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1. From Molecules to Molecular Surfaces. Exploiting the Interplay Between Organic Synthesis and Electrochemistry

   https://doi.org/10.1021/acs.accounts.9b00578  

   Jing, Q. ; Moeller, K. D. ( January 2020 , Accounts of chemical research)

   For many years, we looked at electrochemistry as a tool for exploring, developing, and implementing new synthetic methods for the construction of organic molecules. Those efforts examined electrochemical methods and mechanisms and then exploited them for synthetic gain. Chief among the tools utilized was the fact that in a constant current electrolysis the working potential at the electrodes automatically adjusted to the oxidation (anode) or reduction (cathode) potential of the substrates in solution. This allowed for a systematic examination of the radical cation intermediates that are involved in a host of oxidative cyclization reactions. The result has been a series of structure-activity studies that have led to far greater insight into the behavior of radical cation intermediates and in turn an expansion in our capabilities of using those intermediates to trigger interesting synthetic reactions. With that said, the relationship between synthetic organic chemistry and electrochemistry is not a "one-way" interaction. For example, we have been using modern synthetic methodology to construct complex addressable molecular surfaces on electroanalytical devices that in turn can be used to probe biological interactions between small molecules and biological receptors in "real-time" as the interactions happen. Synthetic chemistry can then be used to recover the molecules that give rise to positive signals so that they can be characterized. The result is an analytical method that both gives accurate data on the interactions and provides a unique level of quality control with respect to the molecules giving rise to that data. Synthetic organic chemistry is essential to this task because it is our ability to synthesize the surfaces that defines the nature of the biological problems that can be studied. But the relationship between the fields does not end there. Recently, we have begun to show that work to expand the scope of microelectrode arrays as bioanalytical devices is teaching us important lessons for preparative synthetic chemistry. These lessons come in two forms. First, the arrays have taught us about the on-site generation of chemical reagents, a lesson that is being used to expand the use of paired electrochemical strategies for synthesis. Second, the arrays have taught us that reagents can be generated and then confined to the surface of the electrode used for that generation. This has led to a new approach to taking advantage of molecular recognition events that occur on the surface of an electrode for controlling the selectivity of a preparative reaction. In short, the confinement strategy developed for the arrays is used to insure that the chemistry in a preparative electrolysis happens at the electrode surface and not in the bulk solution. This account details the interplay between synthetic chemistry and electrochemistry in our group through the years and highlights the opportunities that interplay has provided and will continue to provide in the future. 

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2. X-ray luminosity function of high-mass X-ray binaries: Studying the signatures of different physical processes using detailed binary evolution calculations

   https://doi.org/10.1051/0004-6361/202244929  

   Misra, Devina ; Kovlakas, Konstantinos ; Fragos, Tassos ; Lazzarini, Margaret ; Bavera, Simone S. ; Lehmer, Bret D. ; Zezas, Andreas ; Zapartas, Emmanouil ; Xing, Zepei ; Andrews, Jeff J. ; et al ( April 2023 , Astronomy & Astrophysics)

   Context. Many physical processes taking place during the evolution of binary stellar systems remain poorly understood. The ever-expanding observational sample of X-ray binaries (XRBs) makes them excellent laboratories for constraining binary evolution theory. Such constraints and useful insights can be obtained by studying the effects of various physical assumptions on synthetic X-ray luminosity functions (XLFs) and comparing them with observed XLFs. Aims. In this work we focus on high-mass X-ray binaries (HMXBs) and study the effects on the XLF of various, poorly constrained assumptions regarding physical processes, such as the common-envelope phase, core collapse, and wind-fed accretion. Methods. We used the new binary population synthesis code POSYDON , which employs extensive precomputed grids of detailed stellar structure and binary evolution models, to simulate the entire evolution of binaries. We generated 96 synthetic XRB populations corresponding to different combinations of model assumptions, including different prescriptions for supernova kicks, supernova remnant masses, common-envelope evolution, circularization at the onset of Roche-lobe overflow, and observable wind-fed accretion. Results. The generated HMXB XLFs are feature-rich, deviating from the commonly assumed single power law. We find a break in our synthetic XLF at luminosity ∼10 38 erg s −1 , similar to observed XLFs. However, we also find a general overabundance of XRBs (up to a factor of ∼10 for certain model parameter combinations) driven primarily by XRBs with black hole accretors. Assumptions about the transient behavior of Be XRBs, asymmetric supernova kicks, and common-envelope physics can significantly affect the shape and normalization of our synthetic XLFs. We find that less well-studied assumptions regarding the circularization of the orbit at the onset of Roche-lobe overflow and criteria for the formation of an X-ray-emitting accretion disk around wind-accreting black holes can also impact our synthetic XLFs and reduce the discrepancy with observations. Conclusions. Our synthetic XLFs do not always agree well with observations, especially at intermediate X-ray luminosities, which is likely due to uncertainties in the adopted physical assumptions. While some model parameters leave distinct imprints on the shape of the synthetic XLFs and can reduce this deviation, others do not have a significant effect overall. Our study reveals the importance of large-scale parameter studies, highlighting the power of XRBs in constraining binary evolution theory. 

