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NASA NTRS2005

Optimal Sampling of a Reaction Coordinate in Molecular Dynamics

Estimating how free energy changes with the state of a system is a central goal in applications of statistical mechanics to problems of chemical or biological interest. From these free energy changes it is possible, for example, to establish which states of the system are stable, what are their probabilities and how the equilibria between these states are influenced by external conditions. Free energies are also of great utility in determining kinetics of transitions between different states. A variety of methods have been developed to compute free energies of condensed phase systems. Here, I will focus on one class of methods - those that allow for calculating free energy changes along one or several generalized coordinates in the system, often called reaction coordinates or order parameters . Considering that in almost all cases of practical interest a significant computational effort is required to determine free energy changes along such coordinates it is hardly surprising that efficiencies of different methods are of great concern. In most cases, the main difficulty is associated with its shape along the reaction coordinate. If the free energy changes markedly along this coordinate Boltzmann sampling of its different values becomes highly non-uniform. This, in turn, may have considerable, detrimental effect on the performance of many methods for calculating free energies.

Pohorille, Andrew↗

NASA NTRS1998

Distinct Secondary Structures of the Leucine-Rich Repeat Proteoglycans Decorin and Biglycan: Glycosylation-Dependent Conformational Stability

Biglycan and decorin, closely related small leucine-rich repeat proteoglycans, have been overexpressed in eukaryotic cers and two major glycoforms isolated under native conditions: a proteoglycan substituted with glycosaminoglycan chains; and a core protein form secreted devoid of glycosaminoglycans. A comparative biophysical study of these glycoforms has revealed that the overall secondary structures of biglycan and decorin are different. Far-UV Circular Dichroism (CD) spectroscopy of decorin and biglycan proteoglycans indicates that, although they are predominantly Beta-sheet, biglycan has a significantly higher content of alpha-helical structure. Decorin proteoglycan and core protein are very similar, whereas the biglycan core protein exhibits closer similarity to the decorin glycoforms than to. the biglycan proteoglycan form. However, enzymatic removal of the chondroitin sulfate chains from biglycan proteoglycan does not induce a shift to the core protein structure, suggesting that the fmal form is influenced by polysaccharide addition only during biosynthesis. Fluorescence emission spectroscopy demonstrated that the single tryptophan residue, which is at a conserved position at the C-terminal domain of both biglycan and decorin, is found in similar microenvironments. This indicates that at least in this specific domain, the different glycoforms do exhibit apparent conservation of structure. Exposure of decorin and biglycan to 10 M urea resulted in an increase in fluorescent intensity, which indicates that the emission from tryptophan in the native state is quenched. Comparison of urea-induced protein unfolding curves provided further evidence that decorin and biglycan assume different structures in solution. Decorin proteoglycan and core protein unfold in a manner similar to a classic two-state model, in which there is a steep transition to an unfolded state between 1-2 M urea. The biglycan core protein also shows a similar steep transition. However, biglycan proteoglycan shows a broad unfolding transition between 1-6 M urea, probably indicating the presence of stable unfolding intermediates.

Krishnan, Priya↗

NASA NTRS1989

Oscillator strengths and electron collisional excitation cross sections for atomic oxygen

The electron-impact excitations of 12 states of O I are analyzed using a close-coupling approximation. The absorption oscillator strengths for dipole-allowed transitions among the states are calculated. Cross sections for excitation of the states by electron impact in the energy region 13.87 to 100 eV are compared with the data of Smith (1976) and Doering and Gulcicek. It is observed that there is a correlation between the data at energies 13.87, 20, and 30 eV for the (3)P-3p(5)P transition and at energies 13.87 and 16.5 eV for the (3)P-3s(5)S(0) transitions; however, for the dipole-allowed (3)P-3d(3)D(0) and (3)P-3s(prime)(3)D(0) transitions there are discrepancies in magnitude.

Tayal, S. S.↗

NASA NTRS2006

Exploring the Connection Between Sampling Problems in Bayesian Inference and Statistical Mechanics

