Electron current to a probe in a magnetized, collisional plasma

Collisional analysis of electron collection by a probe in a strongly magnetized, fully ionized plasma is carried out. A solution to the complete set of macroscopic equations with classical transport coefficients that is wholly consistent in the domain is determined; R and le are probe radius and electron gyroradius, respectively. If R2/le 2 is large compared with mi/3me probe large compared with ion gyroradius, ion–electron energy exchange—rather than electron heat diffusion—keeps electrons isothermal. For smaller probes at negative bias, however, electron cooling occurs in the plasma beyond the sheath, with a potential overshoot lying well away from it. The probe characteristic in the electron-retarding range may then mimic the characteristic for a two electron-temperature plasma and lead to an overestimate of electron temperature; the validity of these results for other transport models is discussed

Nonlocal electron heat-flux

Electron thermal conduction in a not quite collisional unmagnetlzed plasma is analysed. The failure of classical results for temperature scale-length up to 100 times larger than thermal mean-free-path for electron scattering, and large ion-charge number Z , is discussed. Recent results from a nonlocal model of conduction at large Z are reviewed. Closed form expressions for Braginskii's coefficients a ,/3 , y for Z =0(1) are derived. An extension of the nonlocal model for Z =0(1) is discussed.

Electron cooling in probe collection from magnetized plasmas with anomalous transport

The electron-retarding range of the current-voltage characteristic of a flat Langmuir probe perpendicular to a strong magnetic field in a fully ionized plasma is analysed allowing for anomalous (Bohm) cross-field transport and temperature changes in the collection process. With probe size and ion thermal gyroradius comparable, and smaller than the electron mean free path, there is an outer quasineutral region with ion viscosity determinant in allowing nonambipolar parallel and cross flow. A potential overshoot lying either at the base or inside the quasineutral region both makes ions follow Boltzmann's law at negative bias and extends the electron-retarding range to probe bias e(j)p ~ +2Too. Electron heating and cooling occur roughly at positive and negative bias, with a re-minimum around efa ~ - 2 7 ^ ; far from the probe heat conduction cools and heats electrons at and radially away from the probe axis, respectively. The potential overshoot with no thermal effects would reduce the electron current Ie, making the In Ie versus 4>p graph downwards-concave,but cooling further reduces Ie substantially, and may tilt the slope upwards past the temperature minimum. The domain of strict validity of our analysis is narrow in case of low ion mass (deuterium), breaking down with the ion Boltzmann law.

Non-Maxwellian electron distributions in time-dependent simulations of low-Z materials illuminated by a high-intensity X-ray laser

The interaction of high intensity X-ray lasers with matter is modeled. A collisional-radiative timedependent module is implemented to study radiation transport in matter from ultrashort and ultraintense X-ray bursts. Inverse bremsstrahlung absorption by free electrons, electron conduction or hydrodynamic effects are not considered. The collisional-radiative system is coupled with the electron distribution evolution treated with a Fokker-Planck approach with additional inelastic terms. The model includes spontaneous emission, resonant photoabsorption, collisional excitation and de-excitation, radiative recombination, photoionization, collisional ionization, three-body recombination, autoionization and dielectronic capture. It is found that for high densities, but still below solid, collisions play an important role and thermalization times are not short enough to ensure a thermal electron distribution. At these densities Maxwellian and non-Maxwellian electron distribution models yield substantial differences in collisional rates, modifying the atomic population dynamics.

Ion acceleration in underdense plasmas by ultra-short laser pulses

We report on the ion acceleration mechanisms that occur during the interaction of an intense and ultrashort laser pulse ( λ > μ I 2 1018 W cm−2 m2) with an underdense helium plasma produced from an ionized gas jet target. In this unexplored regime, where the laser pulse duration is comparable to the inverse of the electron plasma frequency ωpe, reproducible non-thermal ion bunches have been measured in the radial direction. The two He ion charge states present energy distributions with cutoff energies between 150 and 200 keV, and a striking energy gap around 50 keV appearing consistently for all the shots in a given density range. Fully electromagnetic particle-in-cell simulations explain the experimental behaviors. The acceleration results from a combination of target normal sheath acceleration and Coulomb explosion of a filament formed around the laser pulse propagation axis

Double ion implantation and pulsed laser melting processes for third generation solar cells

