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At least 253 records · Page 14

Understanding flavin electronic structure and spectra

Abstract Flavins have emerged as central to electron bifurcation, signaling, and countless enzymatic reactions. In bifurcation, two electrons acquired as a pair are separated in coupled transfers wherein the energy of both is concentrated on one of the two. This enables organisms to drive demanding reactions based on abundant low‐grade chemical fuel. To enable incorporation of this and other flavin capabilities into designed materials and devices, it is essential to understand fundamental principles of flavin electronic structure that make flavins so reactive and tunable by interactions with protein. Emerging computational tools can now replicate spectra of flavins and are gaining capacity to explain reactivity at atomistic resolution, based on electronic structures. Such fundamental understanding can moreover be transferrable to other chemical systems. A variety of computational innovations have been critical in reproducing experimental properties of flavins including their electronic spectra, vibrational signatures, and nuclear magnetic resonance (NMR) chemical shifts. A computational toolbox for understanding flavin reactivity moreover must be able to treat all five oxidation and protonation states, in addition to excited states that participate in flavoprotein's light‐driven reactions. Therefore, we compare emerging hybrid strategies and their successes in replicating effects of hydrogen bonding, the surrounding dielectric, and local electrostatics. These contribute to the protein's ability to modulate flavin reactivity, so we conclude with a survey of methods for incorporating the effects of the protein residues explicitly, as well as local dynamics. Computation is poised to elucidate the factors that affect a bound flavin's ability to mediate stunningly diverse reactions, and make life possible. This article is categorized under: Structure and Mechanism > Computational Biochemistry and Biophysics Electronic Structure Theory > Combined QM/MM Methods Theoretical and Physical Chemistry > Spectroscopy

59 BASIC BIOLOGICAL SCIENCES↗

Investigating the Interaction Between Circulating Tumor Cells and Local Hydrodynamics via Experiment and Simulations

Introduction: The biological and mechanical properties of circulating tumor cells (CTCs) in combination with the hemodynamics affect the preference of metastatic sites in the vasculature. Despite the extensive literature on the effects of biological properties on cell adhesion, the effects of hydrodynamic forces on primary attachment remains an active area of research. Here, using simulations in conjunction with experimentation, we provide new insight into the interplay of CTCs dynamics and local hydrodynamics. Methods: A flow experiment of CTC attachment was performed within a bioprinted, double branching endothelialized vessel. Simulations of fluid flow and CTC transport in the reconstructed and idealized bifurcated vessel were respectively performed by HARVEY, our in-house massively parallel computational fluid dynamics solver. HARVEY is based on the lattice Boltzmann and finite element methods to model the fluid and cells dynamics. The immersed boundary method is employed for resolving the fluid–structure interaction. Results: CTC attachment was quantified experimentally at all regions of the complex vessel. The results demonstrate a clear preference for CTCs to attach at the branch points. To elucidate the effect of the vessel topology on the location of attachment, a fluid-only simulation was performed assessing the differences in the hydrodynamics along the vessel. CTC transport in idealized bifurcated vessels was subsequently studied to examine the effects of cell deformability on the local hydrodynamics patterns and, thus, the preference of attachment sites. Conclusions: The current work provides evidence on the correlation of the hydrodynamics forces arising from the vessel topology and CTC properties on the attachment regions.

60 APPLIED LIFE SCIENCES↗

SubTSBR to tackle high noise and outliers for data-driven discovery of differential equations

Data-driven discovery of differential equations has been an emerging research topic. We propose a novel algorithm subsampling-based threshold sparse Bayesian regression (SubTSBR) to tackle high noise and outliers. The subsampling technique is used for improving the accuracy of the Bayesian learning algorithm. It has two parameters: subsampling size and the number of subsamples. When the subsampling size increases with fixed total sample size, the accuracy of our algorithm goes up and then down. When the number of subsamples increases, the accuracy of our algorithm keeps going up. We demonstrate how to use our algorithm step by step and compare our algorithm with threshold sparse Bayesian regression (TSBR) for the discovery of differential equations. We show that our algorithm produces better results. We also discuss the merits of discovering differential equations from data and demonstrate how to discover models with random initial and boundary condition as well as models with bifurcations. The numerical examples are: (1) predator-prey model with noise, (2) shallow water equations with outliers, (3) heat diffusion with random initial and boundary condition, and (4) fish-harvesting problem with bifurcations.

