Final Snapshot Research Articles

Correspondence between multiple signaling and developmental cellular patterns: a computational perspective.

The spatial arrangement of variant phenotypes during stem cell division plays a crucial role in the self-organization of cell tissues. The patterns observed in these cellular assemblies, where multiple phenotypes vie for space and resources, are largely influenced by a mixture of different diffusible chemical signals. This complex process is carried out within a chronological framework of interplaying intracellular and intercellular events. This includes receiving external stimulants, whether secreted by other individuals or provided by the environment, interpreting these environmental signals, and incorporating the information to designate cell fate. Here, given two distinct signaling patterns generated by Turing systems, we investigated the spatial distribution of differentiating cells that use these signals as external cues for modifying the production rates. By proposing a computational map, we show that there is a correspondence between the multiple signaling and developmental cellular patterns. In other words, the model provides an appropriate prediction for the final structure of the differentiated cells in a multi-signal, multi-cell environment. Conversely, when a final snapshot of cellular patterns is given, our algorithm can partially identify the signaling patterns that influenced the formation of the cellular structure, provided that the governing dynamic of the signaling patterns is already known.

Stellar halo striations from assumptions of axisymmetry

ABSTRACT Motivated by the Large Magellanic Cloud (LMC)’s impact on the integral of motion space of the stellar halo, we run an N-body merger simulation to produce a population of halo-like stars. We subsequently move to a test-particle simulation, in which the LMC perturbs this debris. When an axisymmetric potential is assumed for the final snapshot of the N-body merger remnant, a series of vertical striations in (Lz, E) space form as the LMC approaches its pericentre. These result from the formation of overdensities in angular momentum owing to a relationship between the precession rate of near radial orbits and the torquing of these orbits by the LMC. This effect is heavily dependent on the shape of the inner potential. If a quadrupole component of the potential is included, these striations become significantly less apparent due to the difference in precession rate between the two potentials. The absence of these features in data, and the dramatic change in orbital plane precession rate, discourages the use of an axisymmetric potential for highly eccentric orbits accreted from a massive Gaia Sausage/Enceladus-like merger. Given the link the between appearance of these striations and the shape of the potential, this effect may provide a new method of constraining the axisymmetry of the halo.

Classify QCD phase transition with deep learning

The state-of-the-art pattern recognition method in machine learning (deep convolution neural network) is used to identify the equation of state (EoS) employed in the relativistic hydrodynamic simulations of heavy ion collisions. High-level correlations of particle spectra in transverse momentum and azimuthal angle learned by the network act as an effective EoS-meter in deciphering the nature of the phase transition in QCD. The EoS-meter is model independent and insensitive to other simulation inputs including the initial conditions and shear viscosity for hydrodynamic simulations. Through this study we demonstrate that there is a traceable encoder of the dynamical information from the phase structure that survives the evolution and exists in the final snapshot of heavy ion collisions and one can exclusively and effectively decode these information from the highly complex final output with machine learning when traditional methods fail. Besides the deep neural network, the performance of traditional machine learning classifiers are also provided.

Numerical simulations of the formation of the Milky Way disk of satellites through the accretion of associations of dwarf galaxies

En este artículo se presentan los resultados de simulaciones numéricas newtonianas de N-cuerpos de la caída hacía el halo de materia oscura de la Vía Láctea de asociaciones de galaxias enanas esferoidales con materia oscura y sin ella. Se generaron las condiciones iniciales utilizando el programa ZENO y el GADGET-2 para simular un sistema aislado en donde estas asociaciones de enanas se precipitan hacia el halo de materia oscura de la Vía Láctea. Con el fin de evaluar la posibilidad de que el disco de satélites de la Vía Láctea hubiese tenido su origen en este tipo de procesos de acreción, se analizaron algunas características de las galaxias enanas finales, tales como la distribución en torno al disco de la galaxia, el perfil de densidad, la dispersión de velocidades y las velocidades radiales de las enanas. Las asociaciones se ubicaron a distancias radiales iniciales de 4, 2 y 1 Mpc del centro de la Vía Láctea y se dejó evolucionar el sistema durante 10 giga años en cada una de las simulaciones. Se encontró que las asociaciones ubicadas a distancias iniciales mayores o iguales a 2 Mpc no son apropiadas debido a que su tiempo de acreción es superior a un tiempo de Hubble. Para el caso de asociaciones ubicadas inicialmente a 1 Mpc del centro de la Vía Láctea, se encontró que no es posible que el disco de satélites se haya formado a partir de asociaciones libres de materia oscura, y que una estructura similar al disco de satélites se pudo haber formado mediante la acreción de asociaciones de galaxias enanas con materia oscura que cayeran al halo de la Vía Láctea siguiendo órbitas parabólicas. Sin embargo, las distancias de los remanentes al centro de la galaxia no reproducen aquellas reportadas en la literatura. © 2018. Acad. Colomb. Cienc. Ex. Fis. Nat.

