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Tobin, John J.,Bergin, Edwin A.,Hartmann, Lee,Lee, Jeong-Eun,Maret, Sé,bastien,Myers, Phillip C.,Looney, Leslie W.,Chiang, Hsin-Fang,Friesen, Rachel IOP Publishing 2013 The Astrophysical journal Vol.765 No.1
<P>We present a study on the spatial distribution of N2D+ and N2H+ in 13 protostellar systems. Eight of thirteen objects observed with the IRAM 30 m telescope show relative offsets between the peak N2D+ (J = 2 -> 1) and N2H+ (J = 1 -> 0) emission. We highlight the case of L1157 using interferometric observations from the Submillimeter Array and Plateau de Bure Interferometer of the N2D+ (J = 3 -> 2) and N2H+ (J = 1 -> 0) transitions, respectively. Depletion of N2D+ in L1157 is clearly observed inside a radius of similar to 2000 AU (7 '') and the N2H+ emission is resolved into two peaks at radii of similar to 1000 AU (3 ''.5), inside the depletion region of N2D+. Chemical models predict a depletion zone in N2D+ and N2H+ due to destruction of H2D+ at T similar to 20 K and the evaporation of CO off dust grains at the same temperature. However, the abundance offsets of 1000 AU between the two species are not reproduced by chemical models, including a model that follows the infall of the protostellar envelope. The average abundance ratios of N2D+ to N2H+ have been shown to decrease as protostars evolve by Emprechtinger et al., but this is the first time depletion zones of N2D+ have been spatially resolved. We suggest that the difference in depletion zone radii for N2H+ and N2D+ is caused by either the CO evaporation temperature being above 20 K or an H-2 ortho-to-para ratio gradient in the inner envelope.</P>
Benchmarking all-atom simulations using hydrogen exchange
Skinner, John J.,Yu, Wookyung,Gichana, Elizabeth K.,Baxa, Michael C.,Hinshaw, James R.,Freed, Karl F.,Sosnick, Tobin R. National Academy of Sciences 2014 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.111 No.45
<P><B>Significance</B></P><P>Molecular dynamics simulations have recently become capable of observing multiple protein unfolding and refolding events in a single-millisecond–long trajectory. This major advance produces atomic-level information with nanosecond resolution, a feat unmatched by experimental methods. Such simulations are being extensively analyzed to assess their description of protein folding, yet the results remain difficult to validate experimentally. We apply a combination of hydrogen exchange, NMR, and other techniques to test the simulations with a resolution of single H-bonds. Several significant discrepancies between the simulations and experimental data were uncovered for regions of the energy surface outside of the native basin. This comparison yields suggestions for improving the force fields and provides a general method for experimentally validating folding simulations.</P><P>Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) <I>Science</I> 334(6055):517–520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.</P>
Harris, Robert J.,Cox, Erin G.,Looney, Leslie W.,Li, Zhi-Yun,Yang, Haifeng,Ferná,ndez-Ló,pez, Manuel,Kwon, Woojin,Sadavoy, Sarah,Segura-Cox, Dominique,Stephens, Ian,Tobin, John American Astronomical Society 2018 The Astrophysical journal Vol.861 No.2
<P>We present high-sensitivity (sigma(I) similar to 0.2-0.5 mJy, sigma(QU) similar to 0.05 mJy), high-resolution (similar to 0.'' 12-0.'' 2) observations of polarized 872 mu m dust emission from the young multiple system VLA 1623 in rho Ophiuchus and the protostar L1527 in Taurus. We detect the circumstellar material of VLA 1623A, the extended Keplerian disk surrounding VLA 1623A that we call VLA 1623CBdisk, VLA 1623B, VLA 1623W, and L1527 strongly in the polarized emission, at the similar to 1%-3% level. We spatially resolve VLA 1623A into two sources, VLA 1623Aa and VLA 1623Ab, separated by similar to 30 au and located within a cavity of radius similar to 50 au within the circumbinary Keplerian disk, as well as the edge-on disk of VLA 1623W. The polarization angle of the emission is uniform across each protostellar source and nearly coincides with each disk's minor axis. The offsets between the minor axis position angle and the polarization angle are not uniformly distributed at the P less than or similar to 2 x 10(-4) level. The circumbinary disk surrounding VLA 1623Aab is azimuthally symmetrically polarized. Each compact source's emission is partially optically thick (tau greater than or similar to 1) at 872 mu m, complicating interpretations of polarization involving aligned grains. We find evidence against alignment by radiative flux in each source, particularly in the edge-on VLA 1623W and L1527. We detect astrometric offsets between the polarized emission and the total intensity in VLA 1623Aa, VLA 1623Ab, and VLA 1623B, as predicted if self-scattering in the optically thick limit operates. We conclude that self-scattering is likely responsible for disk-scale polarization at 872 mu m in these systems.</P>
A modest outburst and emission structure of very young protostar HOPS 373
Sung-Yong Yoon,Gregory J. Herczeg,Jeong-Eun Lee,Ho-Gyu Lee,Doug Johnstone,Watson Varricatt,John J. Tobin,Carlos Contreras Peña,Steve Mairs,Klaus Hodapp,P. Manoj,Mayra Osorio,S. Thomas Megeath,the JCM 한국천문학회 2022 天文學會報 Vol.47 No.2