docs: update thesis

docs/others/phd/2025_atc/figures/psp

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+/Users/zijin/projects/psp_conjunction/overleaf

docs/others/phd/2025_atc/figures/scattering

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+/Users/zijin/projects/ion_scattering_by_SWD/overleaf/figures

docs/others/phd/2025_atc/presentation.qmd

@@ -44,15 +44,15 @@ However, these frameworks struggle to explain all the dynamics observed.
 
 ### Dropouts
 
-![Time profiles of lowenergy He ion intensities recorded by the Wind/LEMT sensor showing a gradual SEP event beginning on 1997 November 6. A dropout in ion intensity lasting about 2 hr can be seen during the decay phase of the gradual event. [@tanTurbulentOriginsParticle2023]](./figures/tanTurbulentOriginsParticle2023-fig1b.png)
+![Time profiles of lowenergy He ion intensities recorded by the Wind/LEMT sensor showing a gradual SEP event beginning on 1997 November 6. A dropout in ion intensity lasting about 2 hr can be seen during the decay phase of the gradual event. [@tanTurbulentOriginsParticle2023]](./figures/ref/tanTurbulentOriginsParticle2023-fig1b.png)
 
-![dropout period having $θ_{BV} \sim 0°$](./figures/tanTurbulentOriginsParticle2023-fig4.png)
+![dropout period having $θ_{BV} \sim 0°$](./figures/ref/tanTurbulentOriginsParticle2023-fig4.png)
 
 ### Reservoir
 
 A region where the intensities and energy spectra throughout much of the inner heliosphere (see Fig. 52: top right panel) at different azimuthal, radial, and latitudinal locations are nearly identical
 
-![Intensity-time profiles for protons in the 1979 March 1 event at 3 spacecraft are shown in the upper left panel with times of shock passage indicated by S for each. Energy spectra in the “reservoir” at time R are shown in the upper right panel while the paths of the spacecraft through a sketch of the CME are shown below [@reamesTwoSourcesSolar2013]](figures/reamesTwoSourcesSolar2013-fig6.png)
+![Intensity-time profiles for protons in the 1979 March 1 event at 3 spacecraft are shown in the upper left panel with times of shock passage indicated by S for each. Energy spectra in the “reservoir” at time R are shown in the upper right panel while the paths of the spacecraft through a sketch of the CME are shown below [@reamesTwoSourcesSolar2013]](figures/ref/reamesTwoSourcesSolar2013-fig6.png)
 
 Effective cross-field and non-diffusive transport [@larioHeliosphericEnergeticParticle2010]
 
@@ -67,7 +67,7 @@ $$
 ### Turbulent Magnetic Fluctuations
 
 
-![PDF of the out-of-plane electric current density $J_z$ from a 2D MHD simulation, compared to a reference Gaussian (standard deviation $σ$). For each region I, II, and III, magnetic field lines (contours of constant magnetic potential $A_z$: > 0 solid, < 0 dashed) are shown; the colored (red) regions are places where the selected band (I, II, or III) contributes. [@grecoPartialVarianceIncrements2017]](./figures/grecoPartialVarianceIncrements2017-fig1.png)
+![PDF of the out-of-plane electric current density $J_z$ from a 2D MHD simulation, compared to a reference Gaussian (standard deviation $σ$). For each region I, II, and III, magnetic field lines (contours of constant magnetic potential $A_z$: > 0 solid, < 0 dashed) are shown; the colored (red) regions are places where the selected band (I, II, or III) contributes. [@grecoPartialVarianceIncrements2017]](./figures/ref/grecoPartialVarianceIncrements2017-fig1.png)
 
 ::: {.notes}
 A physically appealing interpretation emerges: region I consists of very low values of fluctuations that lie mainly in the lanes between magnetic islands. Region II consists of sub-Gaussian current cores that populate the central regions of the magnetic islands (or flux tubes). Region III is composed of the coherent small-scale current sheet-like structures that form the sharp boundaries between the magnetic flux tubes. This classification provides a real-space picture of the nature of intermittent MHD turbulence.

docs/others/phd/2025_atc/thesis_outline.qmd

@@ -46,7 +46,7 @@ SEPs are primarily accelerated through two distinct mechanisms [@reamesTwoSource
 
 Gradual SEP events typically last for several days and are predominantly proton-rich, often associated with fast CMEs driving shocks in the solar corona and interplanetary space. These shocks accelerate particles over extended regions, producing widespread and intense radiation storms. In contrast, impulsive SEP events are related to short duration (less than 1 h) solar flares. These events typically have shorter durations, lasting from minutes to a few hours, and feature characteristically higher electron-to-proton ratios and enrichments of heavy ions (${ }^3 \mathrm{He} /{ }^4 \mathrm{He}$ and $\mathrm{Fe} / \mathrm{O}$ ratios).
 
