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Amperometry is a commonly used electrochemical method for studying the process of exocytosis in real-time. Given the high precision of recording that amperometry procedures offer, the volume of data generated can span over several hundreds of megabytes to a few gigabytes and therefore necessitates systematic and reproducible methods for analysis. Though the spike characteristics of amperometry traces in the time domain hold information about the dynamics of exocytosis, these biochemical signals are, more often than not, characterized by time-varying signal properties. Such signals with time-variant properties may occur at different frequencies and therefore analyzing them in the frequency domain may provide statistical validation for observations already established in the time domain. This necessitates the use of time-variant, frequency-selective signal processing methods as well, which can adeptly quantify the dominant or mean frequencies in the signal. The Fast Fourier Transform (FFT) is a well-established computational tool that is commonly used to find the frequency components of a signal buried in noise. In this work, we outline a method for spike-based frequency analysis of amperometry traces using FFT that also provides statistical validation of observations on spike characteristics in the time domain. We demonstrate the method by utilizing simulated signals and by subsequently testing it on diverse amperometry datasets generated from different experiments with various chemical stimulations. To our knowledge, this is the first fully automated open-source tool available dedicated to the analysis of spikes extracted from amperometry signals in the frequency domain., Comment: 34 pages, 16 figures

Elucidating exocytosis processes provide insights into cellular neurotransmission mechanisms, and may have potential in neurodegenerative diseases research. Amperometry is an established electrochemical method for the detection of neurotransmitters released from and stored inside cells. An important aspect of the amperometry method is the sub-millisecond temporal resolution of the current recordings which leads to several hundreds of gigabytes of high-quality data. In this study, we present a universal method for the classification with respect to diverse amperometric datasets using data-driven approaches in computational science. We demonstrate a very high prediction accuracy (greater than or equal to 95%). This includes an end-to-end systematic machine learning workflow for amperometric time series datasets consisting of pre-processing; feature extraction; model identification; training and testing; followed by feature importance evaluation - all implemented. We tested the method on heterogeneous amperometric time series datasets generated using different experimental approaches, chemical stimulations, electrode types, and varying recording times. We identified a certain overarching set of common features across these datasets which enables accurate predictions. Further, we showed that information relevant for the classification of amperometric traces are neither in the spiky segments alone, nor can it be retrieved from just the temporal structure of spikes. In fact, the transients between spikes and the trace baselines carry essential information for a successful classification, thereby strongly demonstrating that an effective feature representation of amperometric time series requires the full time series. To our knowledge, this is one of the first studies that propose a scheme for machine learning, and in particular, supervised learning on full amperometry time series data., Comment: 56 pages, 11 figures

Turbulence is still one of the main challenges for accurately predicting reactive flows. Therefore, the development of new turbulence closures which can be applied to combustion problems is essential. Data-driven modeling has become very popular in many fields over the last years as large, often extensively labeled, datasets became available and training of large neural networks became possible on GPUs speeding up the learning process tremendously. However, the successful application of deep neural networks in fluid dynamics, for example for subgrid modeling in the context of large-eddy simulations (LESs), is still challenging. Reasons for this are the large amount of degrees of freedom in realistic flows, the high requirements with respect to accuracy and error robustness, as well as open questions, such as the generalization capability of trained neural networks in such high-dimensional, physics-constrained scenarios. This work presents a novel subgrid modeling approach based on a generative adversarial network (GAN), which is trained with unsupervised deep learning (DL) using adversarial and physics-informed losses. A two-step training method is used to improve the generalization capability, especially extrapolation, of the network. The novel approach gives good results in a priori as well as a posteriori tests with decaying turbulence including turbulent mixing. The applicability of the network in complex combustion scenarios is furthermore discussed by employing it to a reactive LES of the Spray A case defined by the Engine Combustion Network (ECN)., Comment: Submitted to Combustion Symposium 2020