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At least 127 records · Page 7

PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish

Understanding how neurons interact across the brain to control animal behaviors is one of the central goals in neuroscience. Recent developments in fluorescent microscopy and genetically-encoded calcium indicators led to the establishment of whole-brain imaging methods in zebrafish, which record neural activity across a brain-wide volume with single-cell resolution. Pioneering studies of whole-brain imaging used custom light-sheet microscopes, and their operation relied on commercially developed and maintained software not available globally. Hence it has been challenging to disseminate and develop the technology in the research community. Here, we present PyZebrascope, an open-source Python platform designed for neural activity imaging in zebrafish using light-sheet microscopy. PyZebrascope has intuitive user interfaces and supports essential features for whole-brain imaging, such as two orthogonal excitation beams and eye damage prevention. Its camera module can handle image data throughput of up to 800 MB/s from camera acquisition to file writing while maintaining stable CPU and memory usage. Its modular architecture allows the inclusion of advanced algorithms for microscope control and image processing. As a proof of concept, we implemented a novel automatic algorithm for maximizing the image resolution in the brain by precisely aligning the excitation beams to the image focal plane. PyZebrascope enables whole-brain neural activity imaging in fish behaving in a virtual reality environment. Thus, PyZebrascope will help disseminate and develop light-sheet microscopy techniques in the neuroscience community and advance our understanding of whole-brain neural dynamics during animal behaviors.

59 BASIC BIOLOGICAL SCIENCES↗

Linear and Nonlinear X-ray Spectra of Chiral Molecules: X-ray Circular Dichroism, Sum- and Difference-Frequency Generation of Fenchone and Cysteine

Recent advancements in X-ray light sources enable element-sensitive nonlinear spectroscopies for probing molecular chirality. We simulate X-ray absorption spectroscopy, X-ray circular dichroism (XCD), and nonlinear optical/X-ray SFG and DFG (OX SFG/DFG) signals for two prototypical chiral molecules, fenchone and cysteine. Furthermore, our multireference simulations reproduce experimental data and reveal how novel X-ray spectroscopies exploit the site- and element-sensitivity of X-rays to uncover molecular asymmetry. The XCD spectra show strong asymmetries at chiral centers, while distant atoms contribute weaker signals. The OX SFG/DFG signals, under fixed resonant optical excitation, strongly depend on the core and valence excitations. This allows us to introduce two-dimensional (2D) chirality-sensitive valence-core spectroscopy, which provides insight into the overlap between valence orbitals and local molecular asymmetry. Finally, our estimates using realistic laser and X-ray pulse parameters demonstrate that such nonlinear experiments are feasible at XFELs, offering a promising tool for investigating chiral molecules.

Circular dichroism spectroscopy↗

Wavelength- and irradiance-dependent changes in intracellular nitric oxide level

Photobiomodulation (PBM) refers to beneficial effects of low energy light absorption. Although there is a large and growing body of literature describing down-stream physiological benefits of PBM, there is limited understanding of the molecular mechanisms that initiate and mediate these effects at the level of photon absorption. At present, the leading hypothesis is that light absorption induces release of nitric oxide (NO) from the active site of cytochrome c oxidase (COX), allowing it to bind O 2 instead. This is believed to increase mitochondrial respiration, and result in greater overall health of the cell due to increased ATP production. Aim: Although NO itself is a powerful signaling molecule involved in a host of biological responses, less attention has been devoted to the mechanisms of NO release and subsequent effects on cell signaling. The purpose of this work is to investigate wavelength-specific effects on intracellular NO release in living cells. Approach: We have conducted in depth dosimetry analyses of NO production and function in an in vitro retinal model in response to low energy exposure to one or more wavelengths of laser light. Results: We found statistically significant wavelength-dependent elevations (10-30%) in intracellular NO levels following laser exposures at 447, 532, 635 or 808 nm. Sequential or simultaneous exposures to light at two different wavelengths enhanced the NO modulation up to 50% of unexposed controls. Additionally, the immediate increases in cellular NO levels were independent of the function of nitric oxide synthase, depended greatly on the substrate source of electrons entering the electron transport chain, and did not result in increased levels of cGMP. Conclusions: This study concludes the simple model of light-mediated release of NO from COX is unlikely to explain the wide variety of PBM effects reported in the literature. Our multi-wavelength method provides a novel tool for studying immediate and early mechanisms of PBM, as well as exploring intracellular NO signaling networks.