-![The two-class picture for SEP events. @desaiLargeGradualSolar2016](figures/desaiLargeGradualSolar2016-fig3.png)
+![The two-class picture for SEP events. @desaiLargeGradualSolar2016](figures/ref/desaiLargeGradualSolar2016-fig3.png)
 
 In the decay phase of large gradual SEP events, a characteristic phenomenon known as the **reservoir effect** frequently occurs, where particle intensities measured by widely separated spacecraft become nearly uniform across large regions and exhibit similar temporal evolutions. One traditional explanation for reservoir formation suggests that particles become trapped behind a CME-driven magnetic structure, resulting in spatially uniform spectra that adiabatically decrease in intensity as the confining magnetic bottle expands. However, high heliolatitude observations from the Ulysses mission revealed the three-dimensional character of the reservoir effect and favor the cross-field diffusion explanation [@larioHeliosphericEnergeticParticle2010; @dallaPropertiesHighHeliolatitude2003].
 

docs/others/phd/2026_grad/.gitignore

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+typstapp
+uclathesis

docs/others/phd/2026_grad/_acknowledgments.qmd

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+# Acknowledgments

docs/others/phd/2026_grad/_intro.qmd

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+# Introduction
+
+The solar wind is a hot, magnetized plasma that continuously expands from the solar corona into interplanetary space, driven by the pressure gradient between the dense coronal plasma and the surrounding interstellar medium [@parkerDynamicsInterplanetaryGas1958; @parkerDynamicalTheorySolar1965; @velliSupersonicWindsAccretion1994; @velliHydrodynamicsSolarWind2001]. As it propagates outward, the solar wind accelerates to super-Alfvénic speeds, transporting mass, momentum, and energy throughout the heliosphere.
+
+Because the solar wind is highly electrically conductive, magnetic field lines are frozen into the plasma flow to a good approximation. The resulting large-scale interplanetary magnetic field (IMF) is shaped by the combination of radial expansion and solar rotation, producing the Archimedean spiral geometry described by the Parker model—a configuration well supported by observations when averaged over sufficiently long intervals [@zhaoStatisticsInterplanetaryMagnetic2025; @zhaoStatisticsInterplanetaryMagnetic2025a].
+
+Superposed on this ordered background, however, are substantial fluctuations spanning a broad range of scales. These fluctuations are a manifestation of MHD turbulence [@schekochihinMHDTurbulenceBiased2022; @matthaeusTurbulenceSpacePlasmas2021; @brunoTurbulenceSolarWind2016; @brunoSolarWindTurbulence2013; @tuMHDStructuresWaves1995; @goldsteinMagnetohydrodynamicTurbulenceSolar1995], which is multiscale, intermittent, and strongly non-Gaussian [@chandranIntermittentReflectiondrivenStrong2025; @brunoIntermittencySolarWind2019; @verscharenMultiscaleNatureSolar2019; @matthaeusIntermittencyNonlinearDynamics2015]. A key feature of this turbulence is that energy does not distribute uniformly across space as it cascades from large to small scales. Instead, it concentrates into localized, coherent structures—magnetic flux ropes, magnetic holes, plasma waves, and, most prominently, current sheets [@perroneCoherentEventsIon2020; @khabarovaCurrentSheetsPlasmoids2021; @pezziCurrentSheetsPlasmoids2021]. These structures are not passive byproducts of the cascade; they feed back into the ambient plasma and magnetic environment, contributing significantly to plasma heating, particle acceleration, and departures from classical MHD behavior [@degiorgioCoherentStructureFormation2017; @borovskyContributionStrongDiscontinuities2010; @liEffectCurrentSheets2011; @grecoPartialVarianceIncrements2017].
+
+The heliospheric magnetic field thus exhibits a dual character: while the Parker spiral describes the mean magnetic topology of the heliosphere, a complete physical picture of the solar wind requires explicit consideration of turbulence and embedded coherent structures. This multiscale structure has important consequences for a range of heliophysical processes, particularly the transport and acceleration of energetic particles.
+
+Solar energetic particles (SEPs) are high-energy ions and electrons episodically accelerated in the solar and interplanetary environment [@anastasiadisSolarEnergeticParticles2019; @kleinAccelerationPropagationSolar2017; @desaiLargeGradualSolar2016; @reamesTwoSourcesSolar2013]. They originate either in the low solar corona during eruptive events, or at interplanetary shock fronts driven by fast coronal mass ejections, where diffusive shock acceleration can energize particles over extended spatial and temporal scales. SEP events pose radiation hazards to spacecraft electronics, astronauts, and high-altitude aviation, and they provide a natural laboratory for studying particle acceleration and transport in magnetized plasmas—with implications extending to astrophysical systems more broadly.
+
+Early theoretical descriptions of SEP propagation treated the interplanetary medium as a smooth background threaded by broadband turbulent waves, within which particles scatter quasi-linearly. However, growing observational and numerical evidence demonstrates that the fine-scale magnetic structure of the solar wind can exert a decisive influence on particle dynamics [@malaraEnergeticParticleDynamics2023; @malaraChargedparticleChaoticDynamics2021; @artemyevSuperfastIonScattering2020]. When a particle's gyroradius becomes comparable to the thickness of a current sheet, classical guiding-center theory breaks down: the particle undergoes a non-adiabatic interaction that can produce large, abrupt changes in pitch angle. Because current sheets are abundant throughout the heliosphere and their thickness overlaps with the gyroradii of suprathermal and energetic ions, such interactions are not rare events but a systematic feature of SEP propagation. They can enhance pitch-angle scattering, induce trapping or reflection, enable localized acceleration, and produce non-diffusive transport that cannot be captured by models based solely on homogeneous wave turbulence.