In the framework of the third generation of photovoltaic devices, the intermediate band solar cell is one of the possible candidates to reach higher efficiencies with a lower processing cost. In this work, we introduce a novel processing method based on a double ion implantation and, subsequently, a pulsed laser melting (PLM) process to obtain thicker layers of Ti supersaturated Si. We perform ab initio theoretical calculations of Si impurified with Ti showing that Ti in Si is a good candidate to theoretically form an intermediate band material in the Ti supersaturated Si. From time-of-flight secondary ion mass spectroscopy measurements, we confirm that we have obtained a Ti implanted and PLM thicker layer of 135 nm. Transmission electron microscopy reveals a single crystalline structure whilst the electrical characterization confirms the transport properties of an intermediate band material/Si substrate junction. High subbandgap absorption has been measured, obtaining an approximate value of 104 cm−1 in the photons energy range from 1.1 to 0.6 eV.

Direct Vlasov simulations of electron-attracting cylindrical Langmuir probes in flowing plasmas

Current collection by positively polarized cylindrical Langmuir probes immersed in flowing plasmas is analyzed using a non-stationary direct Vlasov-Poisson code. A detailed description of plasma density spatial structure as a function of the probe-to-plasma relative velocity U is presented. Within the considered parametric domain, the well-known electron density maximum close to the probe is weakly affected by U. However, in the probe wake side, the electron density minimum becomes deeper as U increases and a rarified plasma region appears. Sheath radius is larger at the wake than at the front side. Electron and ion distribution functions show specific features that are the signature of probe motion. In particular, the ion distribution function at the probe front side exhibits a filament with positive radial velocity. It corresponds to a population of rammed ions that were reflected by the electric field close to the positively biased probe. Numerical simulations reveal that two populations of trapped electrons exist: one orbiting around the probe and the other with trajectories confined at the probe front side. The latter helps to neutralize the reflected ions, thus explaining a paradox in past probe theory.