59 BASIC BIOLOGICAL SCIENCES↗

Bipolar Blobs as Evidence of Hidden AGN Activities in the Low-mass Galaxies

Abstract We report evidence of a hidden black hole (BH) in a low-mass galaxy, MaNGA 9885-9102, and provide a new method to identify active BHs in low-mass galaxies. This galaxy is originally selected from the MaNGA survey with distinctive bipolar Hαblobs at the minor axis. The bipolar feature can be associated with active galactic nuclei (AGN) activity, while the two blobs are classified as the Hiiregions on the BPT diagram, making the origins confusing. The Swift UV continuum shows that the two blobs do not have UV counterparts, suggesting that the source of ionization is out of the blobs. Consistent with this, the detailed photoionization models prefer AGN rather than the star-forming origin with a significance of 5.8σ. The estimated BH mass isM BH ∼ 7.2 × 10 5 M ⊙ from theM BH –σ * relationship. This work introduces a novel method for detecting the light echo of BHs, potentially extending to intermediate mass, in low-metallicity environments where the traditional BPT diagram fails.

Astronomy & Astrophysics↗

Device response principles and the impact on energy resolution of epitaxial quantum dot scintillators with monolithic photodetector integration

Abstract Epitaxial quantum dot (QD) scintillator crystals with picosecond-scale timing and high light yield have been created for medical imaging, high energy physics and national security applications. Monolithic photodetector (PD) integration enables the sensing of photons generated within the waveguiding crystal and allows a wide range of scintillator-photodetector coupling geometries. Until recently, these doubly novel devices have suffered from complex, high variance responses to monoenergetic sources which significantly reduces their precision and accuracy. The principles governing the overall device response have now been discerned and embodied by an expression derived within a geometrical optics framework which considers optical properties, surface roughness and photodetector coupling geometry. Response variation due to these factors was sufficiently reduced to obtain material-related energy resolution values of 2.4% with alpha particles. These findings place energy resolution alongside luminescence timescale, photon yield, and radiation hardness as outstanding properties of these engineered materials.

36 MATERIALS SCIENCE↗

Casimir Light in Dispersive Nanophotonics

Time-varying optical media, whose dielectric properties are actively modulated in time, introduce a host of novel effects in the classical propagation of light, and are of intense current interest. In the quantum domain, time-dependent media can be used to convert vacuum fluctuations (virtual photons) into pairs of real photons. Here, we refer to these processes broadly as “dynamical vacuum effects” (DVEs). Despite interest for their potential applications as sources of quantum light, DVEs are generally very weak, presenting many opportunities for enhancement through modern techniques in nanophotonics, such as using media which support excitations such as plasmon and phonon polaritons. Here, we present a theory of weakly modulated DVEs in arbitrary nanostructured, dispersive, and dissipative systems. A key element of our framework is the simultaneous incorporation of time-modulation and “dispersion” through time-translation-breaking linear response theory. As an example, we use our approach to propose a highly efficient scheme for generating entangled surface polaritons based on time-modulation of the optical phonon frequency of a polar insulator.