97 MATHEMATICS AND COMPUTING↗

Stabilizing a strongly nonlinear structure through shaker dynamics in fixed frequency voltage control tests

Bifurcations are commonly encountered during force controlled swept and stepped sine testing of nonlinear structures, which generally leads to the so-called jump-down or jump-up phenomena between stable solutions. There are various experimental closed-loop control algorithms, such as control-based continuation and phase-locked loop, to stabilize dynamical systems through these bifurcations, but they generally rely on specialized control algorithms that are not readily available with many commercial data acquisition software packages. A recent method was developed to experimentally apply sequential continuation using the shaker voltage that can be readily deployed using commercially available software. By utilizing the stabilizing effects of electrodynamic shakers and the force dropout phenomena in fixed frequency voltage control sine tests, this approach has been demonstrated to stabilize the unstable branch of a nonlinear system with three branches, allowing for three multivalued solutions to be identified within a specific frequency bandwidth near resonance. Recent testing on a strongly nonlinear system with vibro-impact nonlinearity has revealed jumping behavior when performing sequential continuation along the voltage parameter, like the jump phenomena seen during more traditional force controlled swept and stepped sine testing. Here, this paper investigates the stabilizing effects of an electrodynamic shaker on strongly nonlinear structures in fixed frequency voltage control tests using both numerical and experimental methods. The harmonic balance method is applied to the coupled shaker-structure system with an electromechanical model to simulate the fixed voltage control tests and predict the stabilization for different parameters of the model. The simulated results are leveraged to inform the design of a set of experiments to demonstrate the stabilization characteristics on a fixture-pylon assembly with a vibro-impact nonlinearity. Through numerical simulation and experimental testing on two different strongly nonlinear systems, the various parameters that influence the stability of the coupled shaker-structure are revealed to better understand the performance of fixed frequency voltage control tests.

42 ENGINEERING↗

First-Principles Insights into Proton-Coupled Electron Transfer versus Hydrogen Evolution Reaction Selectivity from a Base-Appended Cobaltocene Mediator

Performing selective proton-coupled electron transfer (PCET) to substrates such as N 2 , CO 2 , and unsaturated organic molecules under electrochemical conditions requires the suppression of the competing hydrogen evolution reaction (HER). To address this challenge, our laboratory previously demonstrated a PCET mediator strategy using a dimethylaniline-appended cobaltocene complex, [(CpCoCp NMe2 )H] + , which performs selective reductive chemistry while suppressing the HER. However, the origin of the suppressed, yet still observable, HER has not been thoroughly established. In this work, we perform density functional theory (DFT) calculations to elucidate the HER mechanism involving this redox mediator and to provide atomistic insights into the bifurcation between the PCET and HER pathways. We find that protonation of the aniline moiety to form [CpCoCp NMe2H ] + is more favorable, both kinetically and thermodynamically, than formation of the ring-protonated species [(CpCo(Cp-H) NMe2 )] + . Furthermore, PCET to acetophenone is energetically more favorable via [CpCoCp NMe2H ] + than via [(CpCo(Cp-H) NMe2 )] +1/0 . In contrast, the most favorable HER pathway involves the ring-protonated Co(I) species. These results offer mechanistic insights into HER versus PCET bifurcation and establish guiding principles for designing PCET mediators for selective electroreductive transformations.

evolution reactions↗

Fermi acceleration in relativistic collisionless plasma shocks correlates with anisotropic energy gains

Collisionless shocks generated by two colliding relativistic electron-positron plasma shells are studied using particle-in-cell simulations. Shocks are mediated by the Weibel instability (WI), and the kinetic energy of the fastest accelerated particles is found to be anisotropically modified by WI-induced electric fields. Specifically, we show that all particles interacting with the shock bifurcate into two groups based on their final relativistic Lorentz factor γ: slow (γ < γ bf ) and fast (γ < γ bf ), where γ bf is the bifurcation Lorentz factor that was found to be approximately twice the initial (upstream) Lorentz factor γ0. We have found that the kinetic energies of the slow particles are equally affected by the longitudinal and transverse components of the shock electric field, whereas the fast particles are primarily accelerated by the transverse field component.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Conical intersection and coherent vibrational dynamics in alkyl iodides captured by attosecond transient absorption spectroscopy

