ranges produce complementary information. Fast neutrons produce gamma rays by inelastic scattering, which is sensitive to Fe and O. Thermal neutrons produce gamma rays by prompt gamma neutron activation (PGNA) and this is sensitive to Si, Al, Na, K and H. The compaction of the perlite can be measured by the change in gamma ray signal strength which is proportional to the atomic number densities of the constituent elements. The MCNP simulations were made to determine the magnitude of this change. The tank wall was approximated by a I-dimensional slab geometry with an 11/16" outer carbon steel wall, an inner stainless wall and 120 cm thick perlite zone. Runs were made for cases with expanded perlite, compacted perlite or with various void fractions. Runs were also made to simulate the effect of adding a moderator. Tallies were made for decay-time analysis from t=0 to 10 ms; total detected gamma-rays; detected gamma-rays from thermal neutron reactions d. detected gamma-rays from non-thermal neutron reactions and total detected gamma-rays as a function of depth into the annulus volume. These indicated a number of possible independent metrics of perlite compaction. For example the count rate for perlite elements increased from 3600 to 8500 cps for an increase in perlite density from 6 lbs/lcf to 16.5 lbs/cf. Thus the MCNP simulations have confirmed the feasibility of using neutron methods to map the compaction of perlite in the walls of the cryogenic tanks.

Livingston, R. A.↗

The M2 Proton Channel of Influenza Virus: How Does It Work?

The transport of protons across membranes is an essential process for both bioenergetics of modem cells and the origins of cellular life. All living systems make use of proton gradients across cell walls to convert environmental energy into a high-energy chemical compound, adenosine triphosphate (ATR), synthesized from adenosine diphosphate. ATR, in turn, is used as a source of energy to drive many cellular reactions. The ubiquity of this process in biology suggests that even the earliest cellular systems were relying on proton gradient for harvesting environmental energy needed to support their survival and growth. In contemporary cells, proton transfer is assisted by large, complex proteins embedded in membranes. The issue addressed in this study was: how the same process can be accomplished with the aid of similar, but much simpler molecules that could have existed in the protobiological milieu? The model system used in the study contained a bilayer membrane made of phospholipid, dimyristoylphosphatidylcholine (DMPC), which is a good model of the biological membranes focusing cellular boundaries. Both sides of the bilayer were surrounded by water which simulated the environment inside and outside the cell. Embedded in the membrane was a fragment of the Influenza-A M2 protein and enough sodium counterions to maintain system neutrality. This protein has been shown to exhibit remarkably high rates of proton transport and, therefore, is an excellent model to study the formation of proton gradients across membranes. The Influenza M2 protein is 97 amino acids in length, but a fragment 25 amino acids long, which contains a transmembrane domain of 19 amino acids flanked by 3 amino acids on each side, is sufficient to transport protons. Four identical protein fragments, each folded into a helix, aggregate to form small channels spanning the membrane. Protons are conducted through a narrow pore in the middle of the channel in response to applied voltage. This channel is large enough to contain water molecules, and is normally filled with water. In analogy to the mechanism of proton transfer in some other channels, it has been postulated that protons are translocated along the network of water molecules filling the pore of the channel. This mechanism, however, must involve an additional, important step because the channel contains four histidine amino acid residues, one from each of the helices, which are sufficiently large to occlude the pore and interrupt the water network. The histidine residues ensure channel selectivity by blocking transport of small such as sodium or potassium. They have been also implicated in gating protons due to the ability of each histidine to become positively charged by accepting an additional proton. Two mechanisms of gating have been proposed. In one mechanism, all four histidines acquire an additional proton and, due to repulsion between their positive charges, move away from one another, thus opening the channel. The alternative mechanism relies of the ability of protons to move between different atoms in a molecule (tautomerization). Thus, a proton is captured on one side of the gate while another proton is released from the opposite side, and the molecule returns to the initial state through tautomerization. The simulations were designed to test these two mechanisms. Large-scale, atomic-level molecular dynamics simulations of the channel, in which the histidine residues were in different protonation states revealed that all intermediate states of the system involved in the tautomerization mechanism are structurally stable and the arrangement of water molecules in the channel is conducive to the proton transport. In contrast, in the four-protonated state, postulated to exist in the gate-opening mechanism, the electrostatic repulsion between the histidine residues appears to be so large that the channel looses its structural integrity and one helix moves away from the remaining three. This result indicates that such a mechanism of proton transport is unlikely. The simulations revealed that translocation along a network of water molecules in the channel and tautomerization of the histidine residues in the M2 proteins in the most likely mechanism of proton transport. The results not only explain how a remarkably simple protein system can efficiently aid in the formation of proton gradients across cell walls, but also suggest how this system can be genetically re-engineered to become a directional, reversible proton pump. Such a pump can provide energy to laboratory-built models of simple cellular systems. If they were successfully constructed it would greatly advance our understanding of the beginnings of life and find important applications in medicine and pharmacology.