42 ENGINEERING↗

Overcoming Dynamic Disturbances in Imaging Systems

We develop and discuss a methodology with the potential to yield a significant reduction in complexity, cost, and risk of space-borne optical systems in the presence of dynamic disturbances. More robust systems almost certainly will be a result as well. Many future space-based and ground-based optical systems will employ optical control systems to enhance imaging performance. The goal of the optical control subsystem is to determine the wavefront aberrations and remove them. Ideally reducing an aberrated image of the object under investigation to a sufficiently clear (usually diffraction-limited) image. Control will likely be distributed over several elements. These elements may include telescope primary segments, telescope secondary, telescope tertiary, deformable mirror(s), fine steering mirror(s), etc. The last two elements, in particular, may have to provide dynamic control. These control subsystems may become elaborate indeed. But robust system performance will require evaluation of the image quality over a substantial range and in a dynamic environment. Candidate systems for improvement in the Earth Sciences Enterprise could include next generation Landsat systems or atmospheric sensors for dynamic imaging of individual, severe storms. The technology developed here could have a substantial impact on the development of new systems in the Space Science Enterprise; such as the Next Generation Space Telescope(NGST) and its follow-on the Next NGST. Large Interferometric Systems of non-zero field, such as Planet Finder and Submillimeter Probe of the Evolution of Cosmic Structure, could benefit. These systems most likely will contain large, flexible optomechanical structures subject to dynamic disturbance. Furthermore, large systems for high resolution imaging of planets or the sun from space may also benefit. Tactical and Strategic Defense systems will need to image very small targets as well and could benefit from the technology developed here. We discuss a novel speckle imaging technique with the potential to separate dynamic aberrations from static aberrations. Post-processing of a set of image data, using an algorithm based on this technique, should work for all but the lowest light levels and highest frequency dynamic environments. This technique may serve to reduce the complexity of the control system and provide for robust, fault-tolerant, reduced risk operation. For a given object, a short exposure image is "frozen" on the focal plane in the presence of the environmental disturbance (turbulence, jitter, etc.). A key factor is that this imaging data exhibits frame-to-frame linear shift invariance. Therefore, although the Point Spread Function is varying from frame to frame, the source is fixed; and each short exposure contains object spectrum data out to the diffraction limit of the imaging system. This novel speckle imaging technique uses the Knox-Thompson method. The magnitude of the complex object spectrum is straightforward to determine by well-established approaches. The phase of the complex object spectrum is decomposed into two parts. One is a single-valued function determined by the divergence of the optical phase gradient. The other is a multi-valued function determined by the circulation of the optical phase gradient-"hidden phase." Finite difference equations are developed for the phase. The novelty of this approach is captured in the inclusion of this "hidden phase." This technique allows the diffraction-limited reconstruction of the object from the ensemble of short exposure frames while simultaneously estimating the phase as a function of time from a set of exposures.

