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The blood clotting protein fibrin has extraordinary elastomeric properties due to its hierarchical structure. SAXS is combined with computational molecular modeling, providing insight in fibrin elasticity and guidelines for designing new polymers.
A molecular Rayleigh scattering based flow diagnostic is developed to measure time average velocity, density, temperature, and turbulence intensity in a 25.4-mm diameter nozzle free jet facility. The spectrum of the Rayleigh scattered light is analyzed using a Fabry-Perot interferometer operated in the static imaging mode. The resulting fringe pattern containing spectral information of the scattered light is recorded using a low noise CCD camera. Nonlinear least squares analysis of the fringe pattern using a kinetic theory model of the Rayleigh scattered light provides estimates of density, velocity, temperature, and turbulence intensity of the gas flow. Resulting flow parameter estimates are presented for an axial scan of subsonic flow at Mach 0.95 for comparison with previously acquired pitot tube data, and axial scans of supersonic flow in an underexpanded screeching jet. The issues related to obtaining accurate turbulence intensity measurements using this technique are discussed.
Nonintrusive optical point-wise measurement techniques utilizing the principles of molecular Rayleigh scattering have been developed at the NASA Glenn Research Center to obtain time-averaged information about gas velocity, density, temperature, and turbulence, or dynamic information about gas velocity and density in unseeded flows. These techniques enable measurements that are necessary for validating computational fluid dynamics (CFD) and computational aeroacoustic (CAA) codes. Dynamic measurements allow the calculation of power spectra for the various flow properties. This type of information is currently being used in jet noise studies, correlating sound pressure fluctuations with velocity and density fluctuations to determine noise sources in jets. These nonintrusive techniques are particularly useful in supersonic flows, where seeding the flow with particles is not an option, and where the environment is too harsh for hot-wire measurements.
A novel technique for measurement of high frequency temperature fluctuations in unseeded gas flows using molecular Rayleigh scattering is investigated. The spectrum of laser light scattered from molecules in a gas flow is resolved using a Fabry-Perot interferometer. The width of the spectral peak is broadened by thermal motion of the molecules and hence is related to gas temperature. The interference fringe pattern containing spectral information is divided into four concentric regions using a series of mirrors angled with respect to one another. Light from each of these regions is directed towards photomultiplier tubes and sampled at 10 kHz using photon counting electronics. Monitoring the relative change in intensity within each region allows measurement of gas temperature. Independently monitoring the total scattered intensity provides a measure of gas density. This technique also has the potential to simultaneously measure a single component of flow velocity by monitoring the spectral peak location. Measurements of gas temperature and density are demonstrated using a low speed heated air jet surrounded by an unheated air co-flow. Mean values of temperature and density are shown for radial scans across the jet flow at a fixed axial distance from the jet exit plane. Power spectra of temperature and density fluctuations at several locations in the jet are also shown. The instantaneous measurements have fairly high uncertainty; however, long data records provide highly accurate statistically quantities, which include power spectra. Mean temperatures are compared with thermocouple measurements as well as the temperatures derived from independent density measurements. The accuracy for mean temperature measurements was +/- 7 K.
Cross sections for neutron scattering from hydrogen and deuterium taking into account spin correlations, rotations and vibrations
The evaporation and scattering of ND 3 from a dodecane flat liquid jet are investigated and the results are compared with previous studies on molecular beam scattering from liquid surfaces. Evaporation is well-described by a Maxwell–Boltzmann flux distribution with a cos θ angular distribution at the liquid temperature. Scattering experiments at E i = 28.8 kJ mol -1 over a range of deflection angles show evidence for impulsive scattering and thermal desorption. Further, at a deflection angle of 90°, the thermal desorption fraction is 0.49, which is higher than that of other molecules previously scattered from dodecane and consistent with work performed on NH 3 scattering from a squalane-wetted wheel. ND 3 scattering from dodecane results in super-specular scattering, as seen in previous experiments on dodecane. The impulsive scattering channel is fitted to a “soft-sphere” model, yielding an effective surface mass of 55 amu and an internal excitation of 5.08 kJ mol -1 . Overall, impulsively scattered ND 3 behaves similarly to other small molecules scattered from dodecane.
The unfolding dynamics of ubiquitin were studied using a combination of x-ray solution scattering (XSS) and molecular dynamics (MD) simulations. The kinetic analysis of the XSS ubiquitin signals showed that the protein unfolds through a two-state process, independent of the presence of destabilizing salts. In order to characterize the ensemble of unfolded states in atomic detail, the experimental XSS results were used as a constraint in the MD simulations through the incorporation of x-ray scattering derived potential to drive the folded ubiquitin structure toward sampling unfolded states consistent with the XSS signals. We detail how biased MD simulations provide insight into unfolded states that are otherwise difficult to resolve and underscore how experimental XSS data can be combined with MD to efficiently sample structures away from the native state. Our results indicate that ubiquitin samples unfolded in states with a high degree of loss in secondary structure yet without a collapse to a molten globule or fully solvated extended chain. Finally, we propose how using biased-MD can significantly decrease the computational time and resources required to sample experimentally relevant nonequilibrium states.
