Bulletin of the American Physical Society
APS March Meeting 2021
Volume 66, Number 1
Monday–Friday, March 15–19, 2021; Virtual; Time Zone: Central Daylight Time, USA
Session Y18: Dynamics and Kinetics in Chemical PhysicsLive
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Sponsoring Units: DCP Chair: Michael Heaven, Emory University |
Friday, March 19, 2021 11:30AM - 11:42AM Live |
Y18.00001: Predicting second virial coefficients: a Gaussian process regression approach Miruna Cretu, Jesús Pérez-Ríos Second virial coefficients represent a robust tool for describing the departure from ideality of a gas based on 2 body interactions in a system. The applications of second virial coefficients are diverse, ranging from the estimation of fluid properties to crystal growth, hence the broad interest in its calculation over the years. We propose the calculation of second virial coefficients within the new paradigm of data-intensive science, as an alternative to traditional methods. Our approach involves devising a set of predictors based on physical and chemical intuition, which encapsulates the most relevant features to 2-body interactions in a system. This is used jointly with Gaussian process regression to yield predictions of second virial coefficients for both organic and inorganic compounds. We explore the extrapolation and transferability capabilities of our model and show that good accuracy can be obtained in machine learning with the use of physico-chemical properties and molecular fingerprints solely selected using domain intuition and judgement, rather than canonical feature selection algorithms and universal descriptors. |
Friday, March 19, 2021 11:42AM - 11:54AM Live |
Y18.00002: Optimal inference of molecular interaction from live-cell FRET imaging Keita Kamino, Kazuhiro Aoki, Thierry Emonet Signal-to-noise ratio (SNR) ultimately limits what we can learn from data. Intensity-based fluorescence resonance energy transfer (FRET) is a widely-used technique to convert the molecular interaction or conformational change in living cells into fluorescent signals that are detected under a microscope, allowing experimenters to infer molecular states in a non-invasive manner. However, existing data-analysis methods turn to algebraic manipulation of the noise-corrupted observables, resulting in the loss of information stored in the raw data at the cost of interpretability of results. Here, we present a novel computational FRET method by exploiting the framework of Bayesian filtering. Based on the direct computation of the Bayesian posterior, the method provides statistically optimal inference of molecular interaction, and thus achieves significantly higher SNR than existing methods. We quantify how the new approach outperforms existing methods using artificial data with various properties, and demonstrate the efficacy using real data obtained from both unimolecular and bimolecular FRET reporter molecules in living cells. |
Friday, March 19, 2021 11:54AM - 12:06PM Live |
Y18.00003: Feasibility Study of SSTO Programs Using Thermodynamic Properties Conor McGibboney, Eric C. Booth The purpose of this research is to study the feasibility of Liquid Air Cycle Engines (LACE) and Air Collection and Enrichment System (ACES) for single stage to orbit (SSTO) space programs. Various thermodynamic properties such as the Joule-Thomson effect, Para-to-Ortho hydrogen spin conversion, and general heat exchanger performance are used to determine feasibility on a fundamental theoretical level. For LACE we examined the condensation ratio (CR) kg air condensed by kg H2 coolant used, and examined how much variations in pressure, as well as Para-to-Ortho hydrogen conversion would aid heat-exchanger efficiency. No matter what is done, we cannot achieve a desired CR that is close to the needed stoichiometric ratio of 34.4. For ACES we examined CR with and without precooling with excess N2. Remarkably, precooling intake air with nitrogen worsens performance dramatically. The deficiency that causes ACES to be counterproductive is that, below 165 Kelvin, the proportional rise in the constant pressure heat capacity (Cp) of air is much greater than the proportional fall in the Cp of para-H2. Additionally, massive system components needed for precooling and heat-exchange would need to be carried to space on the vehicle thus, further reducing efficiency. |
Friday, March 19, 2021 12:06PM - 12:18PM Live |