Identifying QCD Transition Using Deep Learning

In this proceeding we review our recent work using supervised learning with a deep convolutional neural network (CNN) to identify the QCD equation of state (EoS) employed in hydrodynamic modeling of heavy-ion collisions given only final-state particle spectra ρ(pT, Ф). We showed that there is a traceable encoder of the dynamical information from phase structure (EoS) that survives the evolution and exists in the final snapshot, which enables the trained CNN to act as an effective “EoS-meter” in detecting the nature of the QCD transition.

Pedro de Ribadeneyra's 'Ecclesiastical History of the Schism of the Kingdom of England': A Spanish Jesuit's History of the English Reformation ed. by Spencer J. Weinreich

Reviewed by: Pedro de Ribadeneyra's 'Ecclesiastical History of the Schism of the Kingdom of England': A Spanish Jesuit's History of the English Reformation ed. by Spencer J. Weinreich Victor Houliston Pedro de Ribadeneyra's 'Ecclesiastical History of the Schism of the Kingdom of England': A Spanish Jesuit's History of the English Reformation. Edited and translated by Spencer J. Weinreich. [Jesuit Studies, volume 8.] (Leiden and Boston: Brill. 2017. Pp. xxvi, 839. $253.00. ISBN 978-90-04-32395-7.) Spencer J. Weinreich describes his translation of Ribadeneyra's Historia ecclesiastica as a "labor of love" (p. 103), springing from a desire to commend its merits and interest to scholars. Some have dismissed the Historia as a rhetorical monstrosity, of little value in its own right, useful only as a source of information about Spanish attitudes to England, the run-up to the Armada of 1588, and curiosities and myths of English reformation history. Weinreich urges us not to raid the work but to read it as a whole. His fluent and readable translation is an admirable incentive. Why, then, should we read the Historia? Most English-language scholarship has treated the First Part (1588) as an adaptation of Nicholas Sander's De schismate Anglicano (1585; revised and expanded 1586) and an extension of William Allen and Robert Persons's project to raise awareness of the plight of Catholics in England and drum up support for the Armada. But, as Weinreich argues in the introduction, it is important to see it as a Spanish work in a Spanish context. It elaborates a Spanish vision of English tyranny and Catholic martyrdom, and its Second Part (1593) reflects on the failure of the Armada, complementing Ribadeneyra's Tratado de la tribulacion (1589). If we read it as a continuous narrative-cum-treatise, suspending judgment on historical accuracy and impartiality, we are able to engage with a compelling version of how the English reformation appeared to a devout continental observer. The perspective is largely shared with English exiles such as Sander, Allen, and Persons, but the eulogies of Catherine of Aragon, Mary Tudor, and Mary Queen of Scots, and the prefatory epistles to the future King Philip III, give it a Spanish edge. The description of Mary Stuart's sad end left Luis de Granada in tears. The First Part goes beyond even the English source in its anticipation of the Armada. It dramatizes the state of England on the brink of ruin, after all the folly, injustice, and profanation of reform. It is intended as a final snapshot before divine retribution overwhelms the kingdom—and so it stimulates the historical imagination, to see events through partial contemporary eyes and to envisage what might have been. The Second Part deserves more attention than it has received thus far. [End Page 550] It does not offer a continuation of the narrative from 1588 to 1593, but focuses on the royal proclamation of 1591 against seminary priests and Jesuits, defending the seminaries, excoriating Leicester and Burghley, commiserating Hatton, and portraying Queen Elizabeth at her worst. It is largely a recension of Persons's so-called Philopater (1592), a work that is also badly in need of translation. But what distinguishes Ribadeneyra's version is that the argument about the legitimacy of English Catholic resistance is embedded in a profound and often moving meditation on the experience of defeat. Weinreich's extensive introduction ranges widely from biography to textual history and the treatment of women. The account of the 1586 edition of Sander's De schismate Anglicano, Ribadeneyra's chief source, is particularly welcome, because so much writing about Sander's book focuses on the less influential 1585 edition. The treatment of historical, biographical, and bibliographical context is extremely thorough, in both the introduction and the annotations. Weinreich's diligence re-introduces an eloquent voice into the debate about late sixteenth-century European politics and religious history. Victor Houliston University of the Witwatersrand Copyright © 2018 The Catholic University of America Press

