Electron beam lithography is gaining widespread utilization as the semiconductor industry progresses towards both advanced optical and non-optical lithographic technologies for high resolution patterning. The current resist technologies are based on organic systems that are imaged most commonly through chain scission, networking, or a chemically amplified polarity change in the material. Alternative resists based on inorganic systems were developed and characterized in this research for high resolution electron beam lithography and their interactions with incident electrons were investigated using Monte Carlo simulations. A novel inorganic resist imaging scheme was developed using metal-organic precursors which decompose to form metal oxides upon electron beam irradiation that can serve as inorganic hard masks for hybrid bilayer inorganic-organic imaging systems and also as directly patternable high resolution metal oxide structures. The electron beam imaging properties of these metal-organic materials were correlated to the precursor structure by studying effects such as interactions between high atomic number species and the incident electrons. Optimal single and multicomponent precursors were designed for utilization as viable inorganic resist materials for sub-50nm patterning in electron beam lithography. The electron beam imaging characteristics of the most widely used inorganic resist material, hydrogen silsesquioxane (HSQ), was also enhanced using a dual processing imaging approach with thermal curing as well as a sensitizer catalyzed imaging approach. The interaction between incident electrons and the high atomic number species contained in these inorganic resists was also studied using Monte Carlo simulations. The resolution attainable using inorganic systems as compared to organic systems can be greater for accelerating voltages greater than 50 keV due to minimized lateral scattering in the high density inorganic systems. The effects of loading nanoparticles in an electron beam resist was also investigated using a newly developed hybrid Monte Carlo approach that accounts for multiple components in a solid film. The resolution of the nanocomposite resist process was found to degrade with increasing nanoparticle loading. Finally, the electron beam patterning of self-assembled monolayers, which were found to primarily utilize backscattered electrons from the high atomic number substrate materials to form images, was also investigated and characterized. It was found that backscattered electrons limit the resolution attainable at low incident electron energies.

Biological transport is an essential phenomenon for the living systems. A mechanistic investigation of biological transport processes is highly important for the characterization of physiological and cellular events, the design and functioning of several biomedical devices and the development of new therapies. To investigate the physical-chemical details of this phenomenon, concerted efforts of both experiments and theory are necessary. Motor proteins constitute a major portion of the active transport in the living cell. However, the actual mechanism of how chemical energy is converted into their directed motion has still remained obscure. Recent experiments on motor proteins have been producing exciting results that have motivated theoretical studies. In order to provide deep insight onto motor protein's mechanochemical coupling we have used stochastic modeling based on discrete-state chemical kinetic model. Such models enable us to (1) resolve the contradiction between experimental observations on heterodimeric kinesins and highly popular hand-over-hand mechanism, (2) take into account the free energy landscape modification of individual motor domains due to interdomain interaction, (3) recognize the effect of spatial fluctuations on biochemical properties of molecular motors, and (4) calculate the dynamical properties such as velocities, dispersions of complex biochemical pathways. We have also initiated the investigation of the dynamics of coupled motor assemblies using stochastic modeling. Furthermore, an extensive Monte Carlo lattice simulation based study on facilitated search process of DNA-binding proteins is presented. This simulation shows that the accelerated search compared to pure Smoluchowski limit can be achieved even in the case where the one-dimensional diffusion is order of magnitude slower than the three-dimensional diffusion. We also show that facilitated search is not only the manifestation of dimensionality reduction but correlation times play a crucial role in the overall search times. Finally, a more general field of stochastic processes, namely first-passage time process is investigated. Explicit expressions of important properties, such as splitting probailities and mean first-passage times, that are relevant to (but not limited to) biological transport, are derived for several complex systems.

Monte Carlo simulations have been used in the past to investigate a variety of surfactant systems; however, there is little published literature for double-headed and gemini surfactants with asymmetric tails. We perform Larson-type Monte Carlo simulations of double-headed and gemini surfactant systems with asymmetric tails in two- and three-dimensions. The model predicts that the addition of a second head group to form a double-headed surfactant results in an increase in the critical micelle concentration (CMC) compared to a single-headed surfactant, in agreement with experiment. It also indicates that the placement of the second head group has an impact on the final CMC value. We study a series of gemini surfactants with asymmetric tails and find no change in the value of the CMC as the ratio of the lengths of the two tails increases. This is contrary to the only experimental study that found there was a slight decrease in the CMC as the ratio of the lengths of the two tails increases. We examine this difference in terms of the relatively small effect surfactant asymmetry has on value of the CMC and the fact that the model is capable of qualitatively reproducing the known dependence of the CMC on other architectural properties. This initial probe into systems of double-headed and gemini surfactants with asymmetric tails confirms many of the previously published findings and provides avenues for possible future research using Monte Carlo simulations.