Quantitative lidar measurements of aerosol scattering are hampered by the need for calibrations and the problem of correcting observed backscatter profiles for the effects of attenuation. The University of Wisconsin High Spectral Resolution Lidar (HSRL) addresses these problems by separating molecular scattering contributions from the aerosol scattering; the molecular scattering is then used as a calibration target that is available at each point in the observed profiles. While the HSRl approach has intrinsic advantages over competing techniques, realization of these advantages requires implementation of a technically demanding system which is potentially very sensitive to changes in temperature and mechanical alignments. This paper describes a new implementation of the HSRL in an instrumented van which allows measurements during field experiments. The HSRL was modified to measure depolarization. In addition, both the signal amplitude and depolarization variations with receiver field of view are simultaneously measured. This allows for discrimination of ice clouds from water clouds and observation of multiple scattering contributions to the lidar return.
Optically dense clouds in the interstellar medium composed predominantly of molecular hydrogen, known as molecular clouds, are sensitive to energy injection in the form of photon absorption, cosmic-ray scattering, and dark matter (DM) scattering. The ionization rates in dense molecular clouds are heavily constrained by observations of abundances of various molecular tracers. Recent studies have set constraints on the DM-electron scattering cross section using measurements of ionization rates in dense molecular clouds. Here we calculate the analogous bounds on the DM-proton cross section using the molecular Migdal effect, recently adapted from the neutron scattering literature to the DM context. These bounds may be the strongest limits on a strongly coupled DM subfraction, and represent the first application of the Migdal effect to astrophysical systems. Published by the American Physical Society 2024
A Rayleigh scattering diagnostic for high speed flows is described for the simultaneous, instantaneous measurement of gas temperature and velocity at a number (up to about one hundred) of locations in a plane illuminated by an injection-seeded, frequency doubled Nd:YAG laser. Molecular Rayleigh scattered light is collected and passed through a planar mirror Fabry-Perot interferometer. The resulting image is analyzed to determine the gas temperature and bulk velocity at each of the regions. The Cramer Rao lower bound for measurement uncertainty is calculated. Experimental data is presented for a free jet and for preliminary measurements in the Lewis 4 inch by 10 inch supersonic wind tunnel.
A polar nephelometer for use in studying atmospheric aerosols was developed. The nephelometer detects molecular scatter from air and measures scattering from very clean air using pure molecular scattering for calibration. A compact system using a folded light path with an air cooled argon laser for the light source was designed. A small, sensitive detector unit permits easy angular rotation for changing the scattering angle. A narrow detector field of view of + or - 1/4 degree of scattering along with a single wavelength of incident light is used to minimize uncertainties in the scattering theory. The system is automated for data acquisition of the scattering matrix elements over an angular range from 2 degrees to 178 degrees of scattering. Both laser output and detector sensitivity are monitored to normalize the measured light scattering.
The radiance and color of the twilight sky are calculated for single scattered radiation with the use of spherically symmetric models of the earth's atmosphere. Spherical geometry is used throughout the calculations with no plane parallel approximations. Refraction effects are taken into account through fine subdivision of the atmosphere into spherical shells of fixed index of refraction. Shell's law of refraction is used to calculate a direction of travel each time that a photon traverses the interface between layers. Five different models of the atmosphere were used: a pure molecular scattering atmosphere; molecular atmosphere plus ozone absorption; and three models with aerosol concentrations of 1, 3, and 10 times normal together with molecular scattering and ozone absorption. The results of the calculations are shown for various observation positions and local viewing angles in the solar plane for wavelengths in the range of 0.40 microns to 0.75 microns.
The radiance and color of the twilight sky are calculated for single scattered radiation with the use of spherically symmetric models of the earth's atmosphere. Spherical geometry is used throughout the calculations with no plane-parallel approximations. Refraction effects are taken into account through fine subdivision of the atmosphere into spherical shells of fixed index of refraction. Snell's law of refraction is used to calculate a new direction of travel each time that a photon traverses the interface between layers. Five different models of the atmosphere were used: a pure molecular scattering atmosphere; molecular atmosphere plus ozone absorption; and three models with aerosol concentrations of one, three, and ten times normal together with molecular scattering and ozone absorption. The results of the calculations are shown for various observation positions and local viewing angles in the solar plane for wavelengths in the range from 0.40 to 0.75 micron.
