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At least 55 records · Page 3

Unusual reactivity of a flavin in a bifurcating electron-transferring flavoprotein leads to flavin modification and a charge-transfer complex

From the outset, canonical electron transferring flavoproteins (ETFs) earned a reputation for containing modified flavin. We now show that modification occurs in the recently recognized bifurcating (Bf) ETFs as well. In Bf ETFs, the ’electron transfer’ (ET) flavin mediates single electron transfer via a stable anionic semiquinone state, akin to the FAD of canonical ETFs, whereas a second flavin mediates bifurcation (the Bf FAD). We demonstrate that the ET FAD undergoes trans- formation to two different modified flavins by a sequence of protein-catalyzed reactions that occurs specifically in the ET site, when the enzyme is maintained at pH 9 in an amine-based buffer. Our optical and mass spectrometric characterizations identify 8-formyl flavin early in the process and 8-amino flavins (8AFs) at later times. The latter have not previously been documented in an ETF to our knowledge. Mass spectrometry of flavin products formed in Tris or bis-tris-aminopropane solutions demonstrates that the source of the amine adduct is the buffer. Stepwise reduction of the 8AF demonstrates that it can explain a charge transfer band observed near 726 nm in Bf ETF, as a complex involving the hydroquinone state of the 8AF in the ET site with the oxidized state of unmodified flavin in the Bf site. This supports the possibility that Bf ETF can populate a conformation enabling direct electron transfer between its two flavins, as has been proposed for cofactors brought together in complexes between ETF and its partner proteins.

36 MATERIALS SCIENCE↗

Evidence and modeling of turbulence bifurcation in L-mode confinement transitions on Alcator C-Mod

Analysis and modeling of rotation reversal hysteresis experiments show that a single turbulent bifurcation is responsible for the Linear to Saturated Ohmic Confinement (LOC/SOC) transition and concomitant intrinsic rotation reversal on Alcator C-Mod. Plasmas on either side of the reversal exhibit different toroidal rotation profiles and therefore different turbulence characteristics despite the profiles of density and temperature, which are indistinguishable within measurement uncertainty. Elements of this bifurcation are also shown to persist for auxiliary heated L-modes. The deactivation of subdominant (in the linear growth rate and contribution to heat transport) ion temperature gradient and trapped electron mode instabilities is identified as the only possible change in turbulence within a reduced quasilinear transport model across the reversal, which is consistent with the measured profiles and inferred heat and particle fluxes. Experimental constraints on a possible change from strong to weak turbulence, outside the description of the quasilinear model, are also discussed. These results indicate an explanation for the LOC/SOC transition that provides a mechanism for the hysteresis through the dynamics of subdominant modes and changes in their relative populations and does not involve a change in the most linearly unstable ion-scale drift-wave instability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Bifurcation of equilibrium positions for ellipsoidal particles in inertial shear flows between two walls

We conducted a systematic numerical investigation of spherical, prolate and oblate particles in an inertial shear flow between two parallel walls, using smoothed particle hydrodynamics (SPH). It was previously shown that above a critical Reynolds number, spherical particles experience a supercritical pitchfork bifurcation of the equilibrium position in shear flow between two parallel walls, namely that the central equilibrium position becomes unstable, leading to the emergence of two new off-centre stable positions (Foxet al.,J. Fluid Mech., vol. 915, 2021). This phenomenon was unexpected given the symmetry of the system. In addition to confirming this finding, we found, surprisingly, that ellipsoidal particles can also return to the centre position from the off-centre positions when the particle Reynolds number is further increased, while spherical particles become unstable under this increased Reynolds number. By utilizing both SPH and the finite element method for flow visualization, we explained the underlining mechanism of this reverse of bifurcation by altered streamwise vorticity and symmetry breaking of pressure. Furthermore, we expanded our investigation to include asymmetric particles, a novel aspect that had not been previously modelled, and we observed similar trends in particle dynamics for both symmetric and asymmetric ellipsoidal particles. While further validation through laboratory experiments is necessary, our research paves the road for development of new focusing and separation methods for shaped particles.

