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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Size-dependent femtosecond proton transfer in protonated methanol clusters

Methanol clusters (CH 3 OH) n are prototypical hydrogen-bonded systems that bridge isolated molecules and bulk liquid methanol. Strong-field ionization of these clusters can trigger ultrafast charge migration, proton transfer, and isomerization; however, the onset timescales of these pathways remain largely unexplored despite extensive steady-state mass-spectrometric evidence for protonation and chemical rearrangement. Here we use femtosecond time-resolved strong-field ionization and disruptive probing to directly track the early-time dynamics of methanol clusters. Transient mass spectra yield size-dependent timescales for the formation of protonated clusters H + (CH 3 OH) n (n = 1–3) and an associated CHO˙ + radical cation. We find that both proton-transfer and subsequent stabilization become markedly faster with increasing cluster size. These measurements establish methanol clusters as a complementary benchmark to water for understanding ionization-initiated proton motion and chemical reorganization in hydrogen-bonded liquids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Searching for the most powerful thermonuclear X-ray bursts with the Neil Gehrels Swift Observatory

We searched for thermonuclear X-ray bursts from Galactic neutron stars in all event mode data of the Neil Gehrels Swift Observatory collected until March 31, 2018. In particular, we are interested in the intermediate-duration bursts (shell flashes fueled by thick helium piles) with the ill-understood phenomenon of strong flux fluctuations. Nine such bursts have been discussed in the literature to date. Swift is particularly suitable for finding additional examples. We find and list a total of 134 X-ray bursts; 44 are detected with BAT only, 41 with XRT only, and 49 with both. Twenty-eight bursts involve automatic slews. We find 12 intermediate-duration bursts, all detected in observations involving automatic slews. Five show remarkably long Eddington-limited phases in excess of 200 s. Five show fluctuations during the decay phase; four of which are first discussed in the present study. We discuss the general properties of the fluctuations, considering also 7 additional literature cases. In general two types of fluctuations are observed: fast ones, with a typical timescale of 1 s and up and downward fluctuations of up to 70%, and slow ones, with a typical timescale of 1 min and only downward fluctuations of up to 90%. The latter look like partial eclipses because the burst decay remains visible in the residual emission. We revisit the interpretation of this phenomenon in the context of the new data set and find that it has not changed fundamentally despite the expanded data set. It is thought to be due to a disturbance of the accretion disk by outflowing matter and photons, causing obscuration and reflection due to Thompson scattering in an orbiting highly ionized cloud or structure above or below the disk. Furthermore, we discuss in detail the most pronounced burster SAX J1712.6–3739. One of the bursts from this source is unusual in that it lasts longer than 5600 s, but does not appear to be a superburst.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Color–color diagrams as tools for assessment of the variable absorption in high mass X-ray binaries

High mass X-ray binaries hold the promise of allowing us to understand the structure of the winds of their supermassive companion stars by using the emission from the compact object as a backlight to evaluate the variable absorption in the structured stellar wind. The wind along the line of sight can change on timescales as short as minutes and below. However, such short timescales are not available for the direct measurement of absorption through X-ray spectroscopy with the current generation of X-ray telescopes. In this paper, we demonstrate the usability of color–color diagrams for assessing the variable absorption in wind accreting high mass X-ray binary systems. Furthermore, we employ partial covering models to describe the spectral shape of high mass X-ray binaries and assess the implication of different absorbers and their variability on the shape of color–color tracks. We show that in taking into account, the ionization of the absorber, and in particular accounting for the variation of ionization with absorption depth, is crucial to describe the observed behavior well.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Disturbed, diffuse, or just missing? A global study of the H I content of Hickson compact groups

