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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Understanding protein-complex assembly through grand canonical maximum entropy modeling

Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are far more protein complexes that are yet to be solved because of their dynamic associations with one another. Nevertheless, it is possible to infer these protein complexes through a physical model. However, it is often not clear to physicists what kind of data from biology is necessary for such a modeling endeavor. Here, we aim to model these clusters of coarse-grained protein assemblies from multiple subunits through the constraints of interactions among the subunits and the chemical potential of each subunit. We obtained the constraints on the interactions among subunits from the known protein structures. We inferred the chemical potential that dictates the particle number distribution of each protein subunit from the knowledge of protein abundance from experimental data. Guided by the maximum entropy principle, we formulated an inverse statistical mechanical method to infer the distribution of particle numbers from the data of protein abundance as chemical potentials for a grand canonical multicomponent mixture. Using grand canonical Monte Carlo simulations, we captured a distribution of high-order clusters in a protein complex of succinate dehydrogenase with four known subunits. The complexity of hierarchical clusters varies with the relative protein abundance of each subunit in distinctive cell types such as lung, heart, and brain. When the crowding content increases, we observed that crowding stabilizes emergent clusters that do not exist in dilute conditions. We, therefore, proposed a testable hypothesis that the hierarchical complexity of protein clusters on a molecular scale is a plausible biomarker of predicting the phenotypes of a cell.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A python package for analyzing Resilience of Complex Systems (pyRoCS) v.0.0

SAND2024-01040O PyRoCS software synthesizes mathematical equations from several domains—including information theory, ecology, and engineering sciences—to support resilience analysis for complex systems. Resilience is the ability of the complex system being analyzed to withstand, operate through, and recover from a disruption. The complex system can be a physical system such as an electric grid, an organization such as a company, or even a subfunction of an organization. Existing mathematical equations for resilience analysis are found within multiple domains including information theory, biological sciences, and complex systems. This package synthesizes and refactors equations from these various domains to make them more generalizable for application across different types of complex systems relevant for resilience analysis. Users will be able to apply these equations to characterize different components of complex systems based on available data. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Verzi, Stephen↗
DOE OSTI2024

Forest structural complexity and ignition pattern influence simulated prescribed fire effects

Background: Forest structural characteristics, the burning environment, and the choice of ignition pattern each influence prescribed fire behaviors and resulting fire effects; however, few studies examine the influences and interactions of these factors. Understanding how interactions among these drivers can influence prescribed fire behavior and effects is crucial for executing prescribed fires that can safely and effectively meet management objectives. To analyze the interactions between the fuels complex and ignition patterns, we used FIRETEC, a three-dimensional computational fluid dynamics fire behavior model, to simulate fire behavior and effects across a range of horizontal and vertical forest structural complexities. For each forest structure, we then simulated three different prescribed fires each with a unique ignition pattern: strip-head, dot, and alternating dot. Results: Forest structural complexity and ignition pattern affected the proportions of simulated crown scorch, consumption, and damage for prescribed fires in a dry, fire-prone ecosystem. Prescribed fires in forests with complex canopy structures resulted in increased crown consumption, scorch, and damage compared to less spatially complex forests. The choice of using a strip-head ignition pattern over either a dot or alternating-dot pattern increased the degree of crown foliage scorched and damaged, though did not affect the proportion of crown consumed. We found no evidence of an interaction between forest structural complexity and ignition pattern on canopy fuel consumption, scorch, or damage. Conclusions: We found that forest structure and ignition pattern, two powerful drivers of fire behavior that forest managers can readily account for or even manipulate, can be leveraged to influence fire behavior and the resultant fire effects of prescribed fire. These simulation findings have critical implications for how managers can plan and perform forest thinning and prescribed burn treatments to meet risk management or ecological objectives.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Molecular basis for the distinct cellular functions of the Lsm1–7 and Lsm2–8 complexes

