Optical two-dimensional (2D) coherent spectroscopy excels in studying coupling and dynamics in complex systems. The dynamical information can be learned from lineshape analysis to extract the corresponding linewidth. However, it is usually challenging to fit a 2D spectrum, especially when the homogeneous and inhomogeneous linewidths are comparable. We implemented a machine learning algorithm to analyze 2D spectra to retrieve homogeneous and inhomogeneous linewidths. The algorithm was trained using simulated 2D spectra with known linewidth values. The trained algorithm can analyze both simulated (not used in training) and experimental spectra to extract the homogeneous and inhomogeneous linewidths. This approach can be potentially applied to 2D spectra with more sophisticated spectral features.
more »
« less
Cutting through the Noise: Extracting Dynamics from Ultrafast Spectra Using Dynamic Mode Decomposition
Coherent multidimensional spectroscopy provides experimental access to molecular structure and subpicosecond dynamics in solution. Dynamics are typically inferred from the evolution of lineshapes over a function of waiting time. Numerous spectral analysis methods, such as center/nodal line slope, have been developed to extract these dynamics. However, the extracted dynamics can depend heavily on subjective choices, such as the region selected for CLS analysis or the chosen models. In this study, we introduce a novel approach to extracting dynamics from ultrafast two-dimensional infrared (2D IR) spectra by using dynamic mode decomposition (DMD). As a data-driven method, DMD directly extracts spatiotemporal structures from the complex 2D IR spectra. We evaluated the performance of DMD in simulated and experimental spectra containing overlapped peaks. We show that DMD can retrieve the dynamics of overlapped transitions and cross peaks that are typically challenging to extract with traditional methods. In addition, we demonstrate that combining conditional generative adversarial neural networks with DMD can recover dynamics even at low signal-to-noise ratios. DMD methods do not require preliminary assumptions and can be readily extended to other multidimensional spectroscopies.
more »
« less
- Award ID(s):
- 1847199
- PAR ID:
- 10532363
- Publisher / Repository:
- American Chemical Society
- Date Published:
- Journal Name:
- The Journal of Physical Chemistry A
- Volume:
- 127
- Issue:
- 46
- ISSN:
- 1089-5639
- Page Range / eLocation ID:
- 9853 to 9862
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Currently, it is challenging to investigate aneurismal hemodynamics based on current in vivo data such as Magnetic Resonance Imaging or Computed Tomography due to the limitations in both spatial and temporal resolutions. In this work, we investigate the use of modal analysis at various resolutions to examine its usefulness for analyzing blood flows in brain aneurysms. Two variants of Dynamic Mode Decomposition (DMD): (i) Hankel-DMD; and (ii) Optimized-DMD, are used to extract the time-dependent dynamics of blood flows during one cardiac cycle. First, high-resolution hemodynamic data in patient-specific aneurysms are obtained using Computational Fluid Dynamics. Second, the dynamics modes, along with their spatial amplitudes and temporal magnitudes are calculated using the DMD analysis. Third, an examination of DMD analyses using a range of spatial and temporal resolutions of hemodynamic data to validate the applicability of DMD for low-resolution data, similar to ones in clinical practices. Our results show that DMD is able to characterize the inflow jet dynamics by separating large-scale structures and flow instabilities even at low spatial and temporal resolutions. Its robustness in quantifying the flow dynamics using the energy spectrum is demonstrated across different resolutions in all aneurysms in our study population. Our work indicates that DMD can be used for analyzing blood flow patterns of brain aneurysms and is a promising tool to be explored in in vivo.more » « less
-
The third-order response lies at the heart of simulating and interpreting nonlinear spectroscopies ranging from two-dimensional infrared (2D-IR) to 2D electronic (2D-ES), and 2D sum frequency generation (2D-SFG). The extra time and frequency dimensions in these spectroscopic techniques provide access to rich information on the electronic and vibrational states present, the coupling between them, and the resulting rates at which they exchange energy that are obscured in linear spectroscopy, particularly for condensed phase systems that usually contain many overlapping features. While the exact quantum expression for the third-order response is well established, it is incompatible with the methods that are practical for calculating the atomistic dynamics of large condensed phase systems. These methods, which include both classical mechanics and quantum dynamics methods that retain quantum statistical properties while obeying the symmetries of classical dynamics, such as LSC-IVR, centroid molecular dynamics, and Ring Polymer Molecular Dynamics (RPMD), naturally provide short-time approximations to the multi-time symmetrized Kubo transformed correlation function. Here, we show how the third-order response can be formulated in terms of equilibrium symmetrized Kubo transformed correlation functions. We demonstrate the utility and accuracy of our approach by showing how it can be used to obtain the third-order response of a series of model systems using both classical dynamics and RPMD. In particular, we show that this approach captures features such as anharmonically induced vertical splittings and peak shifts while providing a physically transparent framework for understanding multidimensional spectroscopies.more » « less
-
A method for directly calculating the temperature derivative of two-dimensional infrared (2D-IR) spectra from simulations at a single temperature is presented. The approach is demonstrated by application to the OD stretching spectrum of isotopically dilute aqueous (HOD in H 2 O) solutions of urea as a function of concentration. Urea is an important osmolyte because of its ability to denature proteins, which has motivated significant interest in its effect on the structure and dynamics of water. The present results show that the temperature dependence of both the linear IR and 2D-IR spectra, which report on the underlying energetic driving forces, is more sensitive to urea concentration than the spectra themselves. Additional physical insight is provided by calculation of the contributions to the temperature derivative from different interactions, e.g., water–water, water–urea, and urea–urea, present in the system. Finally, it is demonstrated how 2D-IR spectra at other temperatures can be obtained from only room temperature simulations.more » « less
-
Thiocyanates, nitriles, and azides represent a versatile set of vibrational probes to measure the structure and dynamics in biological systems. The probes are minimally perturbative, the nitrile stretching mode appears in an otherwise uncongested spectral region, and the spectra report on the local environment around the probe. Nitrile frequencies and lineshapes, however, are difficult to interpret, and theoretical models that connect local environments with vibrational frequencies are often necessary. However, the development of both more accurate and intuitive models remains a challenge for the community. The present work provides an experimentally consistent collection of experimental measurements, including IR absorption and ultrafast two-dimensional infrared (2D IR) spectra, to serve as a benchmark in the development of future models. Specifically, we catalog spectra of the nitrile stretching mode of methyl thiocyanate (MeSCN) in fourteen different solvents, including non-polar, polar, and protic solvents. Absorption spectra indicate that π-interactions may be responsible for the line shape differences observed between aromatic and aliphatic alcohols. We also demonstrate that a recent Kamlet–Taft formulation describes the center frequency MeSCN. Furthermore, we report cryogenic infrared spectra that may lead to insights into the peak asymmetry in aprotic solvents. 2D IR spectra measured in protic solvents serve to connect hydrogen bonding with static inhomogeneity. We expect that these insights, along with the publicly available dataset, will be useful to continue advancing future models capable of quantitatively describing the relation between local environments, line shapes, and dynamics in nitrile probes.more » « less
An official website of the United States government