Hickson compact groups (HCGs) are dense configurations of four to ten galaxies, whose H I morphology appears to follow an evolutionary sequence of three phases, with gas initially confined to galaxies, then significant amounts spread throughout the intra-group medium, and finally with almost no gas remaining in the galaxies themselves. It has also been suggested that several groups may harbour a diffuse H I component that is resolved out by interferometric observations. The H I deficiency of HCGs is expected to increase as the H I morphological phase progresses along the evolutionary sequence. If this is the case, H I deficiency would be a rough proxy for the age and evolutionary state of a HCG. We aim to test this hypothesis for the first time using a large sample of HCGs and to investigate the evidence for diffuse H I in HCGs. We performed a uniform reduction of all publicly available VLA H I observations (38 HCGs) with a purpose-built pipeline that also maximises the reproducibility of this study. The resulting H I data cubes were then analysed with the latest software tools to perform a manual separation of emission features into those belonging to galaxies and those extending into the intra-group medium. We thereby classified the H I morphological phase of each group as well as quantified their H I deficiency compared to galaxies in isolation. We find little evidence that H I deficiency can be used as a proxy for the evolutionary phase of a compact group in either of the first two phases, with the distribution of H I deficiency being consistent in both. However, for the final phase, the distribution clearly shifts to high H I deficiencies, with more than 90% of the expected H I content typically missing. Across all HCGs studied, we identify a few cases where there is strong evidence for a diffuse gas component in the intra-group medium, which might be detectable with improved observations. We also classify a new sub-phase where groups contain a lone H I -bearing galaxy, but are otherwise devoid of gas. The new morphological phase we have identified is likely the result of an evolved, gas-poor group acquiring a new, gas-rich member. The large spread of H I deficiencies in the first two morphological phases suggests that there is a broad range of initial H I content in HCGs, which is perhaps influenced by large-scale environment, and that the timescale for morphological changes is, in general, considerably shorter than the timescale for the destruction or consumption of neutral gas in these systems.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

VarIabiLity seLection of AstrophysIcal sources iN PTF (VILLAIN): I. Structure function fits to 71 million objects

Light-curve variability is well-suited to characterizing objects in surveys with high cadence and a long baseline. This is especially relevant in view of the large datasets to be produced by the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST). We aim to determine variability parameters for objects in the Palomar Transient Factory (PTF) and explore differences between quasars (QSOs), stars, and galaxies. We relate variability and colour information in preparation for future surveys. We fit joint likelihoods to structure functions (SFs) of 71 million PTF light curves with a Markov chain Monte Carlo method. For each object, we assume a power-law SF and extract two parameters: the amplitude on timescales of one year, A, and a power-law index, γ. With these parameters and colours in the optical (Pan-STARRS1) and mid-infrared (WISE), we identify regions of parameter space dominated by different types of spectroscopically confirmed objects from SDSS. Candidate QSOs, stars, and galaxies are selected to show their parameter distributions. QSOs show high-amplitude variations in the R band, and the highest γ values. Galaxies have a broader range of amplitudes and their variability shows relatively little dependency on timescale. With variability and colours, we achieve a photometric selection purity of 99.3% for QSOs. Even though hard cuts in monochromatic variability alone are not as effective as seven-band magnitude cuts, variability is useful in characterizing object subclasses. Through variability, we also find QSOs that were erroneously classified as stars in the SDSS. We discuss perspectives and computational solutions in view of the upcoming LSST.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Do not forget the electrons: Extending moderately-sized nuclear networks for multidimensional hydrodynamic codes

Context.Nuclear networks are widely used coupled with hydrodynamical simulations of explosive scenarios to account for the change of nuclear species and energy generation rate due to nuclear reactions. In this way, there is a feedback mechanism between the hydrodynamical state and the nuclear processes. Unfortunately, the timescale of nuclear reactions is orders of magnitude smaller than the dynamical timescale that drives hydrodynamical simulations. Therefore, these nuclear networks are usually very small, reduced in most cases to a dozen elements, especially when simulations are carried out in more than one dimension. Aims.We present here an extended nuclear network, with 90 species, designed for being coupled with hydrodynamic simulations, which includes neutrons, protons, electrons, positrons, and the corresponding neutrino and anti-neutrino emission. This network is also coupled with temperature, making it extremely robust and, together with its size, unique of its kind. The inclusion of electron captures on free protons makes the network very appropriate for multidimensional studies of Type Ia supernova explosions, especially when the exploding object is a massive white dwarf. Methods.We perform several tests that are relevant to simulate explosive scenarios, such as Type Ia supernovae and core-collapse supernovae. We compare the results of the 90 nuclei network with a standardα-chain network with 14 elements to evaluate the differences in the energy generation rate. We also evaluate the relevance of including the electrons in the network in terms of generated yields and how it affects the pressure of a degenerate fluid such as that of white dwarfs. The results obtained with the 90-nuclei network have been verified with a much larger 2000-nuclei network built from REACLIB (WinNet), in terms of nuclear energy generation rate, pressure, and produced yields. Results.The results obtained with the proposed medium-sized network compare fairly well, to a few percent, with those computed withWinNetin scenarios reproducing the gross physical conditions of current Type Ia supernova explosion models. In those cases where the carbon and oxygen fuel ignites at high density, the high-temperature plateau typical of the nuclear statistical equilibrium regime is well defined and stable, allowing large integration time steps. We show that the inclusion of electron captures on free protons substantially improves the estimation of the electron fraction of the mixture. Therefore, the pressure is better determined than in networks where electron captures are excluded, which will ultimately lead to more reliable hydrodynamic models. Explosive combustion of helium at low density, occurring near the surface layer of a white dwarf, is also better described with the proposed network, which gives nuclear energy generation rates much closer toWinNetthan typical reduced alpha networks. Conclusions.A nuclear network withN= 90 species, including electrons, aimed at multidimensional calculations of supernova explosions is described and verified. The proposed network is suitable for the study of Type Ia supernova explosions because it provides better values of pressure and electron abundance than other existing networks with smaller or even a similar size but without including electron capture processes.