High Fidelity Models for Near-Earth Object Dynamics

Motivado por los últimos hallazgos realizados gracias a los recientes avances tecnológicos y misiones espaciales, el estudio de los asteroides ha despertado el interés de la comunidad científica. Tal es así que las misiones a asteroides han proliferado en los últimos años (Hayabusa, Dawn, OSIRIX-REx, ARM, AIMS-DART, ...) incentivadas por su enorme interés científico. Los asteroides son constituyentes fundamentales en la evolución del Sistema Solar, son además grandes concentraciones de valiosos recursos naturales, y también pueden considerarse como objectivos estratégicos para la futura exploración espacial. Desde hace tiempo se viene especulando con la posibilidad de capturar objetos próximos a la Tierra (NEOs en su acrónimo anglosajón) y acercarlos a nuestro planeta, permitiendo así un acceso asequible a los mismos para estudiarlos in-situ, explotar sus recursos u otras finalidades. Por otro lado, las asteroides se consideran con frecuencia como posibles peligros de magnitud planetaria, ya que impactos de estos objetos con la Tierra suceden constantemente, y un asteroide suficientemente grande podría desencadenar eventos catastróficos. Pese a la gravedad de tales acontecimientos, lo cierto es que son ciertamente difíciles de predecir. De hecho, los ricos aspectos dinámicos de los asteroides, su modelado complejo y las incertidumbres observaciones hacen que predecir su posición futura con la precisión necesaria sea todo un reto. Este hecho se hace más relevante cuando los asteroides sufren encuentros próximos con la Tierra, y más aún cuando estos son recurrentes. En tales situaciones en las cuales fuera necesario tomar medidas para mitigar este tipo de riesgos, saber estimar con precisión sus trayectorias y probabilidades de colisión es de una importancia vital. Por ello, se necesitan herramientas avanzadas para modelar su dinámica y predecir sus órbitas con precisión, y son también necesarios nuevos conceptos tecnológicos para manipular sus órbitas llegado el caso. El objetivo de esta Tesis es proporcionar nuevos métodos, técnicas y soluciones para abordar estos retos. Las contribuciones de esta Tesis se engloban en dos áreas: una dedicada a la propagación numérica de asteroides, y otra a conceptos de deflexión y captura de asteroides. Por lo tanto, la primera parte de este documento presenta novedosos avances de apliación a la propagación dinámica de alta precisión de NEOs empleando métodos de regularización y perturbaciones, con especial énfasis en el método DROMO, mientras que la segunda parte expone ideas innovadoras para la captura de asteroides y comenta el uso del “ion beam shepherd” (IBS) como tecnología para deflectarlos. Abstract Driven by the latest discoveries enabled by recent technological advances and space missions, the study of asteroids has awakened the interest of the scientific community. In fact, asteroid missions have become very popular in the recent years (Hayabusa, Dawn, OSIRIX-REx, ARM, AIMS-DART, ...) motivated by their outstanding scientific interest. Asteroids are fundamental constituents in the evolution of the Solar System, can be seen as vast concentrations of valuable natural resources, and are also considered as strategic targets for the future of space exploration. For long it has been hypothesized with the possibility of capturing small near-Earth asteroids and delivering them to the vicinity of the Earth in order to allow an affordable access to them for in-situ science, resource utilization and other purposes. On the other side of the balance, asteroids are often seen as potential planetary hazards, since impacts with the Earth happen all the time, and eventually an asteroid large enough could trigger catastrophic events. In spite of the severity of such occurrences, they are also utterly hard to predict. In fact, the rich dynamical aspects of asteroids, their complex modeling and observational uncertainties make exceptionally challenging to predict their future position accurately enough. This becomes particularly relevant when asteroids exhibit close encounters with the Earth, and more so when these happen recurrently. In such situations, where mitigation measures may need to be taken, it is of paramount importance to be able to accurately estimate their trajectories and collision probabilities. As a consequence, advanced tools are needed to model their dynamics and accurately predict their orbits, as well as new technological concepts to manipulate their orbits if necessary. The goal of this Thesis is to provide new methods, techniques and solutions to address these challenges. The contributions of this Thesis fall into two areas: one devoted to the numerical propagation of asteroids, and another to asteroid deflection and capture concepts. Hence, the first part of the dissertation presents novel advances applicable to the high accuracy dynamical propagation of near-Earth asteroids using regularization and perturbations techniques, with a special emphasis in the DROMO method, whereas the second part exposes pioneering ideas for asteroid retrieval missions and discusses the use of an “ion beam shepherd” (IBS) for asteroid deflection purposes.

Three-dimensional spatial distribution of synapses in the neocortex: A dual-beam electron microscopy study

In the cerebral cortex, most synapses are found in the neuropil, but relatively little is known about their 3-dimensional organization. Using an automated dual-beam electron microscope that combines focused ion beam milling and scanning electron microscopy, we have been able to obtain 10 three-dimensional samples with an average volume of 180 µm(3) from the neuropil of layer III of the young rat somatosensory cortex (hindlimb representation). We have used specific software tools to fully reconstruct 1695 synaptic junctions present in these samples and to accurately quantify the number of synapses per unit volume. These tools also allowed us to determine synapse position and to analyze their spatial distribution using spatial statistical methods. Our results indicate that the distribution of synaptic junctions in the neuropil is nearly random, only constrained by the fact that synapses cannot overlap in space. A theoretical model based on random sequential absorption, which closely reproduces the actual distribution of synapses, is also presented.