Eukaryotes possess eight highly conserved Lsm (like Sm) proteins that assemble into circular, heteroheptameric complexes, bind RNA, and direct a diverse range of biological processes. Among the many essential functions of Lsm proteins, the cytoplasmic Lsm1–7 complex initiates mRNA decay, while the nuclear Lsm2–8 complex acts as a chaperone for U6 spliceosomal RNA. It has been unclear how these complexes perform their distinct functions while differing by only one out of seven subunits. Here, we elucidate the molecular basis for Lsm-RNA recognition and present four high-resolution structures of Lsm complexes bound to RNAs. The structures of Lsm2–8 bound to RNA identify the unique 2',3' cyclic phosphate end of U6 as a prime determinant of specificity. In contrast, the Lsm1–7 complex strongly discriminates against cyclic phosphates and tightly binds to oligouridylate tracts with terminal purines. Lsm5 uniquely recognizes purine bases, explaining its divergent sequence relative to other Lsm subunits. Lsm1–7 loads onto RNA from the 3' end and removal of the Lsm1 carboxy-terminal region allows Lsm1–7 to scan along RNA, suggesting a gated mechanism for accessing internal binding sites. These data reveal the molecular basis for RNA binding by Lsm proteins, a fundamental step in the formation of molecular assemblies that are central to eukaryotic mRNA metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Dynamic, Adaptive, Systems and Materials: Complex, Simple and Emergent Behaviors

This program has been funded by DoE/BES for twenty years. It has moved into and out of various subjects as it has developed, but it has retained its focus on complexity and complex systems. The project has evolved in the following way: Self-Assembly and Biomimetic Self-Assembly: All self-assembling systems depend upon a minimum of two types of interaction: a repulsion and an attraction. For the familiar molecular systems, attractive interactions are typically hydrogen bonds and electrostatic interactions. Repulsive interactions include steric effects, hydrophobic effects (in biological systems), and charge-charge repulsion. We have expanded this repertoire to include surface interactions, magnetic interactions, and others. I list these systems in the order in which we have explored them: i) A key emphasis in current work is in understanding how the movement of ions in a magnetic field (the Lorentz effect) interacts with catalytic systems. We have demonstrated that an acceleration in rate of reduction of CO 2 to CO can be accomplished by applying an external magnetic field. This acceleration is largely due to the application of the Lorentz effect on mass transport at the catalyst’s surface. ii) We have also extensively explored the influence of electrostatics, as exhibited in self-assembling systems, by tribocharging. iii) Another key system involves surface tension effects; examples include interactions between heavy particles floating at a liquid-air interface, and interacting by changes in surface area; interactions of bubbles and bubble rafts, behaviors of bubble trains in microfluidic networks, and behaviors of microorganisms in constraining environments. iv) This work has intentionally de-emphasized biological systems; but it does include some work on protein-ligand interactions and interactions among microorganisms. v) We have also explored applications of some of these effects, these explorations include bubble rafts as diffraction gratings, exploration of the structures that can be obtained by tribocharging and uses of these structures in exploring nucleation and melting of crystals. vi) Although not a major focus of this work, several other topics have emerged and offer opportunities for future work. These include the behavior of bubble trains and bubble rafts in microfluidic systems. A particularly interesting example is the formation of bubble trains that repeat in the alteration of large and small bubbles according to rules we do not presently understand, but are uniquely large-period oscillating systems. These systems offer a new route into understanding the instabilities of the type represented by oscillations. vii) We have also begun exploratory projects on magnetic levitation (especially to determine molecular density), and information storage (in molecules). Magnetic Levitation: Self-assembling and biomimetic systems require both attraction and repulsion. We have used electrostatics (tribocharging), interfacial free-energies (surface tension and related forces) and others. Potential uses include reconfigurable diffraction gratings and liquid lenses; exploration of mechanisms in tribocharging; tunneling in EGaIn junctions; and bubble trains (especially in micro-fluidic systems). Examples of systems representing these topics is included in the following papers: Complexity: Disks rotating at a water-air interface; Benard-Marangoni effects; Vortex-Crystals from spinning magnetic disks (Marangoni effects); EGaIn Electrode to study quantum tunneling; Self-Assembly of electrostatically-charged metallic spheres (electrets); Dynamically reconfigurable lens; Using computational designs of ligands for enzymes; Electrostatic self-assembly by tribocharging; Monodisperse bubble trains in microchannel systems; Inverted dripping faucet; Flames; Printing of micro-organisms to regenerate the “ink” of printing device; Using micro-organisms to move loads (“microoxen”); Motion of bacterial swarms near surfaces; Making monodisperse particles in microfluidic systems; Coding/decoding of information stored in droplet trains in microfluidic networks; Magnetic levitation; and Information storage. i) Tribocharging. The change in focus of this work on electrets from the fundamentals of charging to applications of these materials in studying self-assembly using electrostatic interactions. ii) Bubbles in Microchannels. The realization that systems of bubbles in microchannels represented a major opportunity to study complexity in a very tractable system, and the development of a semi-quantitative theory of this subject. iii) Flames. The growth of “flames” remains an exploratory subject for the research, although their currently relatively little active work involving it ongoing. iv) Systems with Microorganisms. The removal of work in biological systems from this project. Based on work supported in this program, we now have a significant project on the development of microfluidic tools for studying C. elegans (a nematode), but this work was not appropriate for a program focused on complexity, and we developed separate support for it. (It is, however, an example of successful seeding of a new area by BES.) The work on electrets has gone through a period in which a part of the program was the subject of a MURI; the focus of this work was to develop materials that did not charge electrostatically on friction or contact. The MURI is now over, and the work on dynamic self-assembly (supported by BES) is the major focus. “Flames” has also enjoyed synergistic support, in terms of a project supported by DARPA on flame suppression (in the absence of extinguishing agents, using acoustic and electrostatic interactions). This work was helpful in understanding some of the basics of flames, but is entirely distinct from the BES focus in complexity. A growing interest is in the Lorentz effect. The Lorentz effect is the force exerted on charged particles (electrons, ions, charged molecules) when they move through a perpendicular magnetic field. The Lorentz effect is almost ubiquitous in modern technology: examples of applications include electric motors, dynamos, cathode ray tubes, many batteries, and most systems that control electrical currents with magnetic forces. We have begun to explore the Lorentz effect in electrochemical systems and heterogeneous catalytic systems involving charged organic species and inorganic ions. This work is still at an early stage, but initial studies that Lorentz effects can be large when ions move through magnetic fields, or magnetic fields move in the presence of ions.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Hydrodynamic characterization of the redox chemistry of crown-encapsulated uranyl complexes