Astronomy & Astrophysics↗
DOE OSTI2026

Full-polarization millimeter wavelength variability of Sagittarius A * during the 2018 EHT campaign

Context. Sagittarius A* (Sgr A*), the supermassive black hole at the center of the Milky Way, provides a unique laboratory to study accretion dynamics and plasma processes near the event horizon. Aims. We investigated the variability and polarization properties of Sgr A* using ALMA observations during the 2018 Event Horizon Telescope campaign. Methods. We analyzed high-cadence full-polarization light curves from ALMA at millimeter wavelengths, performed time-series analysis, and investigated the temporal behavior during an X-ray flare observed by Chandra on 2018 April 24. The variability characteristics are compared with expectations from standard accretion flow models. Results. We find low variability in total intensity (σ/μ < 10%), but significantly higher variability in linear and circular polarization (∼30% and ∼50%, respectively). A time-series analysis reveals red-noise variability, with power spectral densities between −2 and −3 across all Stokes parameters. Polarized intensity shows stable intra-day timescales, while total intensity exhibits more variable timescales, suggesting distinct emission regions, with polarization likely arising from a coherent structure. On April 24, a statistically significant inter-band delay in polarized intensity coincides with a near-simultaneous X-ray and millimeter peak that deviates from the typical delayed flare scenario. This event also features enhanced millimeter variability and coherent polarization loop evolution. The observed simultaneity challenges standard models of transient synchrotron emission with cooling delays, favoring instead a scenario of continuous energy injection in an optically thin region. Conclusions. Our results offer new constraints on the physical mechanisms driving variability in Sgr A*, and provide key observational input for refining theoretical models of accretion and plasma behavior in the vicinity of supermassive black holes.

Galaxy: center↗
DOE OSTI2026

Modeling rf sheath formation in turbulent tokamak boundary plasma

During ICRF antenna operation, complex interactions between turbulent density profiles, nonlinear RF sheaths, and RF-induced convective transport are observed to alter plasma density in the tokamak edge [D’Ippolito et al., Nucl. Fusion 38, 1543 (1998)]. In this work, we explore the physics of such interactions via numerical modeling, using a nonlinear EM/plasma/sheath code (VSim) and profiles obtained from a fluid plasma turbulence code (Hermes) in a 3D slab domain containing biased side-wall limiters. RF-rectified sheath formation on antenna and limiter surfaces is observed as electromagnetic waves launched by the antenna are refracted through the turbulent density profile. On transport timescales, such sheath potentials have been shown to influence both the mean species density and its RMS fluctuation spectrum [Smithe et al., these proceedings]. On the faster RF timescales, we demonstrate that the converse is also true – regions of high plasma density near material surfaces give rise to the highest sheath potential amplitudes. When density is turbulent and spatially nonuniform, localized regions of high sheath potential (hotspots) may develop where high-density filaments intersect material surfaces. Such hotspots are of particular concern as sources of impurity sputtering, and we explore their behavior in response to changes both to the local plasma density and to antenna operating parameters and structure. Related results exploring the role of Faraday shields and/or enclosing structures in suppressing high sheath potentials for other devices (e.g. SPARC) will also be shown.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