The Bayesian and statistical mechanical communities often share the same objective in their work - estimating and integrating probability distribution functions (pdfs) describing stochastic systems, models or processes. Frequently, these pdfs are complex functions of random variables exhibiting multiple, well separated local minima. Conventional strategies for sampling such pdfs are inefficient, sometimes leading to an apparent non-ergodic behavior. Several recently developed techniques for handling this problem have been successfully applied in statistical mechanics. In the multicanonical and Wang-Landau Monte Carlo (MC) methods, the correct pdfs are recovered from uniform sampling of the parameter space by iteratively establishing proper weighting factors connecting these distributions. Trivial generalizations allow for sampling from any chosen pdf. The closely related transition matrix method relies on estimating transition probabilities between different states. All these methods proved to generate estimates of pdfs with high statistical accuracy. In another MC technique, parallel tempering, several random walks, each corresponding to a different value of a parameter (e.g. "temperature"), are generated and occasionally exchanged using the Metropolis criterion. This method can be considered as a statistically correct version of simulated annealing. An alternative approach is to represent the set of independent variables as a Hamiltonian system. Considerab!e progress has been made in understanding how to ensure that the system obeys the equipartition theorem or, equivalently, that coupling between the variables is correctly described. Then a host of techniques developed for dynamical systems can be used. Among them, probably the most powerful is the Adaptive Biasing Force method, in which thermodynamic integration and biased sampling are combined to yield very efficient estimates of pdfs. The third class of methods deals with transitions between states described by rate constants. These problems are isomorphic with chemical kinetics problems. Recently, several efficient techniques for this purpose have been developed based on the approach originally proposed by Gillespie. Although the utility of the techniques mentioned above for Bayesian problems has not been determined, further research along these lines is warranted

Pohorille, Andrew↗

NASA NTRSDate not supplied

Improving Kinetic Consistency Across Elastic Model Transitions With Quadratic Inequality Constrained Weighted Least Squares (WLSQI)

Flexible body modeling presents a large challenge in the development of simulations to aid in design of flight control systems for launch and landing vehicles. Typically, the flexible body model is not a single continuous model but are rather discrete sets of Linear Time Invariant (LTI) Finite Element Models (FEM) incremented by propellant levels. This introduces the problem of smoothly transitioning modal and physical states of the vehicle when switching from one FEM to the next. This paper introduces a new approach to optimally transition flexible body states with weighted least squares, building off previous methods.

Convex Optimization↗

NASA NTRSDate not supplied

Improving Kinetic Consistency Across Elastic Model Transitions With Quadratic Inequality Constrained Weighted Least Squares (WLSQI)

GN&C↗

NASA NTRS1992

Bypass transition in compressible boundary layers

Transition to turbulence in aerospace applications usually occurs in a strongly disturbed environment. For instance, the effects of free-stream turbulence, roughness and obstacles in the boundary layer strongly influence transition. Proper understanding of the mechanisms leading to transition is crucial in the design of aircraft wings and gas turbine blades, because lift, drag and heat transfer strongly depend on the state of the boundary layer, laminar or turbulent. Unfortunately, most of the transition research, both theoretical and experimental, has focused on natural transition. Many practical flows, however, defy any theoretical analysis and are extremely difficult to measure. Morkovin introduced in his review paper the concept of bypass transition as those forms of transition which bypass the known mechanisms of linear and non-linear transition theories and are currently not understood by experiments. In an effort to better understand the mechanisms leading to transition in a disturbed environment, experiments are conducted studying simpler cases, viz. the effects of free stream turbulence on transition on a flat plate. It turns out that these experiments are very difficult to conduct, because generation of free stream turbulence with sufficiently high fluctuation levels and reasonable homogeneity is non trivial. For a discussion see Morkovin. Serious problems also appear due to the fact that at high Reynolds numbers the boundary layers are very thin, especially in the nose region of the plate where the transition occurs, which makes the use of very small probes necessary. The effects of free-stream turbulence on transition are the subject of this research and are especially important in a gas turbine environment, where turbulence intensities are measured between 5 and 20 percent, Wang et al. Due to the fact that the Reynolds number for turbine blades is considerably lower than for aircraft wings, generally a larger portion of the blade will be in a laminar transitional state. The effects of large free stream turbulence in compressible boundary layers at Mach numbers are examined both in the subsonic and transonic regime using direct numerical simulations. The flow is computed over a flat plate and curved surface. while many applications operate in the transonic regime. Due the nature of their numerical scheme, a non-conservation formulation of the Navier-Stokes equations, it is a non-trivial extension to compute flow fields in the transonic regime. This project aims at better understanding the effects of large free-stream turbulence in compressible boundary layers at mach number both in the subsonic and transonic regime using direct numerical simulations. The present project aims at computing the flow over a flat plate and curved surface. This research will provide data which can be used to clarify mechanisms leading to transition in an environment with high free stream turbulence. This information is useful for the development of turbulence models, which are of great importance for CFD applications, and are currently unreliable for more complex flows, such as transitional flows.

Vandervegt, J. J.↗

NASA NTRS2010

Model-Checking with Edge-Valued Decision Diagrams

We describe an algebra of Edge-Valued Decision Diagrams (EVMDDs) to encode arithmetic functions and its implementation in a model checking library along with state-of-the-art algorithms for building the transition relation and the state space of discrete state systems. We provide efficient algorithms for manipulating EVMDDs and give upper bounds of the theoretical time complexity of these algorithms for all basic arithmetic and relational operators. We also demonstrate that the time complexity of the generic recursive algorithm for applying a binary operator on EVMDDs is no worse than that of Multi-Terminal Decision Diagrams. We have implemented a new symbolic model checker with the intention to represent in one formalism the best techniques available at the moment across a spectrum of existing tools: EVMDDs for encoding arithmetic expressions, identity-reduced MDDs for representing the transition relation, and the saturation algorithm for reachability analysis. We compare our new symbolic model checking EVMDD library with the widely used CUDD package and show that, in many cases, our tool is several orders of magnitude faster than CUDD.