Young, Eric W.↗

Overcoming Dynamic Disturbances in Imaging Systems

We develop and discuss a methodology with the potential to yield a significant reduction in complexity, cost, and risk of space-borne optical systems in the presence of dynamic disturbances. More robust systems almost certainly will be a result as well. Many future space-based and ground-based optical systems will employ optical control systems to enhance imaging performance. The goal of the optical control subsystem is to determine the wavefront aberrations and remove them. Ideally reducing an aberrated image of the object under investigation to a sufficiently clear (usually diffraction-limited) image. Control will likely be distributed over several elements. These elements may include telescope primary segments, telescope secondary, telescope tertiary, deformable mirror(s), fine steering mirror(s), etc. The last two elements, in particular, may have to provide dynamic control. These control subsystems may become elaborate indeed. But robust system performance will require evaluation of the image quality over a substantial range and in a dynamic environment. Candidate systems for improvement in the Earth Sciences Enterprise could include next generation Landsat systems or atmospheric sensors for dynamic imaging of individual, severe storms. The technology developed here could have a substantial impact on the development of new systems in the Space Science Enterprise; such as the Next Generation Space Telescope(NGST) and its follow-on the Next NGST. Large Interferometric Systems of non-zero field, such as Planet Finder and Submillimeter Probe of the Evolution of Cosmic Structure, could benefit. These systems most likely will contain large, flexible optormechanical structures subject to dynamic disturbance. Furthermore, large systems for high resolution imaging of planets or the sun from space may also benefit. Tactical and Strategic Defense systems will need to image very small targets as well and could benefit from the technology developed here. We discuss a novel speckle imaging technique with the potential to separate dynamic aberrations from static aberrations. Post-processing of a set of image data, using an algorithm based on this technique, should work for all but the lowest light levels and highest frequency dynamic environments. This technique may serve to reduce the complexity of the control system and provide for robust, fault-tolerant, reduced risk operation. For a given object, a short exposure image is "frozen" on the focal plane in the presence of the environmental disturbance (turbulence, jitter, etc.). A key factor is that this imaging data exhibits frame-to-frame linear shift invariance. Therefore, although the Point Spread Function is varying from frame to frame, the source is fixed; and each short exposure contains object spectrum data out to the diffraction limit of the imaging system. This novel speckle imaging technique uses the Knox-Thompson method. The magnitude of the complex object spectrum is straightforward to determine by well-established approaches. The phase of the complex object spectrum is decomposed into two parts. One is a single-valued function determined by the divergence of the optical phase gradient. The other is a multi-valued function determined by, the circulation of the optical phase gradient-"hidden phase." Finite difference equations are developed for the phase. The novelty of this approach is captured in the inclusion of this "hidden phase." This technique allows the diffraction-limited reconstruction of the object from the ensemble of short exposure frames while simultaneously estimating the phase as a function of time from a set of exposures.

Young, Eric W.↗

Nonlinear Thomson scattering with ponderomotive control

In nonlinear Thomson scattering, a relativistic electron re-radiates the photons of a laser pulse, converting optical light to x rays or beyond. While this extreme frequency conversion offers a promising source for probing high-energy-density materials and driving uncharted regimes of nonlinear quantum electrodynamics, conventional nonlinear Thomson scattering has inherent tradeoffs in its scaling with laser intensity. Here we discover that the ponderomotive control afforded by spatiotemporal pulse shaping enables novel regimes of nonlinear Thomson scattering that substantially enhance the scaling of the radiated power, emission angle, and frequency with laser intensity. By appropriately setting the velocity of the intensity peak, a spatiotemporally shaped pulse can increase the power radiated by orders of magnitude. Here, the enhanced scaling with laser intensity allows for operation at significantly lower electron energies or intensities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

0D Nanocrystals as Light‐Driven, Localized Charge‐Injection Sources for the Contactless Manipulation of Atomically Thin 2D Materials

A contactless charge‐injection scheme that allows the local and quasi‐permanent manipulation of atomically thin 2D materials, such as monolayer (1L‐)MoS 2 , over spatial extents of several tens of micrometers, is reported. The possibility to precisely position and localize the charge‐injection source to the micrometer scale post‐fabrication allows the investigation of local unperturbed electronic structure of the 2D material. Thanks to this novel approach, the important impact of sample inhomogeneity on the charge‐carrier percolation that occurs over the entire extent of the 2D flake and proliferates up to 40 μm away from the localized charge injection is elucidated. The apparent driving force for carrier relocation is the initial inhomogeneous electronic landscape of the 2D material. These studies demonstrate that local and contactless charge injection with submicrometer precision delivers an alternative route for charge injection and indicates that local 2D material electronic structure can serve as a key element for novel nanoscale device design.