Co-simulation Methodologies for Hybrid and Electric Vehicle Dynamics

In recent decades, full electric and hybrid electric vehicles have emerged as an alternative to conventional cars due to a range of factors, including environmental and economic aspects. These vehicles are the result of considerable efforts to seek ways of reducing the use of fossil fuel for vehicle propulsion. Sophisticated technologies such as hybrid and electric powertrains require careful study and optimization. Mathematical models play a key role at this point. Currently, many advanced mathematical analysis tools, as well as computer applications have been built for vehicle simulation purposes. Given the great interest of hybrid and electric powertrains, along with the increasing importance of reliable computer-based models, the author decided to integrate both aspects in the research purpose of this work. Furthermore, this is one of the first final degree projects held at the ETSII (Higher Technical School of Industrial Engineers) that covers the study of hybrid and electric propulsion systems. The present project is based on MBS3D 2.0, a specialized software for the dynamic simulation of multibody systems developed at the UPM Institute of Automobile Research (INSIA). Automobiles are a clear example of complex multibody systems, which are present in nearly every field of engineering. The work presented here benefits from the availability of MBS3D software. This program has proven to be a very efficient tool, with a highly developed underlying mathematical formulation. On this basis, the focus of this project is the extension of MBS3D features in order to be able to perform dynamic simulations of hybrid and electric vehicle models. This requires the joint simulation of the mechanical model of the vehicle, together with the model of the hybrid or electric powertrain. These sub-models belong to completely different physical domains. In fact the powertrain consists of energy storage systems, electrical machines and power electronics, connected to purely mechanical components (wheels, suspension, transmission, clutch…). The challenge today is to create a global vehicle model that is valid for computer simulation. Therefore, the main goal of this project is to apply co-simulation methodologies to a comprehensive model of an electric vehicle, where sub-models from different areas of engineering are coupled. The created electric vehicle (EV) model consists of a separately excited DC electric motor, a Li-ion battery pack, a DC/DC chopper converter and a multibody vehicle model. Co-simulation techniques allow car designers to simulate complex vehicle architectures and behaviors, which are usually difficult to implement in a real environment due to safety and/or economic reasons. In addition, multi-domain computational models help to detect the effects of different driving patterns and parameters and improve the models in a fast and effective way. Automotive designers can greatly benefit from a multidisciplinary approach of new hybrid and electric vehicles. In this case, the global electric vehicle model includes an electrical subsystem and a mechanical subsystem. The electrical subsystem consists of three basic components: electric motor, battery pack and power converter. A modular representation is used for building the dynamic model of the vehicle drivetrain. This means that every component of the drivetrain (submodule) is modeled separately and has its own general dynamic model, with clearly defined inputs and outputs. Then, all the particular submodules are assembled according to the drivetrain configuration and, in this way, the power flow across the components is completely determined. Dynamic models of electrical components are often based on equivalent circuits, where Kirchhoff’s voltage and current laws are applied to draw the algebraic and differential equations. Here, Randles circuit is used for dynamic modeling of the battery and the electric motor is modeled through the analysis of the equivalent circuit of a separately excited DC motor, where the power converter is included. The mechanical subsystem is defined by MBS3D equations. These equations consider the position, velocity and acceleration of all the bodies comprising the vehicle multibody system. MBS3D 2.0 is entirely written in MATLAB and the structure of the program has been thoroughly studied and understood by the author. MBS3D software is adapted according to the requirements of the applied co-simulation method. Some of the core functions are modified, such as integrator and graphics, and several auxiliary functions are added in order to compute the mathematical model of the electrical components. By coupling and co-simulating both subsystems, it is possible to evaluate the dynamic interaction among all the components of the drivetrain. ‘Tight-coupling’ method is used to cosimulate the sub-models. This approach integrates all subsystems simultaneously and the results of the integration are exchanged by function-call. This means that the integration is done jointly for the mechanical and the electrical subsystem, under a single integrator and then, the speed of integration is determined by the slower subsystem. Simulations are then used to show the performance of the developed EV model. However, this project focuses more on the validation of the computational and mathematical tool for electric and hybrid vehicle simulation. For