Y18.00004: Probing the Water H-Bonding Network in Superconcentrated Aqueous Electrolytes with 2DIR Spectroscopy Nicholas Lewis, Bogdan Dereka, Andrei Tokmakoff Superconcentrated electrolytes have recently emerged as a promising material for various electrochemical applications, such as batteries and supercapacitors. These materials contain ions at concentrations comparable to, or greater than, the concentration of the solvent and can possess beneficial properties such as expanded electrochemical windows. Many fundamental questions about these materials remain, such as the details of the molecular-scale morphology and dynamics and how these relate to the ionic conductivity. Here we use ultrafast 2DIR spectroscopy to study the aqueous LiTFSI solutions as a function of concentration from the dilute to the superconcentrated regimes, focusing on the changes to the water H2O stretch vibrational mode as well as the intra- and inter-molecular coupling to the H2O bend and TFSI- asymmetric SO2 stretch modes. We observe characteristic signatures of the disruption of the H2O H-bonding network at increasing concentration of the salt, with no bulk-like water remaining at the superconcentrated limit, being replaced only by isolated water and linear H-bonding networks. This has important implications for the dominant mechanism of Li+ diffusion in these solutions, supporting the predominance of structural over vehicular transport. |
Friday, March 19, 2021 12:18PM - 12:30PM Live |
Y18.00005: Constructive Quantum Interference in a Photo-Chemical Reaction of BEC Sumit Suresh Kale, Sabre Kais Interferences emerge when multiple pathways coexists together leading towards the same result. A recent study by Yong and coworkers (PRL 121, 073202, 2018) showed that in a photo-association reaction of Raman dressed spin-orbit coupled 87Rb Bose-Einstein Condensate when the reactant spin state is prepared in a coherent superposition of multiple bare spin states it leads to destructive interference between reaction pathways. Here we report a theoretical study suggesting the existence of a reaction scheme which leads to constructive quantum interference. This can be achieved by changing the reactive scattering channel in the reaction and our results show that interferences can be used as a resource for the coherent control of a Photo-chemical reaction. |
Friday, March 19, 2021 12:30PM - 12:42PM Live |
Y18.00006: Kinetics of the reactions of BrHg radical with NO2 and O3 Rongrong Wu, Chuji Wang, Theodore S Dibble Laser photolysis-laser induced fluorescence (LP-LIF) spectroscopy was used for the first experimental kinetic study of the atmospherically important reactions of BrHg + Y, where Y is the abundant free radicals in the atmosphere, such as NO2 and O3. We measured the rate constants of the reactions of BrHg + Y versus temperature (313 – 373 K) and pressure (80 – 700 Torr), and derived the parameters of the Troe expression to assist the modeling of atmospheric mercury redox. The experimental result of the reaction of BrHg + NO2 was compared with the previous computational study, which confirmed that the major competing channel should be assigned to the predicted mercury reduction reaction. The addition rate constants in the high-pressure limit of the two studies are consistent, but the discrepancies suggest that the computation has overestimated the efficiency of collisional energy transfer, which leads to an overestimation of the rate constants in the low-pressure limit. The result of the reaction of BrHg + O3 suggests a significant side reaction – BrHgO + O3 → BrHg + 2O2 – that hasn’t been studied before. |
Friday, March 19, 2021 12:42PM - 12:54PM Live |
Y18.00007: Ultrafast two-dimensional infrared (2DIR) spectroscopy in dense gases and supercritical fluids: Rotational and vibrational energy relaxation, critical slowing, and the onset of liquid character Matthew Rotondaro, Shyamsunder Erramilli, Lawrence Ziegler Ultrafast two-dimensional infrared (2DIR) spectroscopy is used to learn about rotational and vibrational energy relaxation in dense gas and supercritical fluid solutions, special solvation effects near the critical point, and the evolution of liquid phase dynamics as a function of fluid density from that of a gas to the near liquid regime. The echo character of 2DIR results in unique spectral signatures that identify free quantum rotors and solvated liquid-like environments within the same dense fluid sample, and allows evaluation of the adequacy of isolated binary collision (IBC) relaxation models at these high densities. Analysis of the 2DIR spectra of the asymmetric stretching band of N2O in SF6 and Xe reveal efficient rotational energy relaxation rates (1.5 – 3 collisions) but much slower vibrational energy relaxation rates. A critical slowing effect is found on the rate of J relaxation and liquid-like solvation is evident in dense gas solutions at gas state points far from the critical region. This methodology provides new molecular-level insights into the nature of the supercritical region and our understanding of small molecule relaxation in dense fluid environments. |
Friday, March 19, 2021 12:54PM - 1:06PM Live |