The increased interest in the use of light ion therapy is due to the high dose conformity to the target and the dense energy deposition along the tracks resulting in increased relative biological effectiveness compared to conventional radiation therapy. In spite of the good clinical experience, fundamental research on the characteristics of the ion beams is still needed in order to be able to fully explore their use. Therefore, a Monte Carlo track structure code, KITrack, simulating the transport of electrons in liquid water, has been developed and used for calculation of parameters of interest for beam characterization. The influence of the choice of the cross sections for the physical processes on the electron tracks has also been explored. As an alternative to Monte Carlo calculations a semi-analytical approach to calculate the radial dose distribution from ions, has been derived and validated. In advanced radiation therapy, accurate characterization of the beams has to be complemented by comprehensive radiobiological models, which relate the dose deposition into the cells to the outcome of the treatment. The second part of the study has therefore explored the influence of heterogeneity in the dose deposition into the cells as well as the heterogeneity in the cells sensitivity to radiation on the probability of controlling the tumor. Analytical expressions for tumor control probability including heterogeneous dose depositions or variation of radiation sensitivity of cells and tumors have been derived and validated with numerical simulations. The more realistic case of a combination of these effects has also been explored through numerical simulations. The MC code KITrack has evolved into an extremely useful tool for beam characterization. The tumor control probability, given by the analytical derived expression, can help improve radiation therapy. A novel anisotropy index has been proposed. It is a measure of the absence of isotropy and provides deeper understanding of the relationship between beam quality and biological effects. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

We study the dynamical behavior of disordered many-particle systems with long-range Coulomb interactions by means of damage-spreading simulations. In this type of Monte-Carlo simulations one investigates the time evolution of the damage, i.e. the difference of the o ccupation numbers of two systems, subjected to the same thermal noise. We analyze the dependence of the damage on temperature and disorder strength. For zero disorder the spreading transition coincides with the equilibrium phase transition, whereas for finite disorder, we find an evidence for a dynamical phase transition well below the transition temperature of the pure system.

We explore steady-state properties of a driven lattice gas, which is a simple model of interacting many-particle systems, driven far from equilibrium by an external field. First, we study a system on a square lattice with periodic boundary conditions (PBC) along both principal lattice axes, while the drive acts along only one of these axes. For such systems, we analyze the full distribution of structure factors. Next, we investigate the effects of imposing other boundary conditions on the system. In particular, we focus on models with shifted periodic boundary conditions (SPBC) along one axis and open boundary conditions (OBC) along the other axis. The OBC allow us to have a steady flux of particles through the system while the SPBC permits us to drive the system in a range of possibilities. Using Monte Carlo simulation techniques, we discover a rich variety of phenomena, especially at low temperatures. A continuum theory for the densities, based on Langevin equations, is formulated and its predictions compared to simulation data. Many large scale properties are described successfully. / Ph. D.

In an attempt to reach a better understanding of the properties and critical behavior of non-equilibrium systems, we investigate the steady state properties of three simple models, variations of the prototype, the driven Ising lattice gas. Our first system studied is the bilayer model, a stack of two driven Ising lattice gases allowed to interact. We study this model using a very simple analytic approximation, the high temperature expansion. Building on existing simulation data and field theory results, our goal is to test how faithfully the series expansion can reproduce the Monte Carlo phase diagram. We find that the agreement between our calculations and the already reported simulations results is remarkably good. Next, we investigate the critical behavior of a two-dimensional Ising lattice gas driven into a non-equilibrium steady state, subject to a local modification of the dynamics, namely, having anisotropic attempt frequencies for exchanges along different spatial directions. We employ both Monte Carlo simulation techniques and a high temperature expansion approximation and find the phase diagram of the system, perform a finite-size scaling study in order to determine the universality class of the model and compare our simulation results with the phase diagram obtained using the high temperature expansion. We conclude that the bias in the jump rates does not affect the universal critical properties of the system: the modified model is in the same universality class as the driven Ising lattice gas. Our last objective concerns a different inroad into the study of non-equilibrium steady states. Instead of investigating a non-equilibrium steady state via indirect observables, such as correlation functions and order parameters, we seek to compute the steady state probability distribution directly. This is feasible only for systems with a small number of degrees of freedom. We chose to study a one-dimensional version of the so-called two-temperature kinetic Ising model. We solve the master equation exactly for a 1x6 system, and compare the full configurational probability distribution with its equilibrium counterpart. / Ph. D.