Roux, Pierre↗

NASA NTRS1992

Hydroxyl X2Pi pure rotational transitions

We present a list of frequencies, term values, Einstein A values, and assignments for the pure rotational transitions of the X2Pi state of the OH molecule. This list includes transitions from 3 to 2015/cm for Delta-v = 0, v-double-prime = 0-4, and J-double-prime = 0.5-49.5. The A values were computed using recent advances in calculating wave functions for a coupled system and an experimentally derived electric dipole moment function (Nelson et al., 1990) which exhibits curvature.

Goorvitch, D.↗

NASA NTRS1982

X-ray observations of the 1980 Cygnus X-1 'high state'

Observations of intensity transitions in the X-ray emission from the black-hole candidate Cygnus X-1 were made by the Hakucho satellite during the summer of 1980 and are reported here. In addition, the results of hard (20-120 keV) X-ray observations of Cyg X-1 are reported. These data were obtained during the 'high' intensity state by balloon-borne mercuric iodide detectors, and are compared with data obtained at similar energies approximately 1 month earlier (A. Sheepmaker et al., in preparation) during the 'low' intensity state.

Ogawara, Y.↗

NASA NTRS1992

The 10 kW power electronics for hydrogen arcjets

A combination of emerging mission considerations such as 'launch on schedule', resource limitations, and the development of higher power spacecraft busses has resulted in renewed interest in high power hydrogen arcjet systems with specific impulses greater than 1000 s for Earth-space orbit transfer and maneuver applications. Solar electric propulsion systems with about 10 kW of power appear to offer payload benefits at acceptable trip times. This work outlines the design and development of 10 kW hydrogen arcjet power electronics and results of arcjet integration testing. The power electronics incorporated a full bridge switching topology similar to that employed in state of the art 5 kW power electronics, and the output filter included an output current averaging inductor with an integral pulse generation winding for arcjet ignition. Phase shifted, pulse width modulation with current mode control was used to regulate the current delivered to arcjet, and a low inductance power stage minimized switching transients. Hybrid power Metal Oxide Semiconductor Field Effect Transistors were used to minimize conduction losses. Switching losses were minimized using a fast response, optically isolated, totem-pole gate drive circuit. The input bus voltage for the unit was 150 V, with a maximum output voltage of 225 V. The switching frequency of 20 kHz was a compromise between mass savings and higher efficiency. Power conversion efficiencies in excess of 0.94 were demonstrated, along with steady state load current regulation of 1 percent. The power electronics were successfully integrated with a 10 kW laboratory hydrogen arcjet, and reliable, nondestructive starts and transitions to steady state operation were demonstrated. The estimated specific mass for a flight packaged unit was 2 kg/kW.

Hamley, John A.↗

NASA NTRS2017

The Effects of Vegetative Type, Edges, Fire History, Rainfall and Management in Fire-Maintained Ecosystems

The combined effects of repeated fires, climate, and landscape features (e.g., edges) need greater focus in fire ecology studies, which usually emphasize characteristics of the most recent fire and not fire history. Florida scrub-jays are an imperiled, territorial species that prefer medium (1.2-1.7 m) shrub heights. We measured short, medium, and tall habitat quality states annually within 10 ha grid cells that represented potential territories because frequent fires and vegetative recovery cause annual variation in habitat quality. We used multistate models and model selection to test competing hypotheses about how transition probabilities between states varied annually as functions of environmental covariates. Covariates included vegetative type, edges, precipitation, openings (gaps between shrubs), mechanical cutting, and fire characteristics. Fire characteristics not only included an annual presenceabsence of fire covariate, but also fire history covariates: time since the previous fire, the maximum fire-free interval, and the number of repeated fires. Statistical models with support included many covariates for each transition probability, often including fire history, interactions and nonlinear relationships. Tall territories resulted from 28 years of fire suppression and habitat fragmentation that reduced the spread of fires across landscapes. Despite 35 years of habitat restoration and prescribed fires, half the territories remained tall suggesting a regime shift to a less desirable habitat condition. Measuring territory quality states and environmental covariates each year combined with multistate modeling provided a useful empirical approach to quantify the effects of repeated fire in combinations with environmental variables on transition probabilities that drive management strategies and ecosystem change.