Y18.00008: Enhancing the performance of cobalt porphyrin-based electrocatalysts for CO2 reduction Tanglaw Roman, Oliver Conquest, Aleksei Marianov, Yijiao Jiang, Catherine Stampfl The rise in global atmospheric carbon dioxide concentration since the beginning of the industrial era has been found an 'extremely likely' cause of the observed warming of our climate system since the mid-20th century. Concerted efforts among nations to lower CO2 emissions can help avert a crisis, but a possible stronger response is reversing the process through technology that efficiently catalyzes CO2 electroreduction. Carbon-supported first row transition metal complexes drive the reduction of CO2 with remarkable activity and selectivity; however, their durability is quite low and the mechanisms behind the catalysts’ deactivation are still unclear. |
Friday, March 19, 2021 1:06PM - 1:18PM Live |
Y18.00009: Applications of Kinetic Monte Carlo Simulations and Machine Learning to model Atomic Layer Deposition (ALD) of Metal Oxides. David Magness, Emily Justus, Bikash Timalsina, Judy Zhihong Wu, Ridwan Sakidja Metal-oxides such as ZnO or Al2O3 synthesized through Atomic Layer Deposition (ALD) have been of great research interests as the candidate materials for ultra-thin tunnel barrier layers is. In this study, we have applied a 3D on-lattice Kinetic Monte Carlo (kMC) code developed by Timo Weckman’s group to simulate the growth mechanisms of the tunnel barrier layer and to evaluate the role of various experimentally relevant factors of the ALD processes. We have systematically studied the effect of parameters such as the chamber pressure and temperature, pulse/purge times, as well as the coverage of wetting layer on the substrate. The database generated from the kMC simulations was subsequently used as descriptors in the subsequent analyses via Machine Learning algorithms. The results of a combined approach of kMC and ML were then compared to the experimental results. The support from NSF (EPMD Division) Award No. 1809284 and the computational support from NERSC are gratefully acknowledged. |
Friday, March 19, 2021 1:18PM - 1:30PM Live |
Y18.00010: Anharmonic spectroscopic features in quasiclassical dynamics: the importance of the quantum initial conditions Thomas PLE, Simon Huppert, Fabio Finocchi, Philippe Depondt, Sara Bonella Practical approaches for the simulation of quantum nuclear dynamics often combine sampling of a set of quantum initial conditions with their (quasi)classical time-evolution. Observable properties, in particular spectra, are then computed from appropriate averages over these trajectories. In this talk, we combine a perturbative analysis with numerical calculations to examine more in detail the performance of different quasiclassical approaches to capture overtones, combination bands, and Fermi resonances in model systems of increasing complexity. We show that the recently introduced Edgeworth approximation for the sampling of the Wigner quantum density [1] allows capturing these anharmonic spectroscopic features accurately (exactly at lowest perturbation order). Our results highlight the importance of capturing some inherently quantum aspects of the Wigner distribution (in particular position-momentum correlations) in order to reproduce finer spectral features which are often considered out-of-reach of quasiclassical methods due to their lack of quantum coherence effects. |
Friday, March 19, 2021 1:30PM - 1:42PM Live |
Y18.00011: Stochastic thermodynamics of the transition path ensemble Miranda Louwerse, David Sivak The reaction coordinate is a fundamental concept in the theory of chemical reactions, yet a precise definition and methodology for finding the reaction coordinate is an unsolved problem of theoretical and computational interest. In many applications from biology to materials design, a reaction may be studied in simulation by monitoring or controlling a few physical coordinates of the system (ie. dihedral angles, bond lengths, etc.). Currently, this choice of coordinates relies on human intuition about the reaction mechanism and may miss unintuitive but important details. It is thus desirable to develop procedures for determining which physical coordinates contribute to the overall reaction and which coordinates are unimportant. We investigate the committor as a definition of the reaction coordinate, the probability that a trajectory initiated from a given system state will next reach the products before the reactants, and find that the committor is the only 1D coordinate of the system that contains all information about the reaction dynamics. We discuss how work transfer from one coordinate to the rest of the system during a reaction indicates how that coordinate contributes to the reaction mechanism. We use these ideas to study the spin-inversion mechanism for a 2D Ising model. |
Friday, March 19, 2021 1:42PM - 1:54PM Live |
