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At least 271 records · Page 15

On the advantages of exploiting memory in Markov state models for biomolecular dynamics

Biomolecular dynamics play an important role in numerous biological processes. Markov State Models (MSMs) provide a powerful approach to study these dynamic processes by predicting long time scale dynamics based on many short molecular dynamics (MD) simulations. In an MSM, protein dynamics are modeled as a kinetic process consisting of a series of Markovian transitions between different conformational states at discrete time intervals (called “lag time”). To achieve this, a master equation must be constructed with a sufficiently long lag time to allow interstate transitions to become truly Markovian. This imposes a major challenge for MSM studies of proteins since the lag time is bound by the length of relatively short MD simulations available to estimate the frequency of transitions. Here, we show how one can employ the generalized master equation formalism to obtain an exact description of protein conformational dynamics both at short and long time scales without the time resolution restrictions imposed by the MSM lag time. Using a simple kinetic model, alanine dipeptide, and WW domain, we demonstrate that it is possible to construct these quasi-Markov State Models (qMSMs) using MD simulations that are 5–10 times shorter than those required by MSMs. These qMSMs only contain a handful of metastable states and, thus, can greatly facilitate the interpretation of mechanisms associated with protein dynamics. A qMSM opens the door to the study of conformational changes of complex biomolecules where a Markovian model with a few states is often difficult to construct due to the limited length of available MD simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Autoignition study of iso -cetane/tetralin blends at low temperature

iso-Cetane and tetralin are the two fuel components commonly considered in literature diesel surrogates, and are hydrocarbon classes representative of iso-alkanes and naphthoaromatics, respectively. Since both surrogate components are involved in the key reactions controlling the autoignition reactivity of diesel surrogates, autoignition studies of iso-cetane, tetralin, and their blending behavior at low temperatures can be helpful in developing/refining chemical kinetic models of diesel surrogates, in order to better predict diesel ignition response under low temperature combustion conditions. In this investigation, autoignition experiments of iso-cetane, tetralin, and their binary mixtures at varying blending ratios have been conducted in a rapid compression machine (RCM) in the temperature/pressure range of 630–930 K and 10–20 bar. For the neat fuel components, the newly-acquired RCM data have been compared with the literature experimental results at some overlapping conditions. In addition, a chemical kinetic model describing the oxidation of iso-cetane and tetralin compiled/updated from the diesel surrogate model developed by Lawrence Livermore National Laboratory is used to simulate the experimental datasets. It is shown that this model exhibits good agreement with the experimental results of tetralin and also predicts the total ignition delay times of iso-cetane at lower temperatures reasonably well. However, the current model fails to fully capture the increase of total ignition delay time with increasing amount of tetralin in the binary blends observed in the present RCM experiments. Therefore, chemical kinetic analyses of the current model are conducted to help identify possible reasons leading to the discrepancies between simulations and experiments. Furthermore, the chemical kinetic interactions between iso-cetane and tetralin are explored by including additional cross-reactions among iso-cetane, tetralin, and their fuel fragments in the current model to assess their effects on model predictions. As a result, based on the chemical kinetic analysis results, future direction for model refinements is discussed.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Autoignition of CRC diesel surrogates at low temperature combustion conditions: Rapid compression machine experiments and modeling