We explore the nature of driven stochastic lattice systems with non-periodic boundary conditions. The systems consist of particle and holes which move by exchanges of nearest neighbor particle-hole pairs. These exchanges are controlled by the energetics associated with an internal Hamiltonian, an external drive and a stochastic coupling to a heat reservoir. The effect of the drive is to bias particle-hole exchanges along the field in such a way that a particle current can be established. Hard-core volume constraints limit the occupation of only one particle (hole) per lattice site. For certain regimes of the overall particle density and temperature, a system displays a homogeneous disordered phase. We investigate cooperative behavior in this phase by using two-point spatial correlation functions and structure factors. By varying the particle density and the temperature, the system orders into a phase separated state, consisting of particle-rich and particle-poor regions. The temperature and density for the co-existence state depend on the boundary conditions. By using Monte Carlo simulations, we establish co-existence curves for systems with shifted periodic boundary conditions. / Ph. D.

Un milieu poreux ou un matériau poreux comprend deux régions interconnectées : une perméable par un gaz ou un liquide et l’autre imperméable. Beaucoup de substances naturelles comme les roches, le sol et les tissus biologiques (par exemple, os, bio-membranes) sont poreuses ainsi que les matériaux manufacturés comme les ciments et les céramiques, etc. Les matériaux poreux ont des applications technologiques importantes et nombreuses, par exemple, comme tamis moléculaires, catalyseurs ou senseurs chimiques. Il existe un nombre très important d’études en expérience et en théorie pour comprendre la structure des matériaux poreux ainsi que les propriétés des substances confinées dans ces matériaux. Dans leur travail de pionnier, Madden et Glandt ont proposé un modèle très simple pour l’adsorption de fluide dans des milieux poreux désordonnés. Dans ce modèle, on forme la matrice en prenant une configuration figée instantanément d’un système à l’équilibre (“quench” en anglais) et puis un fluide est introduit dans une telle matrice. Récemment, T. Patsahan, M. Holovko et W. Dong ont généralisé la “scaled particle theory” (SPT) aux fluides confinés et obtenu ainsi des équations d’état analytiques pour un fluide de sphère dure dans plusieurs modèles de matrice. Dans un premier temps, j’ai développé la version de la SPT pour un mélange de sphères dures additives confiné en milieu poreux. Les expressions pour les valeurs au contact de différentes fonctions de distribution ont été obtenues également. J’ai effectué aussi des simulations de Monte Carlo. Les résultats de ces simulations sont utilisés pour valider les résultats théoriques. Ensuite, j’ai étudié aussi la séparation de phase d’un mélange binaire des sphères dures non additives confiné dans un milieu poreux. Pour obtenir l’équation d’état, nous avons utilisé une théorie de perturbation en prenant un fluide de sphères dures additive comme système de référence. Les résultats donnés par cette théorie sont en bon accord avec les résultats de simulation Monte Carlo. / A porous medium or a porous material (called as frame or matrix also) usually consists of two interconnected rejoins: one permeable by a gas or a liquid, i.e., pore or void, and the other impermeable. Many natural substances such as rocks, soils, biological tissues (e.g., bio membranes, bones), and manmade materials such as cements, foams and ceramics are porous materials. Porous materials have important technological applications such as molecular sieve, catalyst, chemical sensor, etc. In recent years, there have been considerable investigations for understanding thoroughly the structure of these materials as well as the behavior of substances confined in them. Much effort (both experimental and theoretical) has been devoted to the study of porous materials. In their pioneering work, a very simple model for the fluid adsorption in random porous media was proposed by Madden and Glandt. The matrix in Madden-Glandt model is made by quenching an equilibrium system. Then, a fluid is adsorbed in such a matrix. Recently, T. Patsahan, M. Holovko and W. Dong have extended the scaled particle theory (SPT) to confined fluids and derived analytical equations of state (EOS) for a hard sphere (HS) fluid in some matrix models. In this thesis, using SPT method, I obtained the equation of state of additive hard-sphere (AHS) fluid mixtures confined in porous media. The contact values of the fluid-fluid and fluid-matrix radial distribution functions (RDF) were derived as well. The results of the contact values of the RDFs and the chemical potentials of different species were assessed against Monte Carlo simulations. Moreover, I analyzed also the fluid-fluid phase separation of non-additive hard sphere (NAHS) fluid confined in porous media. An equation of state is derived by using a perturbation theory with a multi-component fluid reference. The results of this theory are in good agreement with those obtained from semi grand canonical ensemble Monte Carlo simulations.

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