Y18.00012: More and Faster: Simultaneously Improving Reaction Coverage and Computational Cost in Automated Reaction Prediction Tasks Qiyuan Zhao, Brett Savoie Automated reaction prediction has the potential to elucidate complex reaction networks for applications ranging from combustion to materials degradation. Although substantial progress has been made in predicting specific reaction pathways, the computational cost and inconsistent reaction coverage of automated reaction prediction are still obstacles to exploring deep reaction networks. Here we show that cost can be reduced and reaction coverage can be increased simultaneously by modifications of the reaction enumeration, geometry initialization, and transition state convergence algorithms. These changes are implemented in the context of Yet Another Reaction Program (YARP), our reaction prediction package. Compared with prevailing methods, YARP near perfectly reproduces established reaction pathways and products, without the use of domain knowledge. In addition, YARP also discovers new kinetically relevant reaction pathways. This is achieved while simultaneously reducing the cost of reaction characterization nearly 100-fold and increasing transition state intended rates over 10-fold. This combination of ultra-low cost and high reaction-coverage creates opportunities to explore the reactivity of larger systems and more complex reaction networks. |
Friday, March 19, 2021 1:54PM - 2:06PM Live |
Y18.00013: Investigating the role of catalyst activity in nanocatalysed self-oscillating chemical reactions via bifurcation analyses Vandana Rajput, Pratyush Dayal Reaction-Diffusion (RD) based self-sustained oscillatory reactions have been used to design various biomimetic stimuli-responsive systems. Belousov Zhabotinsky (BZ) reactions are nonlinear chemical oscillators, that undergo periodic oscillations due to redox-cycle of metal-ion catalyst, by virtue of Hopf bifurcation. Recently, we have shown that the kinetics of BZ reaction is enhanced by using heterogenous nanocatalysts, namely, Ce/Ru nanoparticles decorated graphene nanocomposites and bare Ce nanosheets. Moreover, the kinetics of these nanocatalysed BZ reaction can be modelled by introducing catalyst activity in the Oregonator model. Here, we use bifurcation analysis to investigate the role of catalytic activity on the oscillatory characteristics of BZ reaction. In particular, we compute higher order Lyapunov and frequency coefficients, with catalytic activity as the bifurcation parameter, to determine oscillatory regimes, amplitude and frequency of BZ oscillations. Our investigations reveal re-entrant regions in the bifurcation diagram where sustained oscillations are unexpectedly suppressed, even with high catalytic activity. Our findings can be used to exploit nonlinearity of RD based dynamical systems for biomimetic applications. |
Friday, March 19, 2021 2:06PM - 2:18PM Live |
Y18.00014: Understanding the role of sulfur in controlling carbon monoxide reactivity on iron surface: A DFT and Microkinetic perspective Omotayo Salawu, El Tayeb Bentria, Heesoo Park, Othmane Bouhali, Fadwa El Mellouhi The corrosive disintegration of metals and their alloys into fine particles occurring in carbon saturated environment at catalytic operating temperatures might lead to serious economic implications on several industrial processes especially in the oil and gas sector. One way proposed to tackle this issue during operation involves the addition of Sulfur-based compound/gases. The addition of small concentration of H2S to syngas mixture has been shown to prevent failure of the reactors. In order to effectively validate this approach, it is essential to understand at the atomic scale the role of S on the reaction of CO on the metal surface. A combination of plane waves first principles approach and microkinetic was employed to study clean and defective iron surfaces as well as surfaces with CO, S, CO+S adsorbates, aiming to investigate the effect of S as an inhibiting agent in the carburization process of Fe. Our investigation looks to determine if the blocking effect acts at a short or long-range effect. The presence of S is found to reduce the adsorption energy of CO on Iron hence lowering the sticking and dissociative probabilities. |
Friday, March 19, 2021 2:18PM - 2:30PM On Demand |
Y18.00015: Modeling the Argon bombardment and densification of Low-Temperature Organic Precursors using Reactive Molecular Dynamics Simulations and Machine Learning Kwabena Asante Boahen, Nirmal Baishnab, Ridwan Sakidja In this study, we have systematically modeled the Argon bombardment and densification of the low-temperature processed organic precursors such as orthocarborane molecules to produce structural ceramics such as boron-carbide by using reactive Molecular Dynamics (MD) simulations. The simulations were employed to track and evaluate the interaction of Ar and the precursors to produce radicals and the densification processes of the aggregates generated from the bombardments. In addition, we identified and quantified the key chemical reactions associated with these processes by applying the Machine Learning (ML) algorithm into the database generated from the reactive MD simulations. The combined MD and ML approach has provided us with more insights into the overall mechanism. The support from the NSF-DMREF program (Award No. 1729176) is gratefully acknowledged. |
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