As federal programs require increasingly stringent engine emissions and fuel economy standards, these ambitions can only be met if next-generation combustion technology is developed focusing on high-efficiency and low-emissions engines. Recent research has indicated the need to operate engines at higher compression ratios and with low temperature combustion (LTC) to achieve the needed gains in engine efficiency and reductions in emissions. Because there is a lack of understanding of the chemistry of diesel fuel components and their mixtures at these LTC conditions, this limits the ability to develop predictive chemical kinetic models that can be used to optimize engine combustion. The current study aims to fill in gaps in fundamental combustion data on surrogate fuel mixtures relevant to diesel fuels. Specifically, four multicomponent diesel surrogates formulated by the Coordinating Research Council (CRC) to emulate an ultra-low-sulfur research-grade #2 certification diesel fuel (CFA), namely V0a (4 components), V0b (5 components), V1 (8 components), and V2 (9 components), have been investigated in a rapid compression machine (RCM) through determination of total and first-stage ignition delay times. Autoignition characteristics of lean to rich fuel/O 2 /N 2 mixtures, for the four CRC surrogates and CFA, have been measured using an RCM at LTC relevant pressures and temperatures, in the ranges of 10–20 bar and 650–1000 K, respectively. The equivalence ratios have been varied by independently changing the oxygen mole fraction and the fuel mole fraction in the test mixtures, thereby illustrating the individual effects of oxygen concentration and fuel loading on diesel autoignition. Autoignition results of these four CRC surrogates are compared among them and with those of CFA. Some degree of agreement in autoignition response between each CRC surrogate and CFA is observed, while discrepancies are also identified and discussed. In addition, a detailed chemical kinetic model for diesel surrogates has been developed and validated against these newly-acquired RCM data. We find that this model shows reasonable agreement with the overall ignition delay time results of the current RCM experiments. Chemical kinetic analyses of the developed model were further conducted to help identify the reactions controlling the autoignition processes and the consumption of fuel components in CRC surrogates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Availability and reactivity of N 2 ( v ) for NH 3 synthesis by plasma catalysis

Production of vibrationally excited N 2 (N 2 (v)) in atmospheric pressure nonthermal plasma and loss of N 2 (v) by gas-phase reactions and reactions on catalytic surfaces are analyzed to examine the role of N 2 (v) in NH 3 formation by plasma catalysis. Vibrational state-to-state kinetic models complemented with molecular beam mass spectrometry (MBMS) measurements demonstrate that N 2 (v> 0) is produced with densities 100× greater than the density of N radicals by a radiofrequency atmospheric pressure plasma jet. The experimentally measured loss of N 2 (v) corresponds with a state-to-state kinetic model that describes loss of N 2 (v) by surface-mediated vibrational relaxation without consideration of reactions that convert N 2 (v) to NH 3 over the catalyst surface. Rate constants for vibrational relaxation of N 2 (v) on catalyst surfaces exceed upper bounds on proposed rate constants for NH 3 formation reactions from N 2 (v) over Fe when v < 9, Ni when v < 18, and Ag when v < 39, which indicates that only higher vibrational levels can possibly contribute to catalytic NH 3 formation faster than they undergo vibrational relaxation on the surface. Densities of N 2 (v> 8), vibrational levels that can possibly react over Fe to form NH 3 faster than they undergo vibrational relaxation, are less than or similar to N densities at the inlet of the catalyst bed and measured NH 3 formation for the investigated conditions in this work, while densities of N 2 (v> 17) and N 2 (v> 38) are orders of magnitude below the N density at the inlet of the catalyst bed and the measured NH 3 formation. The loss of N 2 (v) by vibrational relaxation on the surface limits the ability of N 2 (v) to contribute to catalytic NH 3 formation and explains why N 2 (v) does not produce NH 3 in quantities that are comparable to NH 3 formation from N even though N 2 (v > 0) is more abundantly produced by the plasma.

state-to-state kinetic modeling↗

Time-resolved measurements of HO 2 radical in a heated plasma flow reactor

Time-resolved, absolute HO 2 number density in diluted H 2 –O 2 –Ar, CH 4 –O 2 -Ar, and C 2 H 4 –O 2 –Ar mixtures excited by a repetitive ns pulse discharge in a heated plasma flow reactor is measured by Cavity Ringdown Spectroscopy (CRDS). The experimental results are obtained at $\textit{T}$ = 300-600 K and $\textit{P}$ = 130 Torr, both during the discharge pulse burst and in the afterglow. In this work, the HO 2 number density is inferred from the CRDS data using a spectral model exhibiting good agreement with previous measurements of absolute HO 2 absorption cross sections. In the room-temperature H 2 –O 2 mixture, as well as in CH 4 –O 2 and C 2 H 4 –O 2 mixtures over the entire temperature range studied, HO2 is generated only during the discharge burst and decays in the afterglow. However, in the H 2 –O 2 mixture at elevated temperatures, $\textit{T}$ = 400-600 K, HO 2 persists in the afterglow up to 10 ms after the discharge burst, comparable with the flow residence time in the reactor. Comparison with kinetic modeling shows that the sustained reactivity after the source of radicals is turned off is due to a chain propagation / hydrogen oxidation process, which dominates the radical recombination reactions. The kinetic modeling predictions are in good agreement with the relative HO 2 number density measured in all three mixtures, although the model underpredicts the absolute number densities in H 2 –O 2 at $\textit{T}$ = 400-600 K by up to a factor of two. Detection of the sustained low-temperature reactivity in H 2 –O 2 , initiated by the radical generation in the plasma, suggests that the plasma excitation may also affect kinetics of oxidation and reforming of fuels exhibiting low-temperature chemistry below hot ignition point.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Laminar flame speed measurements of a gasoline surrogate and its mixtures with ethanol at elevated pressure and temperature