The strong tendency of lignin to aggregate in solution, coupled with limited understanding of how its molecular structure governs this behavior, hinders its effective utilization in biorefineries. Here, in this study, we investigated the solution behavior of lignin extracted from poplar using γ-valerolactone/water (GVL/H2O, 9:1 wt/wt) through combined small-angle neutron scattering (SANS) and molecular dynamics (MD) simulations. Lignin samples obtained at 100 °C (L100) and 120 °C (L120) differed in β–O–4 content, hydroxyl distribution, and S/G ratio, enabling direct assessment of how molecular composition governs solvation and aggregation. SANS showed that L120 formed rigid and elongated cylindrical aggregates at 25 °C that transitioned to more flexible spheroidal structures by 50 °C and remained stable up to 80 °C, whereas L100 adopted globular aggregates that progressively collapsed with increasing temperature. MD simulations reinforced these observations by showing that S-rich (L120-like) oligomers had larger radii of gyration, stronger solvent coordination driven by methoxy groups, and fewer lignin–lignin contacts. In contrast, G-rich (L100-like) oligomers displayed persistent aggregation and lower solubility. Collectively, these results reveal that increased aromatic methoxylation enhances lignin–solvent interactions and suppresses self-association, whereas reduced methoxylation and higher β–O–4 content promote persistent aggregation into colloid-like structures with restricted solvent penetration into the aggregate interior.
The contribution of inelastic molecular scattering (Rayleigh-Brillouin and rotational Raman scattering) to the filling-in of Fraunhofer lines in the light of the blue sky is studied. Aerosol fluorescence is shown to be negligible, and aerosol scattering is ignored. The angular and polarization dependences of the filling-in detail for single scattering are discussed. An approximate treatment of multiple scattering, using a backward Monte Carlo technique, makes it possible to investigate the effects of the ground albedo. As the molecular scatterings alone produce more line-filling than is observed, it seems likely that aerosols dilute the effect by contributing unaltered sunlight to the observed spectra.
The protein folding process often proceeds through partially folded transient states. Therefore, a structural understanding of these disordered states is crucial for developing mechanistic models of the folding process. Characterization of unfolded states remains challenging due to their disordered nature, and incorporating multiple methods is necessary. Combining the time-resolved x-ray solution scattering (TRXSS) signal with molecular dynamics (MD), we are able to characterize transient partially folded states of bovine α-lactalbumin, a model system widely used for investigation of molten globule states, during its unfolding triggered by a temperature jump. We track the unfolding process between 20 μs and 70 ms and demonstrate that it passes through three distinct kinetic states. The scattering signals associated with these transient species are then analyzed with TRXSS constrained MD simulations to produce protein structures that are compatible with the input signals. Without utilizing any experimentally extracted kinetic information, the constrained MD simulation successfully drove the protein to an intermediate molten globule state; signals for two later disordered states are refined to terminal unfolded states. From our examination of the structural characteristics of these disordered states, we discuss the implications disordered states have on the folding process, especially on the folding pathway. Finally, we discuss the potential applications and limitations of this method.
Lasers with orbital angular momentum (OAM) have potential applications in communication technology, manipulation of particles, and remote sensing. Because of its unusual light-scattering properties, the OAM laser’s interaction with a molecular atmosphere must be studied to ensure that it is not lossy for communication or remote-sensing applications that involve its transmission through an atmospheric environment. In this study, the finite-difference time-domain (FDTD) method [21] is applied to calculate the light scattering of the purely azimuthal (the radial mode number is assumed to be zero) Laguerre-Gaussian (LG) beams with OAM by very small dielectric particles. Not like Lorentz-Mie solutions, the FDTD method can calculate for particles off the central axis of the LG beam. It is found that when the particles are very small, and the topological charge number of the OAM of a laser is not extremely large, the laser’s OAM has little effect on the scattering phase function. This suggests that Rayleigh theory can be applied directly to calculate the light scattering by atmospheric molecules. The transmission of a laser beam with OAM in a molecular atmosphere is not different from that of a regular Gaussian beam.
Speckle-type POZ protein (SPOP) is a substrate adaptor in the ubiquitin proteasome system, and plays important roles in cell-cycle control, development, and cancer pathogenesis. SPOP forms linear higher-order oligomers following an isodesmic self-association model. Oligomerization is essential for SPOP’s multivalent interactions with substrates, which facilitate phase separation and localization to biomolecular condensates. Structural characterization of SPOP in its oligomeric state and in solution is, however, challenging due to the inherent conformational and compositional heterogeneity of the oligomeric species. Here, we develop an approach to simultaneously and self-consistently characterize the conformational ensemble and the distribution of oligomeric states of SPOP by combining small-angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations. We build initial conformational ensembles of SPOP oligomers using coarse-grained molecular dynamics simulations, and use a Bayesian/maximum entropy approach to refine the ensembles, along with the distribution of oligomeric states, against a concentration series of SAXS experiments. Our results suggest that SPOP oligomers behave as rigid, helical structures in solution, and that a flexible linker region allows SPOP’s substrate-binding domains to extend away from the core of the oligomers. Additionally, our results are in good agreement with previous characterization of the isodesmic self-association of SPOP. In the future, the approach presented here can be extended to other systems to simultaneously characterize structural heterogeneity and self-assembly.