this purpose, a detailed study and comparison of different integrators within the MATLAB environment is done. Consequently, the main efforts are directed towards the implementation of co-simulation techniques in MBS3D software. In this regard, it is not intended to create an extremely precise EV model in terms of real vehicle performance, although an acceptable level of accuracy is achieved. The gap between the EV model and the real system is filled, in a way, by introducing the gas and brake pedals input, which reflects the actual driver behavior. This input is included directly in the differential equations of the model, and determines the amount of current provided to the electric motor. For a separately excited DC motor, the rotor current is proportional to the traction torque delivered to the car wheels. Therefore, as it occurs in the case of real vehicle models, the propulsion torque in the mathematical model is controlled through acceleration and brake pedal commands. The designed transmission system also includes a reduction gear that adapts the torque coming for the motor drive and transfers it. The main contribution of this project is, therefore, the implementation of a new calculation path for the wheel torques, based on performance characteristics and outputs of the electric powertrain model. Originally, the wheel traction and braking torques were input to MBS3D through a vector directly computed by the user in a MATLAB script. Now, they are calculated as a function of the motor current which, in turn, depends on the current provided by the battery pack across the DC/DC chopper converter. The motor and battery currents and voltages are the solutions of the electrical ODE (Ordinary Differential Equation) system coupled to the multibody system. Simultaneously, the outputs of MBS3D model are the position, velocity and acceleration of the vehicle at all times. The motor shaft speed is computed from the output vehicle speed considering the wheel radius, the gear reduction ratio and the transmission efficiency. This motor shaft speed, somehow available from MBS3D model, is then introduced in the differential equations corresponding to the electrical subsystem. In this way, MBS3D and the electrical powertrain model are interconnected and both subsystems exchange values resulting as expected with tight-coupling approach.When programming mathematical models of complex systems, code optimization is a key step in the process. A way to improve the overall performance of the integration, making use of C/C++ as an alternative programming language, is described and implemented. Although this entails a higher computational burden, it leads to important advantages regarding cosimulation speed and stability. In order to do this, it is necessary to integrate MATLAB with another integrated development environment (IDE), where C/C++ code can be generated and executed. In this project, C/C++ files are programmed in Microsoft Visual Studio and the interface between both IDEs is created by building C/C++ MEX file functions. These programs contain functions or subroutines that can be dynamically linked and executed from MATLAB. This process achieves reductions in simulation time up to two orders of magnitude. The tests performed with different integrators, also reveal the stiff character of the differential equations corresponding to the electrical subsystem, and allow the improvement of the cosimulation process. When varying the parameters of the integration and/or the initial conditions of the problem, the solutions of the system of equations show better dynamic response and stability, depending on the integrator used. Several integrators, with variable and non-variable step-size, and for stiff and non-stiff problems are applied to the coupled ODE system. Then, the results are analyzed, compared and discussed. From all the above, the project can be divided into four main parts: 1. Creation of the equation-based electric vehicle model; 2. Programming, simulation and adjustment of the electric vehicle model; 3. Application of co-simulation methodologies to MBS3D and the electric powertrain subsystem; and 4. Code optimization and study of different integrators. Additionally, in order to deeply understand the context of the project, the first chapters include an introduction to basic vehicle dynamics, current classification of hybrid and electric vehicles and an explanation of the involved technologies such as brake energy regeneration, electric and non-electric propulsion systems for EVs and HEVs (hybrid electric vehicles) and their control strategies. Later, the problem of dynamic modeling of hybrid and electric vehicles is discussed. The integrated development environment and the simulation tool are also briefly described. The core chapters include an explanation of the major co-simulation methodologies and how they have been programmed and applied to the electric powertrain model together with the multibody system dynamic model. Finally, the last chapters summarize the main results and conclusions of the project and propose further research topics. In conclusion, co-simulation methodologies are applicable within the integrated development environments MATLAB and Visual Studio, and the simulation tool MBS3D 2.0, where equation-based models of multidisciplinary subsystems, consisting of mechanical and electrical components, are coupled and integrated in a very efficient way.