Laminar Flame speed measurements of a gasoline surrogate and mixtures of it with ethanol were conducted using a heated, constant-volume vessel. A spherical propagating flame was observed using a high-speed camera, and laminar flame speed was determined therefrom. Here, the gasoline surrogate, which serves as the baseline for the current study, consisted of four components, namely, iso-octane, n-heptane, toluene, and 1-hexene. Different mixtures of the gasoline surrogate and ethanol were studied, governed by the ethanol percentage in the mixture. That is, E0, E30, E50, and E85 mixtures represent 0%, 30%, 50%, and 85% ethanol in the gasoline surrogate mixture by liquid volume, respectively. Initial temperatures of 335, 359, and 408 K and initial pressures of 1 and 3 bar were investigated. The findings of this study are compared to results in the literature, which show good agreement for E0 but some deviation for the E30 blend. In general, the study showed an increase in laminar flame speed as the ethanol percentage increases in the mixture. Similarly, increasing the initial temperature with fixed ethanol percentage resulted in an increase in laminar flame speed, as expected. In contrast, increasing the initial pressure with fixed Ethanol percentage showed a decrease in laminar flame speed. Finally, the results are compared to an existing chemical kinetics model designed for ethanol and gasoline. Although agreement between the model and data is reasonable and mostly within about 10%, some improvement to the kinetics model is needed to uniformly lower the calculated flame speeds.

09 BIOMASS FUELS↗

Can Third-Body Stabilization of Bimolecular Collision Complexes in Cold Molecular Clouds Happen?

For more than half a century, networks of radiative association, dissociative recombination, and bimolecular reactions have been postulated to drive the low-temperature chemistry of cold molecular clouds. Third-body stabilizations of collision complexes have been assumed to be 'irrelevant' due to short lifetime of such complexes. Here, we conduct crossed molecular beam studies of ground state atomic silicon with diacetylene in combination with electronic structure calculations and microcanonical kinetics models operating under cold molecular cloud conditions. Our combined experimental, electronic structure, and microcanonical kinetics modelling investigations provide compelling evidence that three-body collisions of molecular hydrogen with long-lived reaction intermediates accessed through intersystem crossing are prevalent deep inside molecular clouds. This concept might be exportable to reactions involving polycyclic aromatic hydrocarbons thus affording a versatile machinery to complex organics via third-body stabilizations of bimolecular collision complexes deep inside cold molecular clouds.