The redox properties of actinide-containing species strongly influence their reactivity, speciation, and interfacial behavior, but the experimental quantification of the electrochemical characteristics of molecular actinide complexes in nonaqueous media has not received the attention it deserves. Here, results from hydrodynamic methods and electrochemical simulations of U(VI)/U(V) redox are reported, including quantification of heterogeneous electron-transfer kinetics and estimation of chemical reversibility of U(VI)/U(V) interconversion at electrodes in acetonitrile-based electrolyte. The complexes investigated are recently reported U(VI) and U(V) complexes in which the uranyl ion (UO 2 n+ ) is encapsulated in a macrocyclic 18-crown-6-like moiety templated by a Pt(II) center. These complexes feature the most positive value U VI /U V reduction potential yet reported and are thus particularly relevant to study of facile U(V) generation from U(VI) precursors as well as uranium electroanalysis. Rotating disk electrode (RDE) studies have been used to quantify the diffusion coefficients of the U(VI) and U(V) complexes, and standard heterogeneous electron transfer rate constants ( k 0 ) for the redox have been determined using a conventional Koutecký-Levich analysis. Rotating ring-disk electrode (RRDE) studies have been used to directly interrogate the chemical reversibility of U(VI)-U(V) interconversion, confirming that reduction of the U(VI) complex at an Au disk is associated with formation of the U(V) analogue that can be readily re-oxidized at a Pt ring under hydrodynamic (rotating) conditions. Because measurements of the type reported here are generally associated with current flows that are larger than those found in corresponding quiescent (unstirred) conditions, our findings suggest that hydrodynamic methods could be advantageous for design of electroanalytical approaches to detection of actinide species and study of their redox properties.