Mechanics↗

Very-Low-Frequency transmitters bifurcate energetic electron belt in near-earth space

Very-Low-Frequency (VLF) transmitters operate worldwide mostly at frequencies of 10–30 kilohertz for submarine communications. While it has been of intense scientific interest and practical importance to understand whether VLF transmitters can affect the natural environment of charged energetic particles, for decades there remained little direct observational evidence that revealed the effects of these VLF transmitters in geospace. Here we report a radially bifurcated electron belt formation at energies of tens of kiloelectron volts (keV) at altitudes of ~0.8–1.5 Earth radii on timescales over 10 days. Using Fokker-Planck diffusion simulations, we provide quantitative evidence that VLF transmitter emissions that leak from the Earth-ionosphere waveguide are primarily responsible for bifurcating the energetic electron belt, which typically exhibits a single-peak radial structure in near-Earth space. Since energetic electrons pose a potential danger to satellite operations, our findings demonstrate the feasibility of mitigation of natural particle radiation environment.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Bifurcation-driven vertical plasma displacement

This paper considers vertical plasma motion resulting from plasma current decay during the disruption event. The presented filament-based model describes the motion in the ideal wall limit as an adiabatically slow evolution of the plasma equilibrium. Here, the equilibrium exhibits a pitchfork bifurcation when the decaying plasma current passes a critical value determined by the external magnetic field. This bifurcation affects the disruption-induced mechanical loads on the first wall.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Kinetic-ballooning-bifurcation in tokamak pedestals across shaping and aspect-ratio

We use a new gyrokinetic threshold model to predict a bifurcation in tokamak pedestal width-height scalings that depends strongly on plasma shaping and aspect-ratio. The bifurcation arises from the first and second stability properties of kinetic-ballooning-modes that yields wide and narrow pedestal branches, expanding the space of accessible pedestal widths and heights. The wide branch offers potential for edge-localized-mode-free pedestals with high core pressure. For negative triangularity, low-aspect-ratio configurations are predicted to give steeper pedestals than conventional-aspect-ratio. Both wide and narrow branches have been attained in tokamak experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Neural operator transformers capture bifurcating drift-wave turbulence in fusion plasma simulations

Self-consistent modeling of turbulence-driven transport is critical for optimizing confinement in magnetically confined fusion plasmas, such as tokamaks and stellarators. In particular, capturing the long-term co-evolution of turbulence, flow, and background plasma profiles remains computationally challenging. Direct numerical simulation of these multiscale, highly nonlinear processes is often demanding and impractical for real-time control or design optimization. To address this bottleneck, we investigate transformer-based neural operator partial differential equation surrogates for emulating the dynamics of drift-wave turbulence bifurcation mediated by zonal flows, using the modified Hasegawa–Wakatani (MHW) model as a prototypical system. We find that the finetuned neural operator model has excellent performance in capturing the multi-spatiotemporal-scales of MHW turbulence bifurcation and is robust to testing on rare and out-of-distribution dynamics. Specifically, we demonstrate that a single unified model accurately predicts both quasi-steady-state turbulence and a wide range of dynamical transition processes, such as nonlinear saturation, spontaneous suppression of turbulence, and the emergence of macroscopic zonal flows, over time horizons vastly exceeding the local turbulence correlation time. This computationally efficient approach establishes a strong foundation for fast, AI-based modeling of complex, multiscale phenomena in magnetized fusion plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Bifurcation from L-mode to internal transport barrier triggered by a magnetic island in tokamak plasmas

Magnetic islands are believed to be responsible for triggering the internal transport barrier (ITB) around the rational surface and hence improves confinement in magnetic confinement fusion plasma, for more than two decades. Although some recent theoretical or modelling works support this hypothesis, the direct experimental demonstration on the ITB triggered by a magnetic island is still missing. Here, we report the first experimental observation that the increase in the magnetic island width triggers the bifurcation of the plasma transport state from a low confinement mode (L-mode) to an ITB mode in tokamak plasma. At medium island widths, the bifurcation appears with a dithering phase, i.e. plasma transitions from L-mode to ITB or vice versa quasi-periodically. As the island width further increases, the dithering ITB transitions into a steady ITB. The electron temperature gradient inside the ITB increases with island width. The trigger of the ITB and further enhancement of the ITB performance are also demonstrated by locking the island via applying a resonant magnetic perturbation field. The reduction of density fluctuations in the ITB region is observed and indicates turbulence suppression during ITB formation. These findings offer new insights for understanding ITB formation and robust ITB control.

internal transport barrier↗

Experimental Observation of Magnetic Island Heteroclinic Bifurcation in Tokamaks

We report empirical observations of magnetic island heteroclinic bifurcation for the first time. This behavior is observed in interacting coupled 2/1 tearing modes in the core of a DIII-D tokamak plasma. Poincaré maps constrained by measured magnetic amplitudes and phasing show bifurcation from heteroclinic to homoclinic topology in the 2/1 island as the 4/2 relative amplitude (R 4/2 ) decreases. Initially, the local electron temperature peak in the 2/1 island splits, consistent with two O points. As R 4/2 decreases a single peak forms, consistent with one O point. Lastly, these call for developing tearing stability theory and control solutions for heteroclinic islands in tokamaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Bifurcation Analysis Reveals Solution Structures of Phase Field Models