astrochemistry↗

Towards a UV model of kinetic mixing and portal matter

The nature of dark matter (DM) and how it might interact with the particles of the Standard Model (SM) is an ever-growing mystery. It is possible that the existence of new “dark sector” forces, yet undiscovered, are the key to solving this fundamental problem, and one might hope that in the future such forces might even be “unified” with the ones we already know in some UV-complete framework. In this paper, following a bottom-up approach, we attempt to take the first steps in the construction of such a framework. The much-discussed possibility of the kinetic mixing (KM) of the “dark photon” with the hypercharge gauge boson of the SM via loops of portal matter (PM) fields, charged in both sectors, offers an attractive starting point for these efforts. Given the anticipated finite strength of the KM in a UV-complete theory, the absence of anomalies, and the lifetime constraints on the PM fields arising from cosmic microwave background and nucleosynthesis constraints, PM must behave as vector-like copies of the known SM fermion fields, such as those which appear naturally in, e.g., E 6 -type models. Within such a setup, the SM and their corresponding partner PM fields would be related by a new S U ( 2 ) I gauge symmetry. With this observation as a springboard, we construct a generalization of these ideas where S U ( 2 ) I is augmented by an additional U ( 1 ) I Y factor so that the light dark photon is the result of a symmetry breaking analogous to the SM, i.e., S U ( 2 ) I × U ( 1 ) I Y → U ( 1 ) D , but with U ( 1 ) D now also broken at the ≲ GeV scale. While SM fields are U ( 1 ) D singlets, as in the conventional dark photon approach, they transform nontrivially under the full S U ( 2 ) I × U ( 1 ) I Y gauge group. This approach leads to numerous interesting signatures, both at low energies and at colliders, and can be viewed as an initial step in the construction of a more UV-complete framework.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A neural master equation framework for multiscale modeling of molecular processes: application to atomic-scale plasma processes

Plasma-surface interactions (PSI) play a crucial role in microelectronics fabrication; however, their multiscale nature and array of complex, often unknown interactions make computational modeling of PSIs extremely difficult. To this end, we propose a general neural master equation (NME) framework that uses master equations to describe the dynamics of a molecular process, wherein neural networks learned from atomistic simulations represent unknown transitions between different system states. By leveraging the physics-based structure of master equations and data-driven state transitions, the NME framework promotes generalizability and physics interpretability, and can bridge disparate length and time scales. The framework is demonstrated for multiscale modeling of Si atomic layer etching and reactive ion etching, where the learned NME-based surface kinetic models exhibit good predictive and extrapolative capabilities for predicting experimentally relevant observables as a function of process parameters. The NME-based surface kinetic models obey physical constraints, which are violated in models based on neural ordinary differential equations. The proposed NME framework for multiscale modeling of molecular processes can pave the way for the discovery of new chemistries and materials in atomic-scale plasma processes.

Chemical engineering↗

Toward UV models of kinetic mixing and portal matter. V. Indirect probes of the new physics scale

Kinetic mixing of the dark photon, the gauge boson of a hidden U ( 1 ) D , with the Standard Model (SM) gauge fields to induce an interaction between ordinary matter and dark matter (DM) at 1-loop requires the existence of portal matter (PM) fields having both dark and SM charges. As discussed in earlier work, these same PM fields can also lead to other loop-level mechanisms besides kinetic mixing that can generate significant interactions between SM fermions and the dark photon in a manner analogous to those that can be generated between a Dirac neutrino and a SM photon, i.e., dark moments. In either case, there are reasons to believe, e.g., due to the renormalization group equation running of the U ( 1 ) D gauge coupling, that PM fields may have ∼ TeV -scale masses that lie at or above those directly accessible to the HL-LHC. If they lie above the reach of the HL-LHC, then the only way to possibly explore the physics at this high scale in the short term is via indirect measurements made at lower energies, e.g., at lepton colliders operating in the m Z to 1 TeV range. In particular, processes such as e + e − → γ + DM or e + e − → f ¯ f , where f is a SM fermion, may be most useful in this regard. Here we explore these possibilities within the framework of a simple toy PM model, introduced in earlier work, based on a non-Abelian dark gauge group completion operating at the PM scale. In the kinetic mixing setup, we show these efforts fail due to the inherently tiny cross sections in the face of substantial SM backgrounds. However, in the case of interactions via induced dark moments, since they necessarily take the form of higher dimensional operators whose influence grows with energy, we show that access to PM-scale information may become possible for certain ranges of the toy model parameters for both of these e + e − processes at a 1 TeV collider. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Rotating cylinder electrode in reactive CO 2 capture: Identifying active C species via transport, VLE models and kinetics

Here, this article explores technical challenges and potential methodologies for understanding electrochemical Reactive CO 2 Capture (RCC) mechanisms. RCC offers potential energy cost advantages by directly converting captured CO 2 into fuels and chemicals, unlike traditional carbon capture and utilization (CCU) processes that require sequential capture, concentration, and compression. However, direct conversion of captured CO 2 introduces complexity due to additional equilibrium buffer reactions, making it challenging to identify active species for reduction in electrochemical studies. This article discusses methods to integrate transport, thermodynamics, and kinetics concepts to identify active carbon sources in RCC. Vapor‐Liquid Equilibrium (VLE) and transport models are validated against experimental results obtained in a gastight rotating cylinder electrode reactor and are shown as useful tools for studying RCC in heterogeneous electrocatalysts across different capture agents, solvents, and temperatures. This article establishes an experimental framework for advancing research in electrochemical RCC.