actinides↗
DOE OSTI2021

A Study of the Interaction, Morphology, and Structure in Trypsin-Epigallocatechin-3-Gallate Complexes

Understanding the interaction between proteins and polyphenols is of significance to food industries. The aim of this research was to investigate the mode of aggregation for trypsin-EGCG (Epigallocatechin-3-gallate) complexes. For this, the complex was characterized by fluorescence spectroscopy, circular dichroism (CD) spectra, small-angel X-ray scattering (SAXS), and atomic force microscope (AFM) techniques. The results showed that the fluorescence intensity of trypsin-EGCG complexes decreased with increasing the concentration of EGCG, indicating that the interaction between trypsin and EGCG resulted in changes in the microenvironment around fluorescent amino acid residues. The results of CD analysis showed conformational changes in trypsin after binding with EGCG. The results from SAXS analysis showed that the addition of EGCG results in the formation of aggregates of trypsin-EGCG complexes, and increasing the concentration of EGCG resulted in larger aggregates. AFM images showed that the trypsin-EGCG complex formed aggregates of irregular ellipsoidal shapes with the size of about 200 × 400 × 200 nm, with EGCG interconnecting the trypsin particles. Overall, according to these results, it was concluded that the large aggregates of trypsin-EGCG complexes are formed from several small aggregates that are interconnected. The results of this study shed some light on the interaction between digestive enzymes and EGCG.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Spread Spectrum Time Domain Reflectometry and Steepest Descent Inversion to Measure Complex Impedance

In this paper, we present a method for estimating complex impedances using reflectometry and a modified steepest descent inversion algorithm. We simulate spread spectrum time domain reflectometry (SSTDR), which can measure complex impedances on energized systems for an experimental setup with resistive and capacitive loads. A parametric function, which includes both a misfit function and stabilizer function, is created. The misfit function is a least squares estimate of how close the model data matches observed data. The stabilizer function prevents the steepest descent algorithm from becoming unstable and diverging. Steepest descent iteratively identifies the model parameters that minimize the parametric function. We validate the algorithm by correctly identifying the model parameters (capacitance and resistance) associated with simulated SSTDR data, with added 3 dB white Gaussian noise. With the stabilizer function, the steepest descent algorithm estimates of the model parameters are bounded within a specified range. Furthermore, the errors for capacitance (220pF to 820pF) and resistance (50 Ω to 270 Ω) are < 10%, corresponding to a complex impedance magnitude |R +1/jωC| of 53 Ω to 510 Ω.

14 SOLAR ENERGY↗
NASA NTRS1987

Effect of motion cues during complex curved approach and landing tasks: A piloted simulation study

A piloted simulation study was conducted to examine the effect of motion cues using a high fidelity simulation of commercial aircraft during the performance of complex approach and landing tasks in the Microwave Landing System (MLS) signal environment. The data from these tests indicate that in a high complexity MLS approach task with moderate turbulence and wind, the pilot uses motion cues to improve path tracking performance. No significant differences in tracking accuracy were noted for the low and medium complexity tasks, regardless of the presence of motion cues. Higher control input rates were measured for all tasks when motion was used. Pilot eye scan, as measured by instrument dwell time, was faster when motion cues were used regardless of the complexity of the approach tasks. Pilot comments indicated a preference for motion. With motion cues, pilots appeared to work harder in all levels of task complexity and to improve tracking performance in the most complex approach task.