The photodissociation dynamics of alkyl iodides along the C–I bond are captured by attosecond extreme-ultraviolet (XUV) transient absorption spectroscopy employing resonant ∼20 fs UV pump pulses. The methodology of previous experiments on CH3I [Chang et al., J. Chem. Phys. 154, 234301 (2021)] is extended to the investigation of a C–I bond-breaking reaction in the dissociative A-band of C2H5I, i-C3H7I, and t-C4H9I. Probing iodine 4d core-to-valence transitions in the XUV enables one to map wave packet bifurcation at a conical intersection in the A-band as well as coherent vibrations in the ground state of the parent molecules. Analysis of spectroscopic bifurcation signatures yields conical intersection crossing times of 15 ± 4 fs for CH3I, 14 ± 5 fs for C2H5I, and 24 ± 4 fs for i-C3H7I and t-C4H9I, respectively. Observations of coherent vibrations, resulting from a projection of A-band structural dynamics onto the ground state by resonant impulsive stimulated Raman scattering, indirectly reveal multimode C–I stretch and CCI bend vibrations in the A-bands of C2H5I, i-C3H7I, and t-C4H9I.

Chang, Kristina F. (ORCID:000000022315039X)↗

Thermite and intermetallic projectiles examined experimentally in air and inert gas environments

Intermetallic (aluminum and zirconium) and thermite (aluminum and molybdenum trioxide) projectiles were launched using a high velocity impact ignition testing system. The experiments were designed to simulate reactivity in high (argon) and low (air) altitude environments. The projectiles were launched into a chamber that included a steel target plate for projectile penetration before impacting a rear witness plate. The chamber was semi-sealed and instrumented for quasi-static pressure data. The results provide an understanding of energy release from the projectile materials and of the environmental influence on performance. The transient pressure traces provide insight into reaction kinetics. A bifurcation in transient pressure rise was an indication of a shift in reaction kinetics from the inherent reactive material to metal oxidation with the environment. The bifurcation was delayed by about 0.15 ms for the intermetallic relative to the thermite, evidence that the thermite reaction proceeded faster upon impact than the intermetallic. The two-step process (impact ignition of the reactive material followed by metal oxidation) was shown to produce higher energy conversion efficiencies than projectiles composed of pure fuel (i.e., aluminum) reported previously. Both reactive materials showed energy conversion efficiencies greater than 30% (for air) and 50% (for argon), and an explanation of underestimated efficiency and energy losses is provided. These results have implications for advancing formulations for ballistic applications. Structural reactive materials can be used to modify the effective reactivity of metal-containing formulations in varied atmospheric environments.

36 MATERIALS SCIENCE↗

The multichannel i -propyl + O2 reaction system: A model of secondary alkyl radical oxidation

The i-propyl + O2 reaction mechanism has been investigated by definitive quantum chemical methods to establish this system as a benchmark for the combustion of secondary alkyl radicals. Focal point analyses extrapolating to the ab initio limit were performed based on explicit computations with electron correlation treatments through coupled cluster single, double, triple, and quadruple excitations and basis sets up to cc-pV5Z. The rigorous coupled cluster single, double, and triple excitations/cc-pVTZ level of theory was used to fully optimize all reaction species and transition states, thus, removing some substantial flaws in reference geometries existing in the literature. The vital i-propylperoxy radical (MIN1) and its concerted elimination transition state (TS1) were found 34.8 and 4.4 kcal mol−1 below the reactants, respectively. Two β-hydrogen transfer transition states (TS2, TS2′) lie above the reactants by (1.4, 2.5) kcal mol−1 and display large Born–Oppenheimer diagonal corrections indicative of nearby surface crossings. An α-hydrogen transfer transition state (TS5) is discovered 5.7 kcal mol−1 above the reactants that bifurcates into equivalent α-peroxy radical hanging wells (MIN3) prior to a highly exothermic dissociation into acetone + OH. The reverse TS5 → MIN1 intrinsic reaction path also displays fascinating features, including another bifurcation and a conical intersection of potential energy surfaces. An exhaustive conformational search of two hydroperoxypropyl (QOOH) intermediates (MIN2 and MIN3) of the i-propyl + O2 system located nine rotamers within 0.9 kcal mol−1 of the corresponding lowest-energy minima.