Electrocatalysis↗

Cool flame chemistry of diesel surrogate compounds: n -Decane, 2-methylnonane, 2,7-dimethyloctane, and n -butylcyclohexane

Elucidating the formation of combustion intermediates is crucial to validate reaction pathways, develop reaction mechanisms and examine kinetic modeling predictions. While high-temperature pyrolysis and oxidation intermediates of alkanes have been thoroughly studied, comprehensive analysis of cool flame intermediates from alkane autoxidation is lacking and challenging due to the complexity of intermediate species produced. Here, jet-stirred reactor autoxidation of four C 10 alkanes: n -decane, 2-methylnonane, 2,7-dimethyloctane, and n -butylcyclohexane, as model compounds of diesel fuel, was investigated from 500 to 630 K using synchrotron vacuum ultraviolet photoionization molecular beam mass spectrometry (SVUV-PIMS). Around 100 intermediates were detected for each fuel. The classes of molecular structures present during the autoxidation of the representative paraffinic functional groups in transport fuels, i.e., n -alkanes, branched alkanes, and cycloalkanes were established and were found to be similar from the oxidation of various alkanes. A theoretical approach was applied to estimate the photoionization cross sections of the intermediates with the same carbon skeleton as the reactants, e.g., alkene, alkenyl keto, cyclic ether, dione, keto-hydroperoxide, diketo-hydroperoxide, and keto-dihydroperoxide. These species are indicators of the first, second, and third O 2 addition reactions for the four C 10 hydrocarbons, as well as bimolecular reactions involving keto-hydroperoxides. Chemical kinetic models for the oxidation of these four fuels were examined by comparison against mole fraction of the reactants and final products obtained in additional experiments using gas chromatography analysis, as well as the detailed species pool and mole fractions of aforementioned seven types of intermediates measured by SVUV-PIMS. This works reveals that the models in the literature need to be improved, not only the prediction of the fuel reactivity and final products, but also the reaction network to predict the formation of many previous undetected intermediates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantifying the Variation in the Number of Donors in Quantum Dots Created Using Atomic Precision Advanced Manufacturing

Atomic-precision advanced manufacturing enables unique silicon quantum electronics built on quantum dots fabricated from small numbers of phosphorus dopants. The number of dopant atoms comprising a dot plays a central role in determining the behavior of charge and spin confined to the dots and thus overall device performance. Here in this work, we use both theoretical and experimental techniques to explore the combined impact of lithographic variation and stochastic kinetics on the number of P incorporations in quantum dots made using these techniques and how this variation changes as a function of the size of the dot. Using a kinetic model of PH3 dissociation augmented with novel reaction barriers, we demonstrate that for a 2 × 3 silicon dimer window the probability that no donor incorporates goes to zero, allowing for certainty in the placement of at least one donor. However, this still comes with some uncertainty in the precise number of incorporated donors (either one or two), and this variability may still impact certain applications. We also examine the impact of the size of the initial lithographic window, finding that the incorporation fraction saturates to δ-layer-like coverage as the circumference-to-area ratio decreases. We predict that this incorporation fraction depends strongly on the dosage of the precursor and that the standard deviation of the number of incorporations scales as ~√n, as would be expected for a sequence of largely independent incorporation events. Finally, we characterize an array of 36 experimentally prepared multidonor 3 × 3 nm lithographic windows with scanning tunneling microscopy, measuring the fidelity of the lithography to the desired array and the final location of PH x fragments within these lithographic windows. We use our kinetic model to examine the expected variability due to the observed lithographic error, predicting a negligible impact on incorporation statistics. We find good agreement between our model and the inferred incorporation locations in these windows from scanning tunneling microscope measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Oxidation of an iso-paraffinic alcohol-to-jet fuel and n-heptane mixture: an experimental and modelling study