Scanlon, Charles H.↗
NASA NTRS1989

A high level Ab initio study of the anionic hydrogen-bonded complexes FH-CN-, FH-NC-, H2O-CN- and H2O-NC-

HF, H2O, CN- and their hydrogen-bonded complexes were studied using state-of-the-art ab initio quantum mechanical methods. A large Gaussian one particle basis set consisting of triple zeta plus double polarization plus diffuse s and p functions (TZ2P + diffuse) was used. The theoretical methods employed include self consistent field, second order Moller-Plesset perturbation theory, singles and doubles configuration interaction theory and the singles and doubles coupled cluster approach. The FH-CN- and FH-NC- and H2O-CN-, H2O-NC- pairs of complexes are found to be essentially isoenergetic. The first pair of complexes are predicted to be bound by approx. 24 kcal/mole and the latter pair bound by approximately 15 kcal/mole. The ab initio binding energies are in good agreement with the experimental values. The two being shorter than the analogous C-N hydrogen bond. The infrared (IR) spectra of the two pairs of complexes are also very similar, though a severe perturbation of the potential energy surface by proton exchange means that the accurate prediction of the band center of the most intense IR mode requires a high level of electronic structure theory as well as a complete treatment of anharmonic effects. The bonding of anionic hydrogen-bonded complexes is discussed and contrasted with that of neutral hydrogen-bonded complexes.

Lee, Timothy J.↗
NASA NTRS1989

A high-level ab initio study of the anionic hydrogen-bonded complexes FH-CN(-), FH-NC(-), H2O-CN(-), and H2O-NC(-)

HF, H2O, CN- and their hydrogen-bonded complexes were studied using state-of-the-art ab initio quantum mechanical methods. A large Gaussian one particle basis set consisting of triple zeta plus double polarization plus diffuse s and p functions (TZ2P + diffuse) was used. The theoretical methods employed include self consistent field, second order Moller-Plesset perturbation theory, singles and doubles configuration interaction theory and the singles and doubles coupled cluster approach. The FH-CN- and FH-NC- and H2O-CN-, H2O-NC- pairs of complexes are found to be essentially isoenergetic. The first pair of complexes are predicted to be bound by approx. 24 kcal/mole and the latter pair bound by approximately 15 kcal/mole. The ab initio binding energies are in good agreement with the experimental values. The two being shorter than the analogous C-N hydrogen bond. The infrared (IR) spectra of the two pairs of complexes are also very similar, though a severe perturbation of the potential energy surface by proton exchange means that the accurate prediction of the band center of the most intense IR mode requires a high level of electronic structure theory as well as a complete treatment of anharmonic effects. The bonding of anionic hydrogen-bonded complexes is discussed and contrasted with that of neutral hydrogen-bonded complexes.

Lee, Timothy J.↗
NASA NTRS1991

Krylov Subspace Methods for Complex Non-Hermitian Linear Systems

We consider Krylov subspace methods for the solution of large sparse linear systems Ax = b with complex non-Hermitian coefficient matrices. Such linear systems arise in important applications, such as inverse scattering, numerical solution of time-dependent Schrodinger equations, underwater acoustics, eddy current computations, numerical computations in quantum chromodynamics, and numerical conformal mapping. Typically, the resulting coefficient matrices A exhibit special structures, such as complex symmetry, or they are shifted Hermitian matrices. In this paper, we first describe a Krylov subspace approach with iterates defined by a quasi-minimal residual property, the QMR method, for solving general complex non-Hermitian linear systems. Then, we study special Krylov subspace methods designed for the two families of complex symmetric respectively shifted Hermitian linear systems. We also include some results concerning the obvious approach to general complex linear systems by solving equivalent real linear systems for the real and imaginary parts of x. Finally, numerical experiments for linear systems arising from the complex Helmholtz equation are reported.

Freund, Roland W.↗
NASA NTRS1992

Preliminary analysis of thermal-infrared multispectral scanner data of the Iron Hill, Colorado carbonatite-alkalic rock complex

