Recent Submissions

  • Versatile Porous Poly(arylene ether)s via Pd-Catalyzed C–O Polycondensation

    Guo, Sheng; Swager, Timothy M. (Journal of the American Chemical Society, American Chemical Society (ACS), 2021-07-27) [Article]
  • Molecular library of OLED host materials—Evaluating the multiscale simulation workflow

    Mondal, Anirban; Paterson, Leanne; Cho, Jaeyoung; Lin, Kun-Han; van der Zee, Bas; Wetzelaer, Gert-Jan A. H.; Stankevych, Andrei; Vakhnin, Alexander; Kim, Jang-Joo; Kadashchuk, Andrey; Blom, Paul W. M.; May, Falk; Andrienko, Denis (Chemical Physics Reviews, AIP Publishing, 2021-07-26) [Article]
  • Meta-Optimization of Deep CNN for Image Denoising Using LSTM

    Alawode, Basit O.; Alfarraj, Motaz (arXiv, 2021-07-14) [Preprint]
    The recent application of deep learning (DL) to various tasks has seen the performance of classical techniques surpassed by their DL-based counterparts. As a result, DL has equally seen application in the removal of noise from images. In particular, the use of deep feed-forward convolutional neural networks (DnCNNs) has been investigated for denoising. It utilizes advances in DL techniques such as deep architecture, residual learning, and batch normalization to achieve better denoising performance when compared with the other classical state-of-the-art denoising algorithms. However, its deep architecture resulted in a huge set of trainable parameters. Meta-optimization is a training approach of enabling algorithms to learn to train themselves by themselves. Training algorithms using meta-optimizers have been shown to enable algorithms to achieve better performance when compared to the classical gradient descent-based training approach. In this work, we investigate the application of the meta-optimization training approach to the DnCNN denoising algorithm to enhance its denoising capability. Our preliminary experiments on simpler algorithms reveal the prospects of utilizing the meta-optimization training approach towards the enhancement of the DnCNN denoising capability.
  • A mathematical model of the erosion process in a channel bend

    Herterich, J.G.; Griffiths, I.M. (Tribology International, Elsevier BV, 2021-07-08) [Article]
  • Correcting photodetector nonlinearity in dual-comb interferometry

    Guay, Philippe; Hébert, Nicolas Bourbeau; Tourigny-Plante, and Alex; Michaud-Belleau, Vincent; Genest, Jérôme (arXiv, 2021-07-05) [Preprint]
    Photodetector nonlinearity, the main limiting factor in terms of optical power in the detection chain, is corrected to improve the signal-to-noise ratio of a short-time measurement in dual-comb spectroscopy. An iterative correction algorithm minimizing out-of-band spectral artifacts based on nonlinearity correction methods used in classical Fourier-transform spectrometers is presented. The exactitude of the nonlinearity correction is validated using a low power linear measurement. Spectroscopic lines of H$^{12}$CN are provided and the error caused by the saturation of the detector is corrected yielding residuals limited by the measurement noise.
  • Four-band non-Abelian topological insulator and its experimental realization

    Jiang, Tianshu; Guo, Qinghua; Zhang, Ruo-Yang; Zhang, Zhao-Qing; Yang, Biao; Chan, Che Ting (Research Square Platform LLC, 2021-07-01) [Preprint]
    Very recently, increasing attention has been focused on non-Abelian topological charges, e.g. the quaternion group Q8. Different from Abelian topological band insulators, these systems involve multiple tangled bulk bandgaps and support non-trivial edge states that manifest the non-Abelian topological features. Furthermore, a system with even or odd number of bands will exhibit significant difference in non-Abelian topological classifications. Up to now, there is scant research investigating the even-band non-Abelian topological insulators. Here, we both theoretically explored and experimentally realized a four-band PT (inversion and time-reversal) symmetric system, where two new classes of topological charges as well as edge states are comprehensively studied. We illustrate their difference from four-dimensional rotation senses on the stereographically projected Clifford tori. We show the evolution of bulk topology by extending the 1D Hamiltonian onto a 2D plane and provide the accompanying edge state distributions following an analytical method. Our work presents an exhaustive study of four-band non-Abelian topological insulators and paves the way to other even band systems.
  • Implementing Fluorescence Enhancement, Quenching, and FRET for Investigating Flap Endonuclease 1 Enzymatic Reaction at the Single-Molecule Level