Ghini, Michele↗

Automated Construction of a Photocatalysis Dataset for Water-Splitting Applications

We present an automatically generated dataset of 15,755 records that were extracted from 47,357 papers. These records contain water-splitting activity in the presence of certain photocatalysts, along with additional information about the chemical reaction conditions under which this activity was recorded. These conditions include any co-catalysts and additives that were present during water splitting, the length of time for which the photocatalytic experiment was conducted, and the type of light source used, including its wavelength. Despite the text extraction of such a wide range of chemical reaction attributes, the dataset afforded good precision (71.2%) and recall (36.3%). These figures-of-merit were calculated based on a random sample of open-access papers from the corpus. Mining such a complex set of attributes required the development of novel techniques in knowledge extraction and interdependency resolution, leveraging inter- and intra-sentence relations, which are also described in this paper. We present a new version (version 2.2) of the chemistry-aware text-mining toolkit ChemDataExtractor, in which these new techniques are included.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Roadmap on quantum light spectroscopy

Conventional spectroscopy uses classical light to detect matter properties through the variation of its response with frequencies or time delays. Quantum light opens up new avenues for spectroscopy by utilizing parameters of the quantum state of light as novel control knobs and through the variation of photon statistics by coupling to matter. This Roadmap article focuses on using quantum light as a powerful sensing and spectroscopic tool to reveal novel information about complex molecules that is not accessible by classical light. It aims at bridging the quantum optics and spectroscopy communities which normally have opposite goals: manipulating complex light states with simple matter e.g. qubits versus studying complex molecules with simple classical light, respectively. Here, articles cover advances in the generation and manipulation of state-of-the-art quantum light sources along with applications to sensing, spectroscopy, imaging and interferometry.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The Supercritical Pile GRB Model: The Prompt to Afterglow Evolution

The 'Supercritical Pile' is a very economical gamma ray burst (GRB) model that provides for the efficient conversion of the energy stored in the protons of a Relativistic Blast Wave (RBW) into radiation and at the same time produces - in the prompt GRB phase, even in the absence of any particle acceleration - a spectral peak at an energy sim 1 MeV. We extend this model to include also the evolution of the RBW Lorentz factor Gamma and thus follow the spectral and temporal features of this model into the early GRB afterglow stage. One of the novel features of the present treatment is the inclusion of the feedback of the GRB produced radiation on the evolution of Gamma with radius. This feedback and the presence of kinematic and dynamic thresholds in the model can be the sources of rich time evolution which we have begun to explore. In particular, one can this way obtain afterglow light curves with steep decays followed by the more conventional flatter afterglow slopes, while at the same time preserving the desirable features of the model, i.e. the well defined relativistic electron source and radiative processes that produce the proper peak in the nu F spectra. Furthermore, the existence of a kinematic threshold in this model provides for a operational distinction of the prompt and afterglow GRB stages; in fact, the afterglow stage sets in when the RBW Lorentz factor cannot anymore fulfill the kinematic condition for pair formation in the photon - proton pair production reactions that constitute the fundamental process for the dissipation of the blast wave kinetic energy. We present the results of a specific set of parameters of this model with emphasis on the multiwavelength prompt emission and transition to the early afterglow.

Kazanas, Demosthenes↗

The Supercritical Pile GRB Model: The Prompt to Afterglow Evolution

The "Supercritical Pile" is a very economical GRB model that provides for the efficient conversion of the energy stored in the protons of a Relativistic Blast Wave (RBW) into radiation and at the same time produces - in the prompt GRB phase, even in the absence of any particle acceleration - a spectral peak at energy approx. 1 MeV. We extend this model to include the evolution of the RBW Lorentz factor Gamma and thus follow its spectral and temporal features into the early GRB afterglow stage. One of the novel features of the present treatment is the inclusion of the feedback of the GRB produced radiation on the evolution of Gamma with radius. This feedback and the presence of kinematic and dynamic thresholds in the model can be the sources of rich time evolution which we have began to explore. In particular. one can this may obtain afterglow light curves with steep decays followed by the more conventional flatter afterglow slopes, while at the same time preserving the desirable features of the model, i.e. the well defined relativistic electron source and radiative processes that produce the proper peak in the (nu)F(sub nu), spectra. In this note we present the results of a specific set of parameters of this model with emphasis on the multiwavelength prompt emission and transition to the early afterglow.