Oxidation of ATJ/n-heptane blends was studied over a wide range of test conditions, using single pulse shock tubes. Test conditions were designed to study the effect of pressure (4 and 50 bar), and fuel loading (~100-1400 ppm) on the oxidation of the blends across a wide range of temperatures (800-1300 K). These effects were observed by measuring concentrations of intermediate species formed using in-line Gas Chromatography (GC) and GCxGC TOF-MS. Results showed that increasing the initial fuel load does not have a significant impact on the results. However, increasing the pressure shifts the mixture reactivity to a lower temperature by about 150 K and causes the fuel to be oxidized instead of decomposing pyrolytically as at lower pressures. Additional experiments for pure ATJ and pure n-heptane were performed at conditions matching the ATJ/n-heptane 50 bar experiments to analyze the differences between the pure and mixed fuels. Speciation measurements were compared against predictions from a detailed kinetic model. The ability of the kinetic model to capture the effects of varying experimental test conditions on the evolution of intermediate species is discussed and kinetic analyses have been conducted to identify the important reaction pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep learning surrogate model for kinetic Landau-fluid closure with collision

In this work, the kinetic Landau-fluid (LF) closure with collision and periodic boundary condition is used in the development of the deep learning (DL) surrogate model. A classical neural network, namely, feedforward neural network or sometimes termed multilayer perceptron, is constructed and trained to learn the kinetic LF closure in the static limit and arbitrary mean free path in configuration space. The preliminary relation between best hyperparameters and critical parameters for data generation is found. Compared with the numerical approach (non-Fourier method) of the LF closure, the deep learning surrogate model shows an order of magnitude of improvement in terms of accuracy. Perhaps most importantly, the surrogate model closure has been integrated for the first time with fluid simulations. Our DL-enabled fluid simulations, for the first time, give the correct Landau damping rate for a wide range of wave vectors, while the Hammett–Perkins closure cannot produce the correct damping rate. We correctly connect the collisionless Hammett–Perkins closure and collisional Braginskii closure to reproduce the intrinsic nonlocal feature of the heat flux with DL techniques. We address the most concerning error accumulation problem and find that simulations with the deep learning surrogate model are as good as, if not better than, simulations with the analytic closure in terms of long-term numerical stability in the linear Landau damping test.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Full-dimensional quantum studies of vibrational energy transfer dynamics between H 2 O and Ar: theory assessing experiment

In this work we report the first full-dimensional quantum mechanical calculations of the ro-vibrational inelastic scattering dynamics between water molecules and argon atoms on an accurate potential energy surface, using a recently developed time-independent quantum method based on the close-coupling approach. The state-to-state integral cross-sections and rate coefficients show strong observance of gap laws. The calculated thermal rate coefficients for the relaxation of the stretching fundamental states of H 2 O are in good agreement with experimental values, while those for the bending overtone state are approximately five times smaller than the values extracted through a previous kinetic modeling of fluorescence decay data. Our state-specific quantum scattering results suggest the need to reassess the kinetic modeling of the experimental data. This work advanced our understanding of the quantum dynamics of vibrationally inelastic energy transfer processes involving polyatomic molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Verification of a fully kinetic ion model for electromagnetic simulations of high-frequency waves in toroidal geometry

For the research of high-frequency electromagnetic waves in tokamaks, an electromagnetic simulation model, in which the ion dynamics is described by a six-dimensional Vlasov equation and the electron dynamics is described by a drift kinetic equation, is formulated and implemented in the global gyrokinetic toroidal code (GTC). Analytic dispersion relations are derived in reduced systems and compared with various theories to verify the model. Linear simulations of a generalized ion Bernstein wave and ion cyclotron emission are verified by comparing the GTC simulation results with analytic dispersion relation theory and magnetoacoustic cyclotron instability theory, respectively, in cylindrical geometry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