    Sobhy, Mohamed A.; Tehseen, Muhammad; Takahashi, Masateru; Bralić, Amer; De Biasio, Alfredo; Hamdan, Samir M. (Computational and Structural Biotechnology Journal, Elsevier BV, 2021-07) [Article]
    Flap endonuclease 1 (FEN1) is an important component of the intricate molecular machinery for DNA replication and repair. FEN1 is a structure-specific 5′ nuclease that cleaves nascent single-stranded 5′ flaps during the maturation of Okazaki fragments. Here, we review our research primarily applying single-molecule fluorescence to resolve important mechanistic aspects of human FEN1 enzymatic reaction. The methodology presented in this review is aimed as a guide for tackling other biomolecular enzymatic reactions by fluorescence enhancement, quenching, and FRET and their combinations. Using these methods, we followed in real-time the structures of the substrate and product and 5’ flap cleavage during catalysis. We illustrate that FEN1 actively bends the substrate to verify its features and continues to mold it to induce a protein disorder-to-order transitioning that controls active site assembly. This mechanism suppresses off-target cleavage of non-cognate substrates and promotes their dissociation with an accuracy that was underestimated from bulk assays. We determined that product release in FEN1 after the 5′ flap release occurs in two steps; a brief binding to the bent nicked-product followed by longer binding to the unbent nicked-product before dissociation. Based on our cryo-electron microscopy structure of the human lagging strand replicase bound to FEN1, we propose how this two-step product release mechanism may regulate the final steps during the maturation of Okazaki fragments.
  • Animal tag technology keeps coming of age: an engineering perspective

    Holton, Mark D.; Wilson, Rory P.; Teilmann, Jonas; Siebert, Ursula (Philosophical Transactions of the Royal Society B: Biological Sciences, The Royal Society, 2021-06-28) [Article]
    Animal-borne tags (biologgers) have now become extremely sophisticated, recording data from multiple sensors at high frequencies for long periods and, as such, have become a powerful tool for behavioural ecologists and physiologists studying wild animals. But the design and implementation of these tags is not trivial because engineers have to maximize performance and ability to function under onerous conditions while minimizing tag mass and volume (footprint) to maximize the wellbeing of the animal carriers. We present some of the major issues faced by tag engineers and show how tag designers must accept compromises while maintaining systems that can answer the questions being posed. We also argue that basic understanding of engineering issues in tag design by biologists will help feedback to engineers to better tag construction but also reduce the likelihood that tag-deploying biologists will misunderstand their own results. Finally, we suggest that proper consideration of conventional technology together with new approaches will lead to further step changes in our understanding of wild-animal biology using smart tags. This article is part of the theme issue ‘Measuring physiology in free-living animals (Part II)’.
  • Transcutaneous Measurement of Essential Vitamins Using Near-Infrared Fluorescent Single-Walled Carbon Nanotube Sensors

    Bakh, Naveed A.; Gong, Xun; Lee, Michael A.; Jin, Xiaojia; Koman, Volodymyr B.; Park, Minkyung; Nguyen, Freddy T.; Strano, Michael S (Small, Wiley, 2021-06-27) [Article]
  • Magnon Transport in the Presence of Antisymmetric Exchange in a Weak Antiferromagnet

    Ross, A.; Lebrun, R.; Gomonay, O.; Sinova, J.; Kay, A.; Grave, D. A.; Rothschild, A.; Kläui, M. (arXiv, 2021-06-24) [Preprint]
    The Dzyaloshinskii-Moriya interaction (DMI) is at the heart of many modern developments in the research field of spintronics. DMI is known to generate noncollinear magnetic textures, and can take two forms in antiferromagnets: homogeneous or inter-sublattice, leading to small, canted moments and inhomogeneous or intra-sublattice, leading to formation of chiral structures. In this work, we first determine the strength of the effective field created by the DMI, using SQUID based magnetometry and transport measurements, in thin films of the antiferromagnetic iron oxide hematite, $\alpha$-Fe$_2$O$_3$. We demonstrate that DMI additionally introduces reconfigurability in the long distance magnon transport in these films under different orientations of a magnetic field. This arises as a hysteresis centred around the easy-axis direction for an external field rotated in opposing directions whose width decreases with increasing magnetic field as the Zeeman energy competes with the effective field created by the DMI.
  • Organic electrochemical transistors in bioelectronic circuits

    Rashid, Reem B.; Ji, Xudong; Rivnay, Jonathan (Biosensors and Bioelectronics, Elsevier BV, 2021-06-23) [Article]
  • Coordinated gas release among the physostomous fish sprat (Sprattus sprattus)

    Kaartvedt, Stein; Ugland, Karl I.; Heuschele, Jan; Solberg, Ingrid (Scientific Reports, Springer Science and Business Media LLC, 2021-06-23) [Article]
    AbstractPrevious experimental studies suggest that the production of sound associated with expelling gas from an open swimbladder may play a role in communication. This would suggest non-random gas release. We used deployed echosounders to study patterns of gas release among a fjord population of sprat (Sprattus sprattus). The echosounder records concurrently revealed individual fish and their release of gas. The gas release primarily occurred at night, partly following recurrent temporal patterns, but also varying between nights. In testing for non-randomness, we formulated a data-driven simulation approach. Non-random gas release scaled with the length of the analyzed time intervals from 1 min to 6 h, and above 30 min the release events in more than 50% of the intervals were significantly connected.
  • Influence of static disorder of charge transfer state on voltage loss in organic photovoltaics