Pohorille, Andrew↗

Proton Transport

The transport of protons across membranes is an essential process for both bioenergetics of modern cells and the origins of cellular life. All living systems make use of proton gradients across cell walls to convert environmental energy into a high-energy chemical compound, adenosine triphosphate (ATP), synthesized from adenosine diphosphate. ATP, in turn, is used as a source of energy to drive many cellular reactions. The ubiquity of this process in biology suggests that even the earliest cellular systems were relying on proton gradient for harvesting environmental energy needed to support their survival and growth. In contemporary cells, proton transfer is assisted by large, complex proteins embedded in membranes. The issue addressed in this Study was: how the same process can be accomplished with the aid of similar but much simpler molecules that could have existed in the protobiological milieu? The model system used in the study contained a bilayer membrane made of phospholipid, dimyristoylphosphatidylcholine (DMPC) which is a good model of the biological membranes forming cellular boundaries. Both sides of the bilayer were surrounded by water which simulated the environment inside and outside the cell. Embedded in the membrane was a fragment of the Influenza-A M$_2$ protein and enough sodium counterions to maintain system neutrality. This protein has been shown to exhibit remarkably high rates of proton transport and, therefore, is an excellent model to study the formation of proton gradients across membranes. The Influenza M$_2$ protein is 97 amino acids in length, but a fragment 25 amino acids long. which contains a transmembrane domain of 19 amino acids flanked by three amino acids on each side. is sufficient to transport protons. Four identical protein fragments, each folded into a helix, aggregate to form small channels spanning the membrane. Protons are conducted through a narrow pore in the middle of the channel in response to applied voltage. This channel is large enough to contain water molecules. and is normally filled with water. In analogy to the mechanism of proton transfer in some other channels, it has been postulated that protons are translocated along the network of water molecules filling the pore of the channel. This mechanism, however, must involve an additional important step because the channel contains four histidine amino acid residues, one from each of the helices, which are sufficiently large to occlude the pore and interrupt the water network. The histidine residues ensure channel selectivity by blocking transport of small ions, such as sodium or potassium. They have been also implicated in gating protons due to the ability of each histidine to become positively charged by accepting an additional proton. Two mechanisms of gating have been proposed. In one mechanism, all four histidines acquire an additional proton and, due to repulsion between their positive charges, move away from one another, thus opening the channel. The alternative mechanism relies of the ability of protons to move between different atoms in a molecule (tautomerization). Thus, a proton is captured on one side of the gate while another proton is released from the opposite side, and the molecule returns to the initial state through tautomerization. The simulations were designed to test these two mechanisms. Large-scale, atomic-level molecular dynamics simulations of the channel with the histidine residues in different protonation states revealed that all intermediate states of the system involved in the tautomerization mechanism are structurally stable and the arrangement of water molecules in the channel is conducive to the proton transport. In contrast, in the four-protonated state, postulated to exist in the gate-opening mechanism, the electrostatic repulsion between the histidine residues appears to be so large that the channel loses its structural integrity and one helix moves away from the remaining three. Additional information is contained within the original extended abstract.

Pohorille, Andrew↗