Chemistry↗

Bistable random momentum transfer in a linear on-chip resonator

Optical switches and bifurcation rely on the nonlinear response of materials. Here, we demonstrate linear temporal bifurcation responses in a passive multimode microresonator, with strongly coupled chaotic and whispering gallery modes (WGMs). In microdisks, the chaotic modes exhibit broadband transfer within the deformed cavities, but their transient response is less explored and yields a random output of the analog signal distributed uniformly from “0” to “1.” Here, we build chaotic states by perturbing the multimode microring resonators with densely packed silicon nanocrystals on the waveguide surface. In vivo measurements reveal random and “digitized” output that ONLY populates around 0 and 1 intensity levels. The bus waveguide mode couples first to chaotic modes, then either dissipates or tunnels into stable WGMs. This binary pathway generates high-contrast, digitized outputs. In conclusion, the fully passive device enables real-time conversion of periodic clock signals into binary outputs with contrasts exceeding 12.3 dB, data rates of up to 10 7 · bits per second, and 20 dB dynamic range.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Electron ITB formation in EAST high poloidal beta plasmas under dominant electron heating

Abstract Plasma confinement and transport in tokamaks play a crucial role in the development of high poloidal beta steady-state operation scenarios. Therefore, it is very important to study the relevant mechanism of internal transport barriers (ITBs), which can help plasmas to obtain better confinement in order to achieve higher fusion gain. This paper mainly introduces the analysis of the characteristics of electron heat transport of discharges with ITB in high β P operation regime in Experimental Advanced Superconducting Tokamak (EAST). Based on the statistical analysis of stable discharges with β P > 1.5, it is found that there is an obvious bifurcation of the normalised electron temperature gradient (ETG) ( R / L T e ) in the range of β P = 2–2.2. Then the discharges of lower β P ( β P < 2, where the value of β P is below the bifurcation threshold) and of higher β P ( β P > 2.2, where the value of β P is above the threshold) were selected for analysis. The diagnostic data provided by Thomson scattering, x-ray crystal spectrometry and charge exchange recombination spectroscopy are used to provide reliable parameter profiles and then combined with the data of external magnetic probe measurements and the polarisation interferometer diagnosis system to fully reconstruct the balance. A relevant plasma current calculation model is used to calculate and analyse the current density profiles and power deposition, and then the transport analysis is carried out. Interestingly, in the higher β P discharges, it is found that the turbulence intensity provided by the CO 2 laser collective scattering system gradually decreases and the normalised ETG R / L T e gradually increases. It is also found that the electron heat transport coefficient decreases in the discharge with higher β P and the growth rate of the electron-scale turbulence calculated by transport gyro-Landau fluid (TGLF) is significantly reduced. Meanwhile, similar conclusions are also obtained in the discharges when the β P is further increased.

Wang, Z. H. (ORCID:0009000203431036)↗

Effectiveness and nonlinear characterization of vibro-impact energy harvesting absorbers in controlling base-excited systems