    Yan, Jun; Rezasoltani, Elham; Azzouzi, Mohammed; Eisner, Flurin; Nelson, Jenny (Nature Communications, Springer Science and Business Media LLC, 2021-06-15) [Article]
    AbstractSpectroscopic measurements of charge transfer (CT) states provide valuable insight into the voltage losses in organic photovoltaics (OPVs). Correct interpretation of CT-state spectra depends on knowledge of the underlying broadening mechanisms, and the relative importance of molecular vibrational broadening and variations in the CT-state energy (static disorder). Here, we present a physical model, that obeys the principle of detailed balance between photon absorption and emission, of the impact of CT-state static disorder on voltage losses in OPVs. We demonstrate that neglect of CT-state disorder in the analysis of spectra may lead to incorrect estimation of voltage losses in OPV devices. We show, using measurements of polymer:non-fullerene blends of different composition, how our model can be used to infer variations in CT-state energy distribution that result from variations in film microstructure. This work highlights the potential impact of static disorder on the characteristics of disordered organic blend devices.
  • Current production by non-methanotrophic bacteria enriched from an anaerobic methane-oxidizing microbial community

    Berger, S.; Rangel Shaw, D.; Berben, T.; Ouboter, H.T.; in ’t Zandt, M.H.; Frank, J.; Reimann, J.; Jetten, M.S.M.; Welte, C.U. (Biofilm, Elsevier BV, 2021-06-15) [Article]
    In recent years, the externalization of electrons as part of respiratory metabolic processes has been discovered in many different bacteria and some archaea. Microbial extracellular electron transfer (EET) plays an important role in many anoxic natural or engineered ecosystems. In this study, an anaerobic methane-converting microbial community was investigated with regard to its potential to perform EET. At this point, it is not well-known if or how EET confers a competitive advantage to certain species in methane-converting communities. EET was investigated in a two-chamber electrochemical system, sparged with methane and with an applied potential of +400 mV versus standard hydrogen electrode. A biofilm developed on the working electrode and stable low-density current was produced, confirming that EET indeed did occur. The appearance and presence of redox centers at −140 to −160 mV and at −230 mV in the biofilm was confirmed by cyclic voltammetry scans. Metagenomic analysis and fluorescence in situ hybridization of the biofilm showed that the anaerobic methanotroph ‘Candidatus Methanoperedens BLZ2’ was a significant member of the biofilm community, but its relative abundance did not increase compared to the inoculum. On the contrary, the relative abundance of other members of the microbial community significantly increased (up to 720-fold, 7.2% of mapped reads), placing these microorganisms among the dominant species in the bioanode community. This group included Zoogloea sp., Dechloromonas sp., two members of the Bacteroidetes phylum, and the spirochete Leptonema sp. Genes encoding proteins putatively involved in EET were identified in Zoogloea sp., Dechloromonas sp. and one member of the Bacteroidetes phylum. We suggest that instead of methane, alternative carbon sources such as acetate were the substrate for EET. Hence, EET in a methane-driven chemolithoautotrophic microbial community seems a complex process in which interactions within the microbial community are driving extracellular electron transfer to the electrode.
  • Understanding photodetector nonlinearity in dual-comb interferometry

    Guay, Philippe; Tourigny-Plante, Alex; Michaud-Belleau, Vincent; Hébert, Nicolas Bourbeau; Gouin, Ariane; Genest, Jérôme (arXiv, 2021-06-15) [Preprint]
    The impact of photodetector nonlinearity on dual-comb spectrometers is described and compared to that of Michelson-based Fourier transform spectrometers (FTS). The optical sampling occurring in the dual-comb approach, being the key difference with FTS, causes optical aliasing of the nonlinear spectral artifacts. Measured linear and nonlinear interferograms are presented to validate the model. Absorption lines of H$^{13}$CN are provided to understand the impact of nonlinearity on spectroscopic measurements.
  • Constraining families of dynamic models using geological, geodetic and strong ground motion data: the Mw 6.5, October 30th, 2016, Norcia earthquake, Italy