Breininger, David R.↗

NASA NTRS1976

The long-term intensity behavior of Centaurus X-3

In three years of observation, the X-ray source Cen X-3 appears to alternate between 'high states', with an intensity of 150 counts/s (2-6 keV) or greater, and 'low states', where the source is barely detectable. The time scale of this behavior is of the order of months, and no apparent periodicity has been observed. Analysis of two transitions between these states is reported. During two weeks in July 1972, the source increased from about 20 counts/s to 150 counts/s. The detailed nature of this turn-on is interpreted in terms of a model in which the supergiant's stellar wind decreases in density. A second transition, a turnoff in February 1973, is similarly analyzed and found to be consistent with a simple decrease in accretion rate. The presence of absorption dips during transitions at orbital phases 0.4-0.5 as well as at phase 0.75 is discussed. The data are consistent with a stellar-wind accretion model and with different kinds of extended lows caused by increased wind density masking the X-ray emission or by decreased wind density lowering the accretion rate.

Schreier, E. J.↗

NASA NTRS1989

Frequency and intensity analysis of the nu3, nu4, and nu6 bands of formaldehyde

The infrared spectra of the nu3, nu4, and nu6 bands of formaldehyde in the region from 890/cm to 1580/cm have been obtained at high resolution using tunable diode laser and Fourier transform-infrared spectroscopy. The transition frequencies have been analyzed using a Hamiltonian including terms through sextic in centrifugal distortion and including five interstate vibration-rotation coupling terms. Excited-state pure rotational transitions are also included in the data, and their frequencies are reproduced well. Individual measured line intensities are used to determine dipole derivatives and band strengths using the fully coupled, asymmetric top eigenvectors.

Reuter, D. C.↗

NASA NTRS1995

The Theoretical Transition Probabilities Between the B(sup 3)Pi(sub g) and the A(sup 3)Sigma(Sup +, sub u), W(sup 3)Delta(sub u), B'(sup 3)Sigma(sup -, sub u) States of N2

The electronic transition moment functions between the B(sup 3)Pi(sub g) and the A(sup 3)Sigma(sup +, sub u), W(sup 3)Delta(sub u), B'(sup 3)Sigma(sup -, sub u) states of N2 are studied using the internally contracted multireference configuration interaction (ICMRCI) method based upon complete active space SCF (CASSCF) reference wave-functions. The dependence of the moments on both the one and n-particle basis sets has been investigated in detail. The calculated radiative lifetimes for the vibrational levels of B(sup 3)Pi(sub g) are in excellent agreement with the most recent measurement of Euler and Pipkin (1983)

Thuemmel, Helmar T.↗

NASA NTRS1988

The laboratory millimeter- and submillimeter-wave spectrum of the first two excited torsional states of (C-13)H3OH

The rotational-torsional spectrum of (C-13)H3OH is presented in both the symmetric and degenerate substates of the first two excited torsional states. Of the new transitions reported, 122 lines are from the v(t) = 1 torsional state and 110 lines are from the v(t) = 2 torsional state, and all are confined to the rotational quantum number J = 8 or less. The data are combined with previously reported millimeter and submillimeter data for the v(t) = 0 torsional state and 44 previously measured excited torsional state lines to form a global data set of 596 transitions, which is analyzed and fitted using an extended internal axis method. The fit results in an overall rms deviation of 1.98 MHz. The spectral constants generated by the fit are used to predict an additional 123 lines of (C-13)H3OH in the v(t) = 1,2 excited torsional states with frequencies up to 612 GHz and rotational quantum number J = 11 or less.

Anderson, Todd↗

NASA NTRS1987

Electromagnetic Repulsive Deicer for Aircraft

Scheme for removing ice from airfoils in flight adds little weight and demands relatively small amount of energy. Employing electromagnetic repulsion of conductors embedded in rubber covering on airfoil, scheme breaks up layer of ice by snapping it in manner of snapping rug to remove dust. Layer of elastomer conforms to shape of airfoil in relaxed state. When carrying large electrical currents, conductive ribbons in elastomer repel each other, creating ridged surface on airfoil. Sheet of ice on airfoil broken up in sudden transition from relaxed state to energized state.

Haslim, Leonard A.↗

NASA NTRS1987

Numerical simulations of trailing vortex bursting

Solutions of the steady-state Navier-Stokes equations for the axisymmetric bursting of a laminar trailing vortex are computed with Newton's method and the pseudo-arc length continuation method for wide ranges of vortex strength and Reynolds number. The results indicate that a trailing vortex can undergo a transition from a state in which the core slowly diffuses to a state marked by large amplitude, spatial oscillations of core radius and core axial velocity. At the transition point the core grows rapidly in size. This event is interpreted as vortex bursting. The results also suggest that when the maximum core swirl velocity is sufficiently large the centerline axial flow downstream of transition will be reversed.

Beran, Philip S.↗