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3. SYMBA: An end-to-end VLBI synthetic data generation pipeline: Simulating Event Horizon Telescope observations of M 87

   https://doi.org/10.1051/0004-6361/201936622  

   Roelofs, F. ; Janssen, M. ; Natarajan, I. ; Deane, R. ; Davelaar, J. ; Olivares, H. ; Porth, O. ; Paine, S. N. ; Bouman, K. L. ; Tilanus, R. P. ; et al ( April 2020 , Astronomy & Astrophysics)

   Context. Realistic synthetic observations of theoretical source models are essential for our understanding of real observational data. In using synthetic data, one can verify the extent to which source parameters can be recovered and evaluate how various data corruption effects can be calibrated. These studies are the most important when proposing observations of new sources, in the characterization of the capabilities of new or upgraded instruments, and when verifying model-based theoretical predictions in a direct comparison with observational data. Aims. We present the SYnthetic Measurement creator for long Baseline Arrays ( SYMBA ), a novel synthetic data generation pipeline for Very Long Baseline Interferometry (VLBI) observations. SYMBA takes into account several realistic atmospheric, instrumental, and calibration effects. Methods. We used SYMBA to create synthetic observations for the Event Horizon Telescope (EHT), a millimetre VLBI array, which has recently captured the first image of a black hole shadow. After testing SYMBA with simple source and corruption models, we study the importance of including all corruption and calibration effects, compared to the addition of thermal noise only. Using synthetic data based on two example general relativistic magnetohydrodynamics (GRMHD) model images of M 87, we performed case studies to assess the image quality that can be obtained with the current and future EHT array for different weather conditions. Results. Our synthetic observations show that the effects of atmospheric and instrumental corruptions on the measured visibilities are significant. Despite these effects, we demonstrate how the overall structure of our GRMHD source models can be recovered robustly with the EHT2017 array after performing calibration steps, which include fringe fitting, a priori amplitude and network calibration, and self-calibration. With the planned addition of new stations to the EHT array in the coming years, images could be reconstructed with higher angular resolution and dynamic range. In our case study, these improvements allowed for a distinction between a thermal and a non-thermal GRMHD model based on salient features in reconstructed images. 

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4. SpoTNet: A spoofing-aware Transformer Network for Effective Synthetic Speech Detection

   https://doi.org/10.1145/3592572.3592841  

   Khan, Awais ; Malik, Khalid Mahmood ( June 2023 , MAD '23: Proceedings of the 2nd ACM International Workshop on Multimedia AI against Disinformation)

   The prevalence of voice spoofing attacks in today’s digital world has become a critical security concern. Attackers employ various techniques, such as voice conversion (VC) and text-to-speech (TTS), to generate synthetic speech that imitates the victim’s voice and gain access to sensitive information. The recent advances in synthetic speech generation pose a significant threat to modern security systems, while traditional voice authentication methods are incapable of detecting them effectively. To address this issue, a novel solution for logical access (LA)-based synthetic speech detection is proposed in this paper. SpoTNet is an attention-based spoofing transformer network that includes crafted front-end spoofing features and deep attentive features retrieved using the developed logical spoofing transformer encoder (LSTE). The derived attentive features were then processed by the proposed multi-layer spoofing classifier to classify speech samples as bona fide or synthetic. In synthetic speeches produced by the TTS algorithm, the spectral characteristics of the synthetic speech are altered to match the target speaker’s formant frequencies, while in VC attacks, the temporal alignment of the speech segments is manipulated to preserve the target speaker’s prosodic features. By highlighting these observations, this paper targets the prosodic and phonetic-based crafted features, i.e., the Mel-spectrogram, spectral contrast, and spectral envelope, presenting an effective preprocessing pipeline proven to be effective in synthetic speech detection. The proposed solution achieved state-of-the-art performance against eight recent feature fusion methods with lower EER of 0.95% on the ASVspoof-LA dataset, demonstrating its potential to advance the field of speaker identification and improve speaker recognition systems. 

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5. Next generation synthetic memory via intercepting recombinase function

   Short, A.E. ( October 2023 , Nature communications)

   Ross Cloney (Ed.)

   Here we present a technology to facilitate synthetic memory in a living system via repurposing Transcriptional Programming (i.e., our decision-making technology) parts, to regulate (intercept) recombinase function post-translation. We show that interception synthetic memory can facilitate programmable loss-of-function via site-specific deletion, programmable gain-of-function by way of site-specific inversion, and synthetic memory operations with nested Boolean logical operations. We can expand interception synthetic memory capacity more than 5-fold for a single recombinase, with reconfiguration specificity for multiple sites in parallel. Interception synthetic memory is ~10-times faster than previous generations of recombinase-based memory. We posit that the faster recombination speed of our next-generation memory technology is due to the post-translational regulation of recombinase function. This iteration of synthetic memory is complementary to decision-making via Transcriptional Programming – thus can be used to develop intelligent synthetic biological systems for myriad applications. 

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