Mastichiadis, A.↗

A Bulk Comptonization Model for the Prompt GRM Emission

The "Supercritical Pile" is a very economical GRB model that provides for the efficient conversion of the energy stored in the protons of a Relativistic Blast Wave (RBW) into radiation and at the same time produces - in the prompt GRB phase, even in the absence of any particle acceleration - a spectral peak at energy approximately 1 MeV. We extend this model to include the evolution of the RBW Lorentz factor F and thus follow its spectral and temporal features into the early GRB afterglow stage. One of the novel features of the present treatment is the inclusion of the feedback of the GRB produced radiation on the evolution of Gamma with radius. This feedback and the presence of kinematic and dynamic thresholds in the model are sources of potentially very rich time evolution which we have began to explore. In particular, one can this way obtain afterglow light curves with steep decays followed by the more conventional flatter afterglow slopes, while at the same time preserving the desirable features of the model, i.e. the well defined relativistic electron source and radiative processes that produce the proper peak in the nu F(sub nu) spectra. In this note we present the results of a specific set of parameters of this model with emphasis on the multiwavelength prompt emission and transition to the early afterglow.

Kazanas, Demos↗

Investigation of laser dynamics, modulation and control by means of intra-cavity time varying perturbation

The generation of tunable visible, infrared, and ultraviolet light is examined, along with the control of this light by means of novel mode-locking and modulation techniques. Transient mode-locking of the Nd:YAG laser and generation of short tunable pulses in the visible and the alkali metal inert gas excimer laser systems were investigated. Techniques for frequency conversion of high power and high energy laser radiation are discussed, along with high average power blue and UV laser light sources.

Harris, S. E.↗

The hard x-ray nanotomography microscope at the advanced light source

Beamline 11.3.1 at the Advanced Light Source is a tender/hard (6–17 keV) x-ray bend magnet beamline recently re-purposed with a new full-field, nanoscale transmission x-ray microscope. The microscope is designed to image composite and porous materials possessing a submicrometer structure and compositional heterogeneity that determine materials’ performance and geologic behavior. The theoretical and achieved resolutions are 55 and <100 nm, respectively. The microscope is used in tandem with a <25 nm eccentricity rotation stage for high-resolution volume imaging using nanoscale computed tomography. The system also features a novel bipolar illumination condenser for the illumination of an ~100 μm spot of interest on the sample, followed by a phase-type zone plate magnifying objective of ~52 µm field of view and a phase detection ring. The zone plate serves as the system objective and magnifies the sample with projection onto an indirect x-ray detection system, consisting of a polished single crystal CsI(Tl) scintillator and a range of high-quality Plan Fluorite visible light objectives. The objectives project the final visible light image onto a water-cooled CMOS 2048 × 2048-pixel 2 detector. Here, in this paper, we will discuss the salient features of this instrument and describe early results from imaging the internal three-dimensional microstructure and nanostructure of target materials, including fiber-reinforced composites and geomaterials.

47 OTHER INSTRUMENTATION↗

Correlation-driven attosecond photoemission delay in the plasmonic excitation of C60 fullerene

Extreme light confinement in plasmonic nanosystems enables novel applications in photonics, sensor technology, energy harvesting, biology, and quantum information processing. Fullerenes represent an extreme case for nanoplasmonics: they are sub-nanometer carbon- based molecules showing high-energy and ultrabroad plasmon resonances, however the fundamental mechanisms driving the plasmonic response and the corresponding collective electron dynamics are still elusive. Here, we uncover the dominant role of electron correlations in the dynamics of the giant plasmon resonance (GPR) of the sub-nanometer system C60 by employing attosecond photoemission chronoscopy. We find a characteristic photoemission delay of up to about 300 attoseconds that is purely induced by coherent large-scale electron correlations in the plasmonic potential. These results provide novel insights into the nature of the plasmon resonances in sub-nanometer systems and open new perspectives for advancing nanoplasmonic applications.

Biswas, Shubhadeep [SLAC National Accelerator Labo↗