The Dynamics of Golgi Protein Traffic Visualized in Living Yeast Cells

We describe for the first time the visualization of Golgi membranes in living yeast cells, using green fluorescent protein (GFP) chimeras. Late and early Golgi markers are present in distinct sets of scattered, moving cisternae. The immediate effects of temperature-sensitive mutations on the distribution of these markers give clues to the transport processes occurring. We show that the late Golgi marker GFP-Sft2p and the glycosyltransferases, Anp1p and Mnn1p, disperse into vesicle-like structures within minutes of a temperature shift in sec18, sft1, and sed5 cells, but not in sec14 cells. This is consistent with retrograde vesicular traffic, mediated by the vesicle SNARE Sft1p, to early cisternae containing the target SNARE Sed5p. Strikingly, Sed5p itself moves rapidly to the endoplasmic reticulum (ER) in sec12 cells, implying that it cycles through the ER. Electron microscopy shows that Golgi membranes vesiculate in sec18 cells within 10 min of a temperature shift. These results emphasize the dynamic nature of Golgi cisternae and satisfy the kinetic requirements of a cisternal maturation model in which all resident proteins must undergo retrograde vesicular transport, either within the Golgi complex or from there to the ER, as anterograde cargo advances.

Ultrafast diffraction and structural dynamics: The nature of complex molecules far from equilibrium

Studies of molecular structures at or near their equilibrium configurations have long provided information on their geometry in terms of bond distances and angles. Far-from-equilibrium structures are relatively unknown—especially for complex systems—and generally, neither their dynamics nor their average geometries can be extrapolated from equilibrium values. For such nonequilibrium structures, vibrational amplitudes and bond distances play a central role in phenomena such as energy redistribution and chemical reactivity. Ultrafast electron diffraction, which was developed to study transient molecular structures, provides a direct method for probing the nature of complex molecules far from equilibrium. Here we present our ultrafast electron diffraction observations of transient structures for two cyclic hydrocarbons. At high internal energies of ≈4 eV, these molecules display markedly different behavior. For 1,3,5-cycloheptatriene, excitation results in the formation of hot ground-state structures with bond distances similar to those of the initial structure, but with nearly three times the average vibrational amplitude. Energy is redistributed within 5 ps, but with a negative temperature characterizing the nonequilibrium population. In contrast, the ring-opening reaction of 1,3-cyclohexadiene is shown to result in hot structures with a C—C bond distance of over 1.7 Å, which is 0.2 Å away from any expected equilibrium value. Even up to 400 ps, energy remains trapped in large-amplitude motions comprised of torsion and asymmetric stretching. These studies promise a new direction for studying structural dynamics in nonequilibrium complex systems.

Domain structure and dynamics in the helical filaments formed by RecA and Rad51 on DNA

Both the bacterial RecA protein and the eukaryotic Rad51 protein form helical nucleoprotein filaments on DNA that catalyze strand transfer between two homologous DNA molecules. However, only the ATP-binding cores of these proteins have been conserved, and this same core is also found within helicases and the F1-ATPase. The C-terminal domain of the RecA protein forms lobes within the helical RecA filament. However, the Rad51 proteins do not have the C-terminal domain found in RecA, but have an N-terminal extension that is absent in the RecA protein. Both the RecA C-terminal domain and the Rad51 N-terminal domain bind DNA. We have used electron microscopy to show that the lobes of the yeast and human Rad51 filaments appear to be formed by N-terminal domains. These lobes are conformationally flexible in both RecA and Rad51. Within RecA filaments, the change between the “active” and “inactive” states appears to mainly involve a large movement of the C-terminal lobe. The N-terminal domain of Rad51 and the C-terminal domain of RecA may have arisen from convergent evolution to play similar roles in the filaments.

Excited-state dynamics in photosystem II: Insights from the x-ray crystal structure

The heart of oxygenic photosynthesis is photosystem II (PSII), a multisubunit protein complex that uses solar energy to drive the splitting of water and production of molecular oxygen. The effectiveness of the photochemical reaction center of PSII depends on the efficient transfer of excitation energy from the surrounding antenna chlorophylls. A kinetic model for PSII, based on the x-ray crystal structure coordinates of 37 antenna and reaction center pigment molecules, allows us to map the major energy transfer routes from the antenna chlorophylls to the reaction center chromophores. The model shows that energy transfer to the reaction center is slow compared with the rate of primary electron transport and depends on a few bridging chlorophyll molecules. This unexpected energetic isolation of the reaction center in PSII is similar to that found in the bacterial photosystem, conflicts with the established view of the photophysics of PSII, and may be a functional requirement for primary photochemistry in photosynthesis. In addition, the model predicts a value for the intrinsic photochemical rate constant that is 4 times that found in bacterial reaction centers.

Two-dimensional protein crystallization via metal-ion coordination by naturally occurring surface histidines.

A powerful and potentially general approach to the targeting and crystallization of proteins on lipid interfaces through coordination of surface histidine residues to lipid-chelated divalent metal ions is presented. This approach, which should be applicable to the crystallization of a wide range of naturally occurring or engineered proteins, is illustrated here by the crystallization of streptavidin on a monolayer of an iminodiacetate-Cu(II) lipid spread at the air-water interface. This method allows control of the protein orientation at interfaces, which is significant for the facile production of highly ordered protein arrays and for electron density mapping in structural analysis of two-dimensional crystals. Binding of native streptavidin to the iminodiacetate-Cu lipids occurs via His-87, located on the protein surface near the biotin binding pocket. The two-dimensional streptavidin crystals show a previously undescribed microscopic shape that differs from that of crystals formed beneath biotinylated lipids.