Qualitative methods III

In this, our third and final snapshot of contemporary qualitative research methods, we pick up on the proliferation of non-representational theory across human geography and focus on research methods concerned with practices that exceed (more than) representation or are non-representational. We chart work that pays attention to the non-visible, the non-verbal and the non-obvious, as well as methods and methodologies that enable researchers to grasp and grapple with assemblages, relationalities, and life as it unfolds. We characterize these ‘more-than representational’ methodologies as: experimenting with approaches to research, using picturing as an embedded research methodology, and highlighting research as sensing. We conclude that these have opened new forms of knowledge, including into subdisciplines like health geography. Nonetheless, a privileging of written and visual modes of thinking and representing remain, and the discipline must be vigilant to nurture and value the emerging work on neural diversity and non-Western modes of thinking.

Wavefield reconstruction in attenuating media: A checkpointing-assisted reverse-forward simulation method

Three-dimensional implementations of reverse time migration (RTM) and full-waveform inversion (FWI) require efficient schemes to access the incident field to apply the imaging condition of RTM or build the gradient of FWI. Wavefield reconstruction by reverse propagation using final snapshot and saved boundaries appears quite efficient but unstable in attenuating media, whereas the checkpointing strategy is a stable alternative at the expense of increased computational cost through repeated forward modeling. We have developed a checkpointing-assisted reverse-forward simulation (CARFS) method in the context of viscoacoustic wave propagation with a generalized Maxwell body. At each backward reconstruction step, the CARFS algorithm makes a smart decision between forward modeling using checkpoints and reverse propagation based on the minimum time-stepping cost and an energy measure. Numerical experiments demonstrated that the CARFS method allows accurate wavefield reconstruction using less timesteppings than optimal checkpointing, even if seismic attenuation is very strong. For RTM and FWI applications involving a huge number of independent sources and/or applications on architectures with limited memory, CARFS will provide an efficient tool with adequate accuracy in practical implementation.

Wavefield reconstruction by interpolating significantly decimated boundaries

Many practical seismic applications such as reverse time migration (RTM) and full-waveform inversion (FWI) are usually computation and memory intensive. To perform crosscorrelation in RTM or build the gradient for FWI, it is mandatory to access the forward and adjoint wavefields simultaneously. To do this, there are three methods: One is to read the stored forward wavefield from the disk, the second is using the final snapshot and the stored boundaries via reverse propagation, and the third is remodeling using checkpointing from stored state to another state. Among these techniques, wavefield reconstruction by reverse propagation appears to be a quite straightforward approach; however, it suffers a stringent memory bottleneck for 3D large-scale imaging applications. The Courant-Friedrichs-Lewy (CFL) condition is a fundamental criterion to determine temporal sampling to achieve stable wavefield extrapolation. The injection of the boundary sequence in time is essentially determined by Nyquist sampling principle, rather than the time interval given by CFL, which is much smaller than the Nyquist requirement. Based on this recognition, we have developed three boundary interpolation techniques, such as the discrete Fourier transform (DFT) interpolation, Kaiser windowed sinc interpolation, and Lagrange polynomial interpolation, for wavefield reconstruction to move from CFL to the Nyquist limit. Wavefield reconstruction via DFT interpolation can be implemented by folding and unfolding steps in the forward simulation and backward reconstruction on the fly. Compared with the DFT interpolation, the wavefield reconstruction methods using Kaiser windowed sinc interpolation and Lagrange polynomial interpolation have better efficiency while remaining a competitive accuracy. These methods allow us to dramatically decimate the boundary without significant loss of information, and they nicely reconstruct the boundary elements in between the samples, making the in-core memory saving of the boundaries feasible in 3D large-scale imaging applications.