The phase field method is playing an increasingly important role in understanding and predicting morphological evolution in materials and biological systems. Here, in this study, we develop a new analytical approach based on the bifurcation analysis to explore the mathematical solution structure of phase field models. Revealing such solution structures not only is of great mathematical interest but also may provide guidance to experimentally or computationally uncover new morphological evolution phenomena in materials undergoing electronic and structural phase transitions. To elucidate the idea, we apply this analytical approach to three representative phase field equations: the Allen-Cahn equation, the Cahn-Hilliard equation, and the Allen-Cahn-Ohta-Kawasaki system. The solution structures of these three phase field equations are also verified numerically by the homotopy continuation method.

97 MATHEMATICS AND COMPUTING↗

Bistable dynamics and Hopf bifurcation in a refined model of early stage HIV infection

Recent clinical studies have shown that HIV disease pathogenesis can depend strongly on many factors at the time of transmission, including the strength of the initial viral load and the local availability of CD4+ T-cells. In this article, a new within-host model of HIV infection that incorporates the homeostatic proliferation of T-cells is formulated and analyzed. Due to the effects of this biological process, the influence of initial conditions on the proliferation of HIV infection is further elucidated. The identifiability of parameters within the model is investigated and a local stability analysis, which displays additional complexity in comparison to previous models, is conducted. The current study extends previous theoretical and computational work on the early stages of the disease and leads to interesting nonlinear dynamics, including a parameter region featuring bistability of infectious and viral clearance equilibria and the appearance of a Hopf bifurcation within biologically relevant parameter regimes.

59 BASIC BIOLOGICAL SCIENCES↗

Experimental observations of bifurcated power decay lengths in the near Scrape-Off Layer of ST40 High Field Spherical Tokamak

The scrape-off layer parallel heat flux decay lengths measured at ST40, a high field, low aspect ratio spherical tokamak, have been observed to bifurcate into two groups. The wide group follows established H-mode scalings (ranging between 2 to 8 mm) while the narrow group falls up to 10 times below these scalings (between 0.2 and 0.8 mm), being comparable to the ion total Larmor radius rather than the ion poloidal Larmor radius. The heat flux profiles of the latter group can only be described by a multi-exponential function, rather than the single exponential function convoluted with a Gaussian. The onset of the narrow scrape-off layer width is observed to be associated with suppressed magnetic fluctuations, suggesting reduced electromagnetic turbulence levels in the SOL.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Modeling the Effects of Drift Orbit Bifurcation on Radiation Belt Electrons

Abstract Drift orbit bifurcation (DOB) has been suggested to play a major role in the loss and transport of radiation belt electrons since it violates the second adiabatic invariants of particles and makes the third invariant undefined. Results from our guiding‐center test particle simulations using the Tsyganenko‐1989c magnetic field model show that the DOB could affect a broad region of the outer radiation belt, which can penetrate inside the geosynchronous orbit at Kp ≥ 3, and its effects are more significant further away from the Earth, at a higher Kp and for higher electron energies. Specifically, the short‐term simulation results after one electron drift show both traditional and nontraditional DOB transport of electrons, with the nontraditional DOB, caused by a third minimum of the magnetic field strength near the equator, reported here for the first time. Moreover, our results show large ballistic jumps in the second invariant and radial distance for electrons at high equatorial pitch angles after one drift. In addition, long‐term DOB transport coefficients of electrons over many drifts are calculated based on our simulation results. We find that the pitch angle and radial diffusion coefficients of electrons due to DOB could be comparable to or even larger than those caused by electron interactions with chorus and Ultra‐Low‐Frequency waves, respectively. In sum, our results demonstrate that DOB could cause effective loss and transport of radiation belt electrons even in the absence of waves.

Astronomy & Astrophysics↗

Modeling the Effects of Drift Orbit Bifurcation on the Magnetopause Shadowing Loss of Radiation Belt Electrons

Abstract Last closed drift shell (LCDS) has been identified as a crucial parameter for investigating the magnetopause shadowing loss of radiation belt electrons. However, drift orbit bifurcation (DOB) effects have not been physically incorporated into the LCDS calculation. Here we calculate event‐specific LCDS using different approaches to dealing with the DOB effects, that is, tracing field lines ignoring DOB, tracing test particles rejecting field lines with DOB, and tracing particles including field lines with DOB, and then incorporate them into a radial diffusion model to simulate the fast electron dropout observed by Van Allen Probes in May 2017. The model effectively captures the fast dropout at high L* and exhibits the best agreement with data when LCDS is calculated by tracing test particles with DOB more physically included. This study represents the first quantitative modeling of the DOB effects on radiation belt magnetopause shadowing loss via a more physical specification of LCDS.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Mapping wave packet bifurcation at a conical intersection in CH 3 I by attosecond XUV transient absorption spectroscopy