+
+Despite their importance, a quantitative understanding of how current sheets influence SEP transport has remained incomplete, for two reasons. First, the statistical properties of kinetic-scale current sheets—their occurrence rate, thickness distribution, and internal magnetic configuration—have not been systematically characterized across different regions of the heliosphere. Second, the connection between these microphysical structural properties and macroscopic transport coefficients has not been rigorously established. This dissertation addresses both gaps.
+
+Specifically, this dissertation (1) develops a coherent observational framework to characterize the properties and occurrence rates of current sheets from kinetic to large scales across different heliospheric regions, and (2) constructs a quantitative, statistics-based model of SEP interactions with current sheets that describes pitch-angle scattering induced by these structures and estimates the resulting spatial transport coefficients. Together, these contributions provide a bridge between the microphysics of individual current sheet encounters and the macroscopic diffusion of energetic particles through the heliosphere, offering new insight into heliospheric particle dynamics and a foundation for improved space weather prediction.
+
+## Thesis Organization
+
+<!-- 
+Part I (Chapters 2–3) provides the observational and theoretical background. Chapter 2 reviews the properties of solar wind current sheets—their identifaction, internal structure, and relationship to turbulence intermittency. Chapter 3 introduces the solar energetic particle context, the transport frameworks within which particle scattering is parameterized, and the quasi-adiabatic theory of non-adiabatic particle interactions with magnetic field reversals. Part II (Chapters 4–5) presents the observational characterization of kinetic-scale current sheets across the inner heliosphere, using multi-spacecraft data from PSP, Wind, ARTEMIS, STEREO, and Juno. Part III (Chapters 6–7) develops the quantitative model of particle scattering and transport, connecting the observed current sheet properties to pitch-angle diffusion coefficients and spatial transport coefficients. Part IV (Chapters 8–9) presents supporting methodological developments: a multi-fluid current sheet model and the Julia-based computational framework that enables the large-scale analyses performed throughout. Chapter 10 summarizes the principal findings and discusses open questions and future directions. 
+-->
+
+This thesis is organized into four parts, progressing from background reviews through observational characterization of current sheets, to their impact on energetic particle transport, and finally to the methodological developments that support and extend the primary scientific results.
+
+**Part I** (Chapters 2–3) provides the observational and theoretical background. *Chapter 2* reviews the observational properties of solar wind current sheets, including the identification and characterization methods, their kinetic nature, and the statistical characteristics reported in the literature. *Chapter 3* introduces the solar energetic particle context: the sources and classification of SEP events, the transport frameworks within which particle scattering is parameterized, and the motivation—rooted in solar wind intermittency—for going beyond classical quasilinear theory. This chapter develops the quasi-adiabatic theory of particle motion near magnetic field reversals and the mechanisms by which the quasi-adiabatic invariant is destroyed at separatrix crossings.
+
+**Part II** (Chapters 4–5) presents the observational characterization of kinetic-scale current sheets across the inner heliosphere from a coordinated set of spacecraft: Parker Solar Probe (PSP) at distances as close as 0.1 AU, Wind, ARTEMIS, and STEREO near 1 AU, and Juno during its cruise phase out to 5 AU. These chapters systematically quantify the statistical distributions of current sheet thickness and current density—two parameters that directly determine the magnetic field configurations. Because the magnetic field geometry directly influences particle motion, these structural properties serve as essential inputs for understanding particle scattering and transport processes. The observational results therefore provide the empirical foundation for the particle-transport studies that follow.
+
+**Part III** (Chapters 6–7) investigates how kinetic-scale current sheets scatter and transport energetic particles. *Chapter 6* quantifies pitch-angle scattering through test-particle simulations and statistical analysis, establishing how specific current sheet configurations produce non-adiabatic behavior and how an ensemble of current sheets contributes to long-term pitch-angle diffusion. *Chapter 7* extends this analysis to spatial transport, deriving parallel and perpendicular diffusion coefficients from ensembles of particles interacting with statistically representative current sheet populations. Together, these chapters bridge microscopic scattering physics between local structure physics and macroscopic heliospheric transport.
+
+**Part IV** (Chapters 8–9) presents two complementary developments. *Chapter 8* introduces a multi-fluid current sheet model developed to interpret plasma velocity structure and magnetic field configuration within a current sheet. It is constructed to allow non-zero normal magnetic field components while maintaining constant magnetic field magnitude, thereby extending beyond simplified one-dimensional MHD configurations. *Chapter 9* describes the Julia-based software ecosystem designed to support the large-scale statistical and computational analyses performed throughout this work. This computational framework allows interactive scientific exploration while maintaining near-compiled performance, making large ensemble studies computationally feasible.
+
+*Chapter 10* summarizes the principal findings and discusses open questions and future directions, with emphasis on the origins of solar wind current sheets and on strategies for incorporating intermittency effects into operational SEP transport models.