In this study, model derivations are carried out of a dynamical system under base excitations with a piezoelectric energy harvesting absorber as the tuned-mass-damper. Additionally, amplitude stoppers are included to the absorber in order to create a broadband resonant response, increasing the window of operational use for energy harvesting and system's control. This study is unique in the fact that the energy harvester is coupled to the source of its excitation. A nonlinear reduced-order model is developed using Euler–Lagrange principle and the Galerkin method to accurately estimate the energy harvesting absorber's displacement, harvested power, and the oscillating response of the primary structure. The nonlinear interaction of the energy harvesting absorber and the amplitude stoppers are the focus of this study, where an in-depth investigation of bifurcation points of the primary structure and energy harvesting absorber responses is performed. Due to a transfer of energy between the primary structure and the absorber, it is shown that a soft stopper with stiffness $5 \times {10^3}\,{\text{N}}\;{{\text{m}}^{ - 1}}\,$ has great control of the primary structure with 60% of the uncontrolled amplitude being reduced, as well as an increase of the harvested energy. Medium stoppers with small initial gaps size and hard stoppers do not control the primary structure and show a decrease in the energy harvesting capabilities due to the activation of the nonlinear contact-impact interactions. Finally, these stoppers also generate aperiodic regions due to the possible presence of grazing bifurcations.

36 MATERIALS SCIENCE↗

Progress in DIII-D towards validating divertor power exhaust predictions

In this study, UEDGE simulations highlight the role of cross-field drifts on the onset of detached conditions, and new calibrated divertor vacuum ultra violet (VUV) spectroscopy is used to challenge the predictions of radiative constituents in these simulations. UEDGE simulations for DIII-D H-mode plasmas with the open divertor with the ion ∇B-drift towards the X-point show a bifurcated onset of the low field side (LFS) divertor detachment, consistent with experimentally observed step-like detachment onset (Jaervinen A.E. et al 2018 Phys. Rev. Lett. 121 075001). The divertor plasma in the simulations exhibits hysteresis in upstream separatrix density between attached and detached solution branches. Reducing the drift magnitude by a factor of 3 eliminates the step-like detachment onset in the simulations, confirming the strong role of drifts in the bifurcated detachment onset. When measured local plasma densities and temperatures are within proximity of predicted values in the simulations, there is no shortfall of the local emission of the dominant resonant radiating lines. However, the simulations systematically predict a factor of two lower total integrated radiated power than measured by the bolometer with the difference lost through radial heat flow out of the computational domain. Even though there is no shortfall in the emission of the dominant lines, a shortfall of total radiated power can be caused by underpredicted spatial extent of the radiation front, indicating a potential upstream or divertor transport physics origin for the radiation shortfall, or shortfall of radiated power in the spectrum between the dominant lines. In addition to the underpredicted spatial extent, in detached conditions, the simulations overpredict the peak radiation and dominant carbon lines near the X-point, which can be alleviated by manually increasing divertor diffusivity in the simulations, highlighting the ad hoc cross-field transport as one of the key limitations of the predictive capability of these divertor fluid codes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Experimental inference of flux tunneling between magnetic island chains in tokamaks

We report confinement bifurcations due to flux tunneling in magnetic islands in toroidal plasmas. This occurs in 2/1 islands, triggered by decoupling of non-overlapping adjacent 5/2 islands. While subject to electron cyclotron current drive (ECCD), the temperature at the 2/1 O-point is flat before but peaks after decoupling. Here, this is shown to be due to a bifurcation from stochastic to nested magnetic structure, caused by the removal of flux tunneling through intersecting manifolds of overlapping heteroclinic tangles. 2/1 island stability correlates with coupling events in an ITER baseline scenario plasma where ECCD can not stabilize the coupled islands, showing the critical impact of flux tunneling on disruption avoidance in tokamaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Validation of density pump-out by pedestal-foot magnetic island formation prior to ELM suppression in KSTAR and DIII-D tokamaks

Abstract TM1 nonlinear two-fluid simulations reveal key characteristics of density pump-out caused by pedestal-foot island formation when applying resonant magnetic perturbation (RMP). These characteristics include a bifurcation in pump-out with a low RMP coil current threshold, a sensitivity of pump-out magnitude to q 95 , and the magnitude of pump-out scaling as the square root of the RMP coil current. Dedicated experiments are carried out in the KSTAR and DIII-D tokamaks to validate these features and show that: (1) a staircase bifurcation in density pump-out is observed when slowly ramping up the n = 1 RMP current, and the density fluctuations are found to be slightly decreased from the pedestal-foot to the pedestal-top; (2) the magnitude of density pump-out becomes weaker when decreasing q 95 from 5.5 to 4.9, and a partial recovery of density pump-out is observed when q 95 is ramped down to lower than 4.9; and (3) analysis of a DIII-D database of n = 3 RMP edge-localized mode control experiments finds that the magnitude of density pump-out is proportional to the square root of RMP coil current Δ n e / n e ∝ I RMP 0.5 . These experimental observations are consistent with TM1 simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Access to stable, high pressure tokamak pedestals using local electron cyclotron current drive