The Iron Hill carbonatite-alkalic igneous rock complex is in the Powderhorn mining district, approximately 40 km south-southwest of Gunnison, Colorado. The complex, which occupies about 30 sq km, was emplaced in metasedimentay and metavolcanic rocks during the later Precambrian or early Cambrian. The main rock types in the complex, from oldest to youngest, are fenite, pyroxenite, uncompahgrite, ijolite, nepheline syenite, and dolomitic carbonatite. The carbonatite is limonitic and forms an elliptially shaped 4 sq km stock. Calcitic and dolomitic carbonatite dikes are also numerous throughout the complex and in the pre-existing rocks. Pyroxenite is the most widespread rock type within the complex, but pyroxene is extensively altered to biotite, phlogopite, and vermiculite. Fenite, which formed through Na, K-metasomatism of the country rocks, typically contains more feldspar and less quartz than the equivalent unaltered country rocks. The other alkalic rock types are less widespread and less well exposed. Parts of the complex are covered by Oligocene ash-flow tuff and alluvial, colluvial, and glacial deposits. Sagebrush and grass cover is moderately dense to very dense at low to intermediate elevations; coniferous tree cover is dense at high elevations and on some north-facing slopes at lower elevations. A new algorithm was used to compute spectral emissivity ratios, independent of any emissivity assumptions. This algorithm has the advantage that any of the possible emissivity ratios can be computed and, thus, a large variety of composite ratio images can be constructed, which permits examination of various geologic hypotheses based on the spectral properties of the surface materials.

Rowan, Lawrence C.↗
NASA NTRS1982

Matrix isolation infrared spectra of hydrogen halide and halogen complexes with nitrosyl halides

Matrix isolation infrared spectra of nitrosyl halide (XNO) complexes with HX and X2 (X = Cl, Br) are presented. The relative frequency shifts of the HX mode are modest (ClNO H-Cl, delta-nu/nu = -0.045; BrNO H-Br, delta-nu/nu = -0.026), indicating weak hydrogen bonds 1-3 kcal/mol. These shifts are accompanied by significant shifts to higher frequencies in the XN-O stretching mode (CIN-O HCl, delta-nu/nu = +0.016; BrN-O HBr, delta-nu/nu = +0.011). Similar shifts were observed for the XN-O X2 complexes (ClN-O Cl2, delta-nu/nu = +0.009; BrN-O-Br2, delta-nu/nu = +0.013). In all four complexes, the X-NO stretching mode relative shift is opposite in sign and about 1.6 times that of the NO stretching mode. These four complexes are considered to be similar in structure and charge distribution. The XN-O frequency shift suggests that complex formation is accompanied by charge withdrawal from the NO bond ranging from about .04 to .07 electron charges. The HX and X2 molecules act as electron acceptors, drawing electrons out of the antibonding orbital of NO and strengthening the XN-O bond. The implications of the pattern of vibrational shifts concerning the structure of the complexes are discussed.

Allamandola, Louis J.↗
NASA NTRS1993

Reduction of Model Complexity by Active Control

The mathematical models of many dynamic systems of interest in the aerospace industry are inherently complex and of high order. Rather than grapple with the full-complexity models for such systems, the control designers often elect to derive low-order, reduced-complexity models for which a control system can be designed. The subject of model-order reduction has received a significant amount of attention in control engineering literature. This paper describes and demonstrates a novel active-control methodology that can be used to design a control system that automatically forces the original system to behave like a chosen reduced-complexity model by treating the effects of the original complexity-related terms as disturbances acting on the reduced-complexity system. The method is demonstrated by several worked examples involving both linear and nonlinear systems, supported by simulation results.

Bukley, Angelia P.↗
NASA NTRS2004

Complex Chromosomal Rearrangements Induced in Vivo by Heavy Ions

It has been suggested that the ratio complex/simple exchanges can be used as a biomarker of exposure to high-LET radiation. We tested this hypothesis in vivo, by considering data from several studies that measured complex exchanges in peripheral blood from humans exposed to mixed fields of low- and high-LET radiation. In particular, we studied data from astronauts involved in long-term missions in low-Earth-orbit, and uterus cancer patients treated with accelerated carbon ions. Data from two studies of chromosomal aberrations in astronauts used blood samples obtained before and after space flight, and a third study used blood samples from patients before and after radiotherapy course. Similar methods were used in each study, where lymphocytes were stimulated to grow in vitro, and collected after incubation in either colcemid or calyculin A. Slides were painted with whole-chromosome DNA fluorescent probes (FISH), and complex and simple chromosome exchanges in the painted genome were classified separately. Complex-type exchanges were observed at low frequencies in control subjects, and in our test subjects before the treatment. No statistically significant increase in the yield of complex-type exchanges was induced by the space flight. Radiation therapy induced a high fraction of complex exchanges, but no significant differences could be detected between patients treated with accelerated carbon ions or X-rays. Complex chromosomal rearrangements do not represent a practical biomarker of radiation quality in our test subjects. Copyright 2003 S. Karger AG, Basel.

