Pump Slice Amplitudes: A Simple and Robust Method for Connecting Two-Dimensional Infrared and Fourier Transform Infrared Spectra

Valentine, Mason L.; Al-Mualem, Ziareena; Baiz, Carlos R.

doi:10.1021/acs.jpca.1c04558

Cited by 24 publications

(21 citation statements)

References 51 publications

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“…This analysis generates a spectrum that is comparable to the absorption spectrum of the same system. 58 The comparison between the reconstructed and ground truth PSA spectra in the figure more clearly shows that the reconstructed spectra closely match the ground truth. However, it is apparent that the peaks in the reconstructed spectra are slightly broader compared to the ground truth.…”

Section: ■ Results and Discussionmentioning

confidence: 69%

“…The PSA analysis is described elsewhere, but in brief, the difference between the maximum and minimum amplitudes along ω 3 for a given ω 1 slice is measured. This analysis generates a spectrum that is comparable to the absorption spectrum of the same system . The comparison between the reconstructed and ground truth PSA spectra in the figure more clearly shows that the reconstructed spectra closely match the ground truth.…”

Section: Resultsmentioning

confidence: 77%

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Generative Adversarial Neural Networks for Denoising Coherent Multidimensional Spectra

Al-Mualem

Baiz

2022

J. Phys. Chem. A

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Ultrafast spectroscopy often involves measuring weak signals and long data acquisition times. Spectra are typically collected as a "pump−probe" spectrum by measuring differences in intensity across laser shots. Shot-to-shot intensity fluctuations are most often the primary source of noise in ultrafast spectroscopy. Here, we present a novel approach for denoising ultrafast twodimensional infrared (2D IR) spectra using conditional generative adversarial neural networks (cGANNs). The cGANN approach is able to eliminate shot-toshot noise and reconstruct the line shapes present in the noisy input spectrum. We

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Section: ■ Results and Discussionmentioning

confidence: 69%

Section: Resultsmentioning

confidence: 77%

Generative Adversarial Neural Networks for Denoising Coherent Multidimensional Spectra

Al-Mualem

Baiz

2022

J. Phys. Chem. A

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“…PSA analysis has been described in detail previously. [36] In brief, PSA is the difference between the maximum and minimum amplitudes along ω3 at slices along the excitation (pump) axis, which gives spectra that are comparable to the linear absorption spectra. Signal-to-noise ratios (SNR) were calculated for each waiting time and compared between fast-scan BoxCARS and pump-probe geometries (Figure 66a) in order to quantify the improvement in signal.…”

Section: Resultsmentioning

confidence: 99%

BoxCARS 2D IR Spectroscopy with Pulse Shaping

Al-Mualem

Chen

Shirley

et al. 2022

Preprint

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BoxCARS and pump-probe geometries are common implementations of two dimensional infrared (2D IR) spectroscopy. BoxCARS is background-free, generally offering greater signal to noise ratio, which enables measuring weak vibrational echo signals. Pulse shapers have been implemented in the pump probe geometry to accelerate data collection and suppress scatter and other unwanted signals by precise control of the pump pulse delay and carrier phase. Here, we introduce a 2D IR optical setup in the BoxCARS geometry that implements a pulse shaper for rapid acquisition of background-free 2D IR spectra. We show a 3x signal to noise improvement using this new fast-scan BoxCARS setup versus the pump probe geometry within the same configuration.

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“…The mathematical formalism for calculating TDS spectra using 2D IR spectroscopy has been described previously (35,36) and is summarized in the SI. In Figure 2, we overlay 2D IR linear traces (black) calculated via the pump slice amplitude method (38) with the corresponding calculated TDS spectra (red) for KFE8 and AcKFE8 after 24 hours of aggregation. While the linear slices are nearly identical for both variants, the TDS spectra differ considerably.…”

Section: Bodymentioning

confidence: 99%

Label-free detection of β-sheet polymorphism

Weeks

Buchanan

2022

Preprint

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The ability to detect and characterize multiple secondary structures or polymorphs within peptide and protein aggregates is crucial to treatment and prevention of amyloidogenic diseases, production of novel biomaterials, and many other applications. Here we report a label-free method to distinguish multiple β-sheet configurations within a single peptide aggregate using two-dimensional infrared spectroscopy. By calculating the transition dipole strength (TDS) spectrum from the ratio of linear and two-dimensional signals, we can extract maximum TDS values which provide higher sensitivity to vibrational coupling, and thus specifics of protein structure, than vibrational frequency alone. TDS spectra of AcKFE8 aggregates reveal two distinct β-sheet structures within fibers that appear homogenous by other techniques. Furthermore, TDS spectra taken during early stages of aggregation show additional peaks that may indicate the presence of more weakly coupled β-sheet structures. These results demonstrate a unique and powerful spectroscopic method capable of distinguishing multiple oligomeric and polymorphic motifs throughout the aggregation using only native vibrational modes.

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Pump Slice Amplitudes: A Simple and Robust Method for Connecting Two-Dimensional Infrared and Fourier Transform Infrared Spectra

Cited by 24 publications

References 51 publications

Generative Adversarial Neural Networks for Denoising Coherent Multidimensional Spectra

Generative Adversarial Neural Networks for Denoising Coherent Multidimensional Spectra

BoxCARS 2D IR Spectroscopy with Pulse Shaping

Label-free detection of β-sheet polymorphism

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