Extreme ultraviolet (XUV) transient absorption spectroscopy has emerged as a sensitive tool for mapping the real-time structural and electronic evolution of molecules. Here, attosecond XUV transient absorption is used to track dynamics in the A-band of methyl iodide (CH 3 I). Gaseous CH 3 I molecules are excited to the A-band by a UV pump (277 nm, ~20 fs) and probed by attosecond XUV pulses targeting iodine I(4d) core-to-valence transitions. Owing to the excellent temporal resolution of the technique, passage through a conical intersection is mapped through spectral signatures of nonadiabatic wave packet bifurcation observed to occur at 15 ± 4 fs following UV photoexcitation. The observed XUV signatures and time dynamics are in agreement with previous simulations [H. Wang, M. Odelius, and D. Prendergast, J. Chem. Phys. 151, 124106 (2019)]. Furthermore, due to the short duration of the UV pump pulse, coherent vibrational motion in the CH 3 I ground state along the C-I stretch mode (538 ± 7 cm -1 ) launched by resonant impulsive stimulated Raman scattering and dynamics in multiphoton excited states of CH 3 I are also detected.

36 MATERIALS SCIENCE↗

Physics-based compact modeling of electro-thermal memristors: Negative differential resistance, local activity, and non-local dynamical bifurcations

Leon Chua's Local Activity theory quantitatively relates the compact model of an isolated nonlinear circuit element, such as a memristor, to its potential for desired dynamical behaviors when externally coupled to passive elements in a circuit. However, the theory's use has often been limited to potentially unphysical toy models and analyses of small-signal linear circuits containing pseudo-elements (resistors, capacitors, and inductors), which provide little insight into required physical, material, and device properties. Furthermore, the Local Activity concept relies on a local analysis and must be complemented by examining dynamical behavior far away from the steady-states of a circuit. In this work, we review and study a class of generic and extended one-dimensional electro-thermal memristors (i.e., temperature is the sole state variable), re-framing the analysis in terms of physically motivated definitions and visualizations to derive intuitive compact models and simulate their dynamical behavior in terms of experimentally measurable properties, such as electrical and thermal conductance and capacitance and their derivatives with respect to voltage and temperature. Within this unified framework, we connect steady-state phenomena, such as negative differential resistance, and dynamical behaviors, such as instability, oscillations, and bifurcations, through a set of dimensionless nonlinearity parameters. In particular, we reveal that the reactance associated with electro-thermal memristors is the result of a phase shift between oscillating current and voltage induced by the dynamical delay and coupling between the electrical and thermal variables. We thus, demonstrate both the utility and limitations of local analyses to understand non-local dynamical behavior. Critically for future experimentation, the analyses show that external coupling of a memristor to impedances within modern sourcing and measurement instruments can dominate the response of the total circuit, making it impossible to characterize the response of an uncoupled circuit element for which a compact model is desired. However, these effects can be minimized by proper understanding of the Local Activity theory to design and utilize purpose-built instruments.

Brown, Timothy D. (ORCID:0000000347068355)↗

Bifurcation Buckling Analysis and Non-Linear Collapse Analysis of Teardrop Shaped Vacuum Chamber

The Spallation Neutron Source (SNS) accelerator is being upgraded to increase the beam power from 1.4MW at 1GeV to 2.8MW at 1.3GeV. The currents in the middle two injection chicane magnets cannot simply be scaled up to accommodate the increased injection energy of 1.3GeV due to potential excessive H- stripping; the magnets must be replaced with longer, lower-field magnets and the associated vacuum chambers need to be redesigned. A new teardrop-shaped vacuum chamber was initially designed to accommodate the new magnets and the updated beam paths and instrumentation. This paper focuses on the structural stability study of the teardrop shape vacuum chamber based on buckling analysis. Protection against collapse from buckling according to the ASME BPVC requirement has been evaluated in depth. First, a Type-1 bifurcation buckling analysis using a linear eigenvalue solution to determine the critical load factor was performed. Subsequently, a Type-3 nonlinear collapse analysis was conducted using the static Riks method with elastic-plastic material properties and imperfections explicitly considered in the model geometry. The critical buckling load for the teardrop shape vacuum chamber was confidently estimated based upon this two-stage approach.

Jiang, Hao↗