Ions/adverse effects/therapeutic use↗
NASA NTRS2008

On Convergence of Development Costs and Cost Models for Complex Spaceflight Instrument Electronics

Development costs of a few recent spaceflight instrument electrical and electronics subsystems have diverged from respective heritage cost model predictions. The cost models used are Grass Roots, Price-H and Parametric Model. These cost models originated in the military and industry around 1970 and were successfully adopted and patched by NASA on a mission-by-mission basis for years. However, the complexity of new instruments recently changed rapidly by orders of magnitude. This is most obvious in the complexity of representative spaceflight instrument electronics' data system. It is now required to perform intermediate processing of digitized data apart from conventional processing of science phenomenon signals from multiple detectors. This involves on-board instrument formatting of computational operands from row data for example, images), multi-million operations per second on large volumes of data in reconfigurable hardware (in addition to processing on a general purpose imbedded or standalone instrument flight computer), as well as making decisions for on-board system adaptation and resource reconfiguration. The instrument data system is now tasked to perform more functions, such as forming packets and instrument-level data compression of more than one data stream, which are traditionally performed by the spacecraft command and data handling system. It is furthermore required that the electronics box for new complex instruments is developed for one-digit watt power consumption, small size and that it is light-weight, and delivers super-computing capabilities. The conflict between the actual development cost of newer complex instruments and its electronics components' heritage cost model predictions seems to be irreconcilable. This conflict and an approach to its resolution are addressed in this paper by determining the complexity parameters, complexity index, and their use in enhanced cost model.

Kizhner, Semion↗
NASA NTRS2011

Atomic Simulation of Complex DNA DSBs and the Interactions with the Ku70/80 Heterodimer

DNA double strand breaks (DSBs) induced by ionizing radiation (IR) usually contain modified bases such as 8-oxo-7,8-dihydroguanine (8-oxoG) and thymine glycol, apurinic/apyrimidinic (AP) sites, 2-deoxyribonolactone, or single-strand breaks (SSBs). The presence of such lesions in close proximity to the DSB terminus makes the DNA nicks more difficult to repair and rejoin than endogenously induced simple DSBs, and as such a major determinant of the biological effects of high linear energy transfer (LET) radiation as encountered in space travel. In this study we conducted molecular dynamics simulations on a series of DNA duplexes with various complex lesions of 8-oxoG and AP sites, in an effort to investigate the effects of such lesions to the structural integrity and stability of DNA after insulted by IR. We also simulated the interaction of such complex DSBs with the Ku70/80 heterodimer, the first protein in mammalian cells to embark the non-homologous end joining (NHEJ) DNA repair pathway. The results indicate, compared to DNA with simple DSBs, the complex lesions can enhance the hydrogen bonds opening rate at the DNA terminus, and increase the mobility of the whole duplex, thus they present more deleterious effects to the genome integrity if not captured and repaired promptly in cells. Simulations also demonstrate the binding of Ku drastically reduces structural disruption and flexibility caused by the complex lesions, and the interactions of Ku with complex DSBs have a different potential energy landscape from the bound structure with simple DSB. In all complex DSBs systems, the binding of DSB terminus with Ku70 is softened while the binding of the middle duplex with Ku80 is tightened. This energy shift may help the Ku protein to secure at the DSB terminus for a longer time, so that other end processing factors or repair pathways can proceed at the lesions before NHEJ repair process starts. These atomic simulations may provide valuable new insight into the selective action of repair proteins on damaged DNA.

Hu, Shaowen↗