Comparison for non-local hydrodynamic thermal conduction models

Inertial confinement fusion and specifically shock ignition involve temperatures and temperature gradients for which the classical Spitzer-Haerm thermal conduction breaks down and a non-local operator is required. In this article, two non-local electron thermal conduction models are tested against kinetic Vlasov-Fokker-Planck simulations. Both models are shown to reproduce the main features of thermal heat front propagation at kinetic timescales. The reduction of the thermal conductivity as a function of the scalelength of the temperature gradient is also recovered. Comparisons at nanosecond timescales show that the models agree on the propagation velocity of the heat front, but major differences appear in the thermal precursor.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

Multi-photon UV photolysis of gaseous polycyclic aromatic hydrocarbons: Extinction spectra and dynamics

The extinction spectra of static naphthalene and static biphenylene vapor, each buffered with a noble gas at room temperature, were measured as a function of time in the region between 390 and 850 nm after UV multi-photon laser photolysis at 308 nm. Employing incoherent broadband cavity enhanced absorption spectroscopy (IBBCEAS), the spectra were found to be unstructured with a general lack of isolated features suggesting that the extinction was not solely based on absorption but was in fact dominated by scattering from particles formed in the photolysis of the respective polycyclic aromatic hydrocarbon. Following UV multi-photon photolysis, the extinction dynamics of the static (unstirred) closed gas-phase system exhibits extraordinary quasi-periodic and complex oscillations with periods ranging from seconds to many minutes, persisting for up to several hours. Depending on buffer gas type and pressure, several types of dynamical responses could be generated (classified as types I, II, and III). They were studied as a function of temperature and chamber volume for different experimental conditions and possible explanations for the oscillations are discussed. A conclusive model for the observed phenomena has not been established. However, a number of key hypotheses have made based on the measurements in this publication: (a) Following the multi-photon UV photolysis of naphthalene (or biphenylene), particles are formed on a timescale not observable using IBBCEAS. (b) The observed temporal behavior cannot be described on basis of a chemical reaction scheme alone. (c) The pressure dependence of the system's responses is due to transport phenomena of particles in the chamber. (d) The size distribution and the refractive indices of particles are time dependent and evolve on a timescale of minutes to hours. The rate of particle coagulation, involving coalescent growth and particle agglomeration, affects the observed oscillations. (e) The walls of the chamber act as a sink. The wall conditions (which could not be quantitatively characterized) have a profound influence on the dynamics of the system and on its slow return to an equilibrium state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Ultrafast x-ray photoelectron spectroscopy in the microsecond time domain

We introduce a new approach for ultrafast in situ high-resolution X-ray photoelectron spectroscopy (XPS) to study surface processes and reaction kinetics on the microsecond timescale. The main idea is to follow the intensity at a fixed binding energy using a commercial 7 channeltron electron analyzer with a modified signal processing setup. This concept allows for flexible switching between measuring conventional XP spectra and ultrafast XPS. The experimental modifications are described in detail. As an example, we present measurements for the adsorption and desorption of CO on Pt(111), performed at the synchrotron radiation facility BESSY II, with a time resolution of 500 μs. Due to the ultrafast measurements, we are able to follow adsorption and desorption in situ at pressures of 2 × 10{sup −6} mbar and temperatures up to 500 K. The data are consistently analyzed using a simple model in line with data obtained with conventional fast XPS at temperatures below 460 K. Technically, our new approach allows measurement on even shorter timescales, down to 20 μs.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models

The dynamics of complex molecules can be directly probed by inelastic neutron scattering experiments. However, many of the underlying dynamical processes may exist on similar timescales, which makes it difficult to assign processes seen experimentally to specific structural rearrangements. Here, we show how Markov models can be used to connect structural changes observed in molecular dynamics simulation directly to the relaxation processes probed by scattering experiments. For this, a conformational dynamics theory of dynamical neutron and X-ray scattering is developed, following our previous approach for computing dynamical fingerprints of time-correlation functions [F. No , S. Doose, I. Daidone, M. L llmann, J. Chodera, M. Sauer, and J. Smith, Proc. Natl. Acad. Sci. U.S.A.108, 4822 (2011)]. Markov modeling is used to approximate the relaxation processes and timescales of the molecule via the eigenvectors and eigenvalues of a transition matrix between conformational substates. Furthermore, this procedure allows the establishment of a complete set of exponential decay functions and a full decomposition into the individual contributions, i.e., the contribution of every atom and dynamical process to each experimental relaxation process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