Reconstructing the timescale of a catastrophic fan‐forming event on Earth using a Mars model

AbstractThe calculation of formation timescales of alluvial fans and deltas on Mars is important as it has direct implications for understanding the planet's hydrologic history. The robustness of sediment transport models is not in doubt but validation of the broad approach using a terrestrial example of similar scale and likely origin, where hydraulic parameters and timescales are known, is useful. Using a catastrophically formed terrestrial fan, where abundant sedimentological information is available, we find that the modeled hydraulic parameters and formation timescales are in very close agreement with the known values of the event. This supports the general modeling approach as applied to Mars fans but also highlights the added value of detailed sedimentary information when reconstructing hydraulics and timescales on Earth and Mars, which cannot be confidently gleaned from the final snapshot of surface geomorphology alone.

Dynamic Binding of PKA Regulatory Subunit RIα

Recent crystal structures have revealed that regulatory subunit RIalpha of PKA undergoes a dramatic conformational change upon complex formation with the catalytic subunit. Molecular dynamics studies were initiated to elucidate the contributions of intrinsic conformational flexibility and interactions with the catalytic subunit in formation and stabilization of the complex. Simulations of a single RIalpha nucleotide binding domain (NBD), missing cAMP, showed that its C helix spontaneously occupies two distinct conformations: either packed against the nucleotide binding domain as in its cAMP bound structure, or extended into an intermediate form resembling that of the holoenzyme structure. C helix extension was not seen in a simulation of either RIalpha NBD. In a model complex containing both NBDs and the catalytic subunit, well-conserved residues at the interface between the NBDs in the cAMP bound form were found to stabilize the complex through contacts with the catalytic subunit. The model structure is consistent with available experimental data.

The Conformationally Dynamic C Helix of the RIα Subunit of Protein Kinase A Mediates Isoform-specific Domain Reorganization upon C Subunit Binding

Different isoforms of the full-length protein kinase A (PKA) regulatory subunit homodimer (R2) and the catalytic (C) subunit-bound holoenzyme (R2C2) have very different global structures despite similar molecular weights and domain organization within their primary sequences. To date, it has been the linker sequence between the R subunit dimerization/docking domain and cAMP-binding domain A that has been implicated in modulating domain interactions to give rise to these differences in global structure. The small angle solution scattering data presented here for three different isoforms of PKA heterodimer (deltaR-C) complexes reveal a role for another conformationally dynamic sequence in modulating inter-subunit and domain interactions, the C helix that connects the cAMP-binding domains A and B of the R subunit. The deltaR-C heterodimer complexes studied here were each formed with a monomeric N-terminal deletion mutant of the R subunit (deltaR) that contains the inhibitor sequence and both cAMP-binding domains. The scattering data show that type IIalpha and type IIbeta deltaR-C heterodimers are relatively compact and globular, with the C subunit contacting the inhibitor sequence and both cAMP-binding domains. In contrast, the type Ialpha heterodimer is significantly more extended, with the C subunit interacting with the inhibitor sequence and cAMP-binding domain A, whereas domain B extends out such that its surface is almost completely solvent exposed. These data implicate the C helix of RIalpha in modulating isoform-specific interdomain communication in the PKA holoenzyme, adding another layer of structural complexity to our understanding of signaling dynamics in this multisubunit, multidomain protein kinase.

Experiments to measure melt-wave erosion in railgun armatures

This paper describes experiments to measure melt-wave erosion (MWE) damage in railgun armatures. C-armatures were launched on the Medium Caliber Launcher at the Institute for Advanced Technology (IAT), Leander, TX, and recovered by "soft catching" in a tube filled with cotton rags. Recovered armatures were mechanically profiled to measure erosion depth as a function of position on the contacting surfaces. Although recovered armatures provide only a final snapshot of the erosion process, one can show how erosion proceeds by recovering armatures at different stages of the launch. This type of study requires the use of a crowbar switch at the breech of the railgun to rapidly shunt current out of the armature, thereby interrupting the erosion process at the desired point in the launch. We describe the experimental setup and summarize the results of 11 experiments. The experiments investigated the effect of linear current density (ranging from 35 to 45 kA/mm) and rail material (copper and aluminum) on MWE damage. Lastly, we present some thoughts on contact transition mechanisms that, in some cases, prevented the collection of MWE data.