Abstract Experiments on the DIII-D tokamak demonstrate that edge localized mode (ELM) stability can be manipulated using localized electron cyclotron current drive (ECCD) in conjunction with resonant magnetic perturbations (RMPs). The injection of counter-plasma-current edge ECCD reduces the RMP amplitude required to suppress ELMs and bifurcates the pedestal into a high-confinement regime with 7 kPA pedestal pressure. This is the first time such a high confinement regime has been accessed through the bifurcation from the ballooning stability branch predicted by existing models. These observations are consistent with modeled ECCD manipulation of magnetic islands induced by the RMPs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Enhancement of ECCD by the current condensation effect for stabilizing large magnetic islands caused by neoclassical tearing modes in tokamak plasmas

The radio frequency current condensation effect reported in Reiman and Fisch (2018 Phys. Rev. Lett. 121 225001) is modeled in the nonlinear resistive magnetohydrodynamic code. A series of numerical investigations have been performed to investigate the enhancement of electron cyclotron current drive (ECCD) by the current condensation effect during the control of neoclassical tearing mode (NTM) in tokamak plasmas. In the numerical model, both the parallel transport and the perpendicular transport of electron temperature are considered. The EC driven current and driven perturbed electron temperature can nonlinearly evolve within the given magnetic configuration and eventually reach saturation states. The input power threshold of ECCD and the fold bifurcation phenomenon are numerically verified via nonlinear simulations. The numerical results show good agreements with the analytical results. Moreover, spatial distributions of EC current for the two solutions at different condensed level are displayed. The control effectiveness of ECCD for large NTM islands has been evaluated while considering the current condensation effect. While taking into account current condensation effect, for a sufficiently large input power, a larger island can be more effectively stabilized than a smaller one, which suggests a reassessment of the previous idea that the ECCD should always be turned on as early as possible. The potential physics mechanism behind the ECCD control have all been discussed in detail. Furthermore, the condensation effect is found to have favorable effects on the radial misalignment of ECCD. In the consideration of the situation for extremely localized control needs, a highly peaked heating profile is adopted to verify that the fold bifurcation phenomenon still exists and the current condensation effect can still take effect in this extreme condition.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Recent advances in plasma control and physics research in the Large Helical Device

The Large Helical Device (LHD), the largest superconducting helical system in the world, is equipped with advanced heating and diagnostic tools, facilitating plasma control and physics research. Data assimilation was employed for electron temperature control using a real-time Thomson scattering system and real time prediction code. A virtual LHD environment enabled visualization of escaping high-energy tritium ions and demonstrated that these ions impact the rear side of the divertor plate. Pioneering results crucial to plasma control have also been achieved. Real-time wall conditioning using Lithium granule dropping improved bulk ion energy and particle transport while simultaneously enhancing the heavy impurity transport. Progress has also been made in the investigation of turbulence-driven transport. At the confinement bifurcation, ion-scale turbulence decreased, while electron-scale turbulence increased. A change in the anisotropy of turbulent eddies was also observed at the confinement bifurcation. Coexistence of local and non-local turbulence was identified in electron-scale turbulence. Non-local turbulence exhibited the rapid spatial propagation of perturbations throughout the plasma, while local turbulence followed the temperature gradient. A transition between drift-wave turbulence and magnetohydrodynamics (MHD) turbulence was observed with the turbulence minimized at the transition condition. Machine learning analysis was employed to evaluate the temperate and density conditions of this turbulence transition. Then, real-time control of fueling and heating was applied to maintain the turbulence transition condition, improving the energy confinement enhancement factor by 20%. In addition, evidence was obtained for collisionless ion heating by energetic-ion-driven geodesic acoustic modes and MHD bursts. These achievements represent unique contributions to the development of fusion reactors.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