Application of AXUV diode detectors at ASDEX Upgrade

In the ASDEX Upgrade tokamak, a radiation measurement for a wide spectral range, based on semiconductor detectors, with 256 lines of sight and a time resolution of 5μs was recently installed. In combination with the foil based bolometry, it is now possible to estimate the absolutely calibrated radiated power of the plasma on fast timescales. This work introduces this diagnostic based on AXUV (Absolute eXtended UltraViolet) n-on-p diodes made by International Radiation Detectors, Inc. The measurement and the degradation of the diodes in a tokamak environment is shown. Even though the AXUV diodes are developed to have a constant sensitivity for all photon energies (1 eV-8 keV), degradation leads to a photon energy dependence of the sensitivity. The foil bolometry, which is restricted to a time resolution of less than 1 kHz, offers a basis for a time dependent calibration of the diodes. The measurements of the quasi-calibrated diodes are compared with the foil bolometry and found to be accurate on the kHz time scale. Therefore, it is assumed, that the corrected values are also valid for the highest time resolution (200 kHz). With this improved diagnostic setup, the radiation induced by edge localized modes is analyzed on fast timescales.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

NMR spin relaxation in proteins: The patterns of motion that dissipate power to the bath

We developed in recent years the two-body coupled-rotator slowly relaxing local structure (SRLS) approach for the analysis of NMR relaxation in proteins. The two bodies/rotators are the protein (diffusion tensor D{sub 1}) and the spin-bearing probe, e.g., the {sup 15}N−{sup 1}H bond (diffusion tensor, D{sub 2}), coupled by a local potential (u). A Smoluchowski equation is solved to yield the generic time correlation functions (TCFs), which are sums of weighted exponentials (eigenmodes). By Fourier transformation one obtains the generic spectral density functions (SDFs) which underlie the experimental relaxation parameters. The typical paradigm is to characterize structural dynamics in terms of the best-fit values of D{sub 1}, D{sub 2}, and u. Additional approaches we pursued employ the SRLS TCFs, SDFs, or eigenmodes as descriptors. In this study we develop yet another perspective. We consider the SDF as function of the angular velocity associated with the fluctuating fields underlying NMR relaxation. A parameter called j-fraction, which represents the relative contribution of eigenmode, i, to a given value of the SDF function at a specific frequency, ω, is defined. j-fraction profiles of the dominant eigenmodes are derived for 0 ≤ ω ≤ 10{sup 12} rad/s. They reveal which patterns of motion actuate power dissipation at given ω-values, what are their rates, and what is their relative contribution. Simulations are carried out to determine the effect of timescale separation, D{sub 1}/D{sub 2}, axial potential strength, and local diffusion axiality. For D{sub 1}/D{sub 2} ≤ 0.01 and strong local potential of 15 k{sub B}T, power is dissipated by global diffusion, renormalized (by the strong potential) local diffusion, and probe diffusion on the surface of a cone (to be called cone diffusion). For D{sub 1}/D{sub 2} = 0.1, power is dissipated by mixed eigenmodes largely of a global-diffusion-type or cone-diffusion-type, and a nearly bare renormalized-local-diffusion eigenmode. For D{sub 1}/D{sub 2} > 0.1, most eigenmodes are of a mixed type. The analysis is affected substantially by reducing the potential strength from 15 to 5 k{sub B}T, and/or allowing for axial D{sub 2} with D{sub 2,∥}/D{sub 2,⊥} = 10. The scheme developed is applied to {sup 15}N−{sup 1}H relaxation from the β-sheet residue K19 and the α-helix residue A34 of the third immunoglobulin-binding domain of streptococcal protein G. Previous studies revealed rhombic local potentials with different rhombicity around C{sub i−1}{sup α}−C{sub i}{sup α}, and different timescale separation (0.047 for K19 and 0.102 for A34). Here, we find that K19 and A34 dissipate power to the bath through global diffusion, mixed cone-diffusion-related and mixed renormalized-local-diffusion-related motions. At small ω-values, A34 is more effective than K19 in dissipating power. In general, it executes faster cone-diffusion-type, and slower renormalized-local-diffusion-type and local-probe-fluctuation-type motions. K19 experiences faster N−H fluctuations than A34. Eigenmode clustering, experienced by K19 to a larger extent, is observed in the fast-probe-fluctuation regime. New information on the effect of the structural context on N−H bond dynamics has been obtained. The patterns of motion that dissipate NMR-relaxation-related power illuminate protein dynamics from a new perspective. They constitute yet another qualifier of N−H bond dynamics. This study sets the stage for developing ways for enhancing the contribution of desired pathways for power dissipation at selected angular velocities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Model reduction for slow–fast stochastic systems with metastable behaviour