    Tinti, Elisa; Casarotti, Emanuele; Ulrich, Thomas; Li, D.; Taufiqurrahman, Taufiqurrahman; Gabriel, Alice-Agnes (California Digital Library (CDL), 2021-06-14) [Preprint]
    The 2016 Central Italy earthquake sequence is characterized by remarkable rupture complexity, including highly heterogeneous slip across multiple faults in an extensional tectonic regime. The dense coverage and high quality of geodetic and seismic data allow to image intriguing details of the rupture kinematics of the largest earthquake of the sequence, the Mw 6.5 October 30th, 2016 Norcia earthquake, such as an energetically weak nucleation phase. Several kinematic models suggest multiple fault planes rupturing simultaneously, however, the mechanical viability of such models is not guaranteed.Using 3D dynamic rupture and seismic wave propagation simulations accounting for two fault planes, we constrain 'families' of spontaneous dynamic models informed by a high-resolution kinematic rupture model of the earthquake. These families differ in their parameterization of initial heterogeneous shear stress and strength in the framework of linear slip weakening friction.First, we dynamically validate the kinematically inferred two-fault geometry and rake inferences with models based on only depth-dependent stress and constant friction coefficients. Then, more complex models with spatially heterogeneous dynamic parameters allow us to retrieve slip distributions similar to the target kinematic model and yield good agreement with seismic and geodetic observations. We discuss the consistency of the assumed constant or heterogeneous static and dynamic friction coefficients with mechanical properties of rocks at 3-10 km depth characterizing the Italian Central Apennines and their local geological and lithological implications. We suggest that suites of well-fitting dynamic rupture models belonging to the same family generally exist and can be derived by exploiting the trade-offs between dynamic parameters.Our approach will be applicable to validate the viability of kinematic models and classify spontaneous dynamic rupture scenarios that match seismic and geodetic observations at the same time as geological constraints.
  • Experimental observation of non-Abelian earring nodal links in phononic crystals

    Wang, Mudi; Liu, Shan; Ma, Qiyun; Zhang, Ruo-Yang; Wang, Dongyang; Guo, Qinghua; Yang, Biao; Ke, Manzhu; Liu, Zhengyou; Chan, C. T. (arXiv, 2021-06-12) [Preprint]
    Nodal lines are symmetry-protected one-dimensional band degeneracies in momentum space, which can appear in numerous topological configurations such as nodal rings, chains, links, and knots. Very recently, non-Abelian topological physics has been proposed in space-time inversion (PT) symmetric systems, and attract widespread attention. One of the most special configurations in non-Abelian system is the earring nodal link, composing of a nodal chain linking with an isolated nodal line, is signature of non-Abelian topology and cannot be elucidated using Abelian topological classifications. However, the earring nodal links have not been yet observed in real system. Here we design the phononic crystals with earring nodal links, and verify its non-Abelian topologicial charge in full-wave simulations. Moreover, we experimentally observed two different kinds of earring nodal links by measuring the band structures for two phononic crystals. Specifically, we found that the order of the nodal chain and line can switch after band inversion but their link cannot be severed. Our work provides experimental evidence for phenomena unique to non-Abelian band topology and our simple acoustic system provides a convenient platform for studying non-Abelian charges.
  • Externally driven broadband transmission in strongly disordered materials

    Bachelard, Nicolas; Ropp, Chad; Yang, Sui; Zhang, Xiang (Applied Physics Letters, AIP Publishing, 2021-06-07) [Article]
  • A Review of Spatial Causal Inference Methods for Environmental and Epidemiological Applications

    Reich, Brian J.; Yang, Shu; Guan, Yawen; Giffin, Andrew B.; Miller, Matthew J.; Rappold, Ana (International Statistical Review, Wiley, 2021-05-31) [Article]
  • Modifying redox properties and local bonding of Co3O4 by CeO2 enhances oxygen evolution catalysis in acid

    Huang, Jinzhen; Sheng, Hongyuan; Ross, R. Dominic; Han, Jiecai; Wang, Xianjie; Song, Bo; Jin, Song (Nature Communications, Springer Science and Business Media LLC, 2021-05-24) [Article]
    AbstractDeveloping efficient and stable earth-abundant electrocatalysts for acidic oxygen evolution reaction is the bottleneck for water splitting using proton exchange membrane electrolyzers. Here, we show that nanocrystalline CeO2 in a Co3O4/CeO2 nanocomposite can modify the redox properties of Co3O4 and enhances its intrinsic oxygen evolution reaction activity, and combine electrochemical and structural characterizations including kinetic isotope effect, pH- and temperature-dependence, in situ Raman and ex situ X-ray absorption spectroscopy analyses to understand the origin. The local bonding environment of Co3O4 can be modified after the introduction of nanocrystalline CeO2, which allows the Co$^{III}$ species to be easily oxidized into catalytically active Co$^{IV}$ species, bypassing the potential-determining surface reconstruction process. Co3O4/CeO2 displays a comparable stability to Co3O4 thus breaks the activity/stability tradeoff. This work not only establishes an efficient earth-abundant catalysts for acidic oxygen evolution reaction, but also provides strategies for designing more active catalysts for other reactions.

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