The quasi-steady-state approximation (or stochastic averaging principle) is a useful tool in the study of multiscale stochastic systems, giving a practical method by which to reduce the number of degrees of freedom in a model. The method is extended here to slow–fast systems in which the fast variables exhibit metastable behaviour. The key parameter that determines the form of the reduced model is the ratio of the timescale for the switching of the fast variables between metastable states to the timescale for the evolution of the slow variables. The method is illustrated with two examples: one from biochemistry (a fast-species-mediated chemical switch coupled to a slower varying species), and one from ecology (a predator–prey system). Numerical simulations of each model reduction are compared with those of the full system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Aspects of the non-zonal transition

The non-zonal transition, a process which can bring about very large heat fluxes in gyrokinetic simulations, occurs once a certain threshold plasma β is reached. This threshold is parameterized via a simulation database, yielding an expression estimating at what β a given system may approach the transition. Furthermore, the diffusive outward transport of a heat blob in a temperature profile marginally stable with respect to the non-zonal transition is discussed: the resulting transport timescale combines the underlying turbulent transport timescale and the linear instability growth time, thus demonstrating that the non-zonal transition provides a mechanism for very fast heat dissipation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Communication: Two-step explosion processes of highly charged fullerene cations C{sub 60}{sup q+} (q = 20–60)

To establish the fundamental understanding of the fragmentation dynamics of highly positive charged nano- and bio-materials, we carried out on-the-fly classical trajectory calculations on the fragmentation dynamics of C{sub 60}{sup q+} (q = 20–60). We used the UB3LYP/3-21G level of density functional theory and the self-consistent charge density-functional based tight-binding theory. For q ≥ 20, we found that a two-step explosion mechanism governs the fragmentation dynamics: C{sub 60}{sup q+} first ejects singly and multiply charged fast atomic cations C{sup z+} (z ≥ 1) via Coulomb explosions on a timescale of 10 fs to stabilize the remaining core cluster. Thermal evaporations of slow atomic and molecular fragments from the core cluster subsequently occur on a timescale of 100 fs to 1 ps. Increasing the charge q makes the fragments smaller. This two-step mechanism governs the fragmentation dynamics in the most likely case that the initial kinetic energy accumulated upon ionization to C{sub 60}{sup q+} by ion impact or X-ray free electron laser is larger than 100 eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

The non-uniform early structural response of globular proteins to cold denaturing conditions: A case study with Yfh1

The mechanism of cold denaturation in proteins is often incompletely understood due to limitations in accessing the denatured states at extremely low temperatures. Using atomistic molecular dynamics simulations, we have compared early (nanosecond timescale) structural and solvation properties of yeast frataxin (Yfh1) at its temperature of maximum stability, 292 K (T{sub s}), and the experimentally observed temperature of complete unfolding, 268 K (T{sub c}). Within the simulated timescales, discernible “global” level structural loss at T{sub c} is correlated with a distinct increase in surface hydration. However, the hydration and the unfolding events do not occur uniformly over the entire protein surface, but are sensitive to local structural propensity and hydrophobicity. Calculated infrared absorption spectra in the amide-I region of the whole protein show a distinct red shift at T{sub c} in comparison to T{sub s}. Domain specific calculations of IR spectra indicate that the red shift primarily arises from the beta strands. This is commensurate with a marked increase in solvent accessible surface area per residue for the beta-sheets at T{sub c}. Detailed analyses of structure and dynamics of hydration water around the hydrophobic residues of the beta-sheets show a more bulk water like behavior at T{sub c} due to preferential disruption of the hydrophobic effects around these domains. Our results indicate that in this protein, the surface exposed beta-sheet domains are more susceptible to cold denaturing conditions, in qualitative agreement with solution NMR experimental results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