TCAD approaches to multidimensional simulation of advanced semiconductor devices

Technology scaling increasingly emphasizes complexity and non-ideality of the electrical behavior of semiconductor devices and boosts interest on alternatives to the conventional planar MOSFET architecture. TCAD simulation tools are fundamental to the analysis and development of new technology generations. However, the increasing device complexity is reflected in an augmented dimensionality of the problems to be solved. The trade-off between accuracy and computational cost of the simulation is especially influenced by domain discretization: mesh generation is therefore one of the most critical steps and automatic approaches are sought. Moreover, the problem size is further increased by process variations, calling for a statistical representation of the single device through an ensemble of microscopically different instances. The aim of this thesis is to present multi-disciplinary approaches to handle this increasing problem dimensionality in a numerical simulation perspective. The topic of mesh generation is tackled by presenting a new Wavelet-based Adaptive Method (WAM) for the automatic refinement of 2D and 3D domain discretizations. Multiresolution techniques and efficient signal processing algorithms are exploited to increase grid resolution in the domain regions where relevant physical phenomena take place. Moreover, the grid is dynamically adapted to follow solution changes produced by bias variations and quality criteria are imposed on the produced meshes. The further dimensionality increase due to variability in extremely scaled devices is considered with reference to two increasingly critical phenomena, namely line-edge roughness (LER) and random dopant fluctuations (RD). The impact of such phenomena on FinFET devices, which represent a promising alternative to planar CMOS technology, is estimated through 2D and 3D TCAD simulations and statistical tools, taking into account matching performance of single devices as well as basic circuit blocks such as SRAMs. Several process options are compared, including resist- and spacer-defined fin patterning as well as different doping profile definitions. Combining statistical simulations with experimental data, potentialities and shortcomings of the FinFET architecture are analyzed and useful design guidelines are provided, which boost feasibility of this technology for mainstream applications in sub-45 nm generation integrated circuits.

DNA hybrid materials consisting of oligonucleotides and organic molecules: synthesis, characterization and applications

The goal of this thesis was to increase the functionality of pristine DNA scaffolds by functionalizing them with fluorescent dyes and hydrophobic moieties. Two important steps were necessary to realize this aim successfully. First, nucleic acids needed to be synthesized making use of multidisciplinary toolbox for the generation and manipulation of polynucleic acids. The most important techniques were the solid phase synthesis involving the incorporation of standard and modified phosphoramidite building blocks as well as molecular biology procedures like the polymerase chain reaction, the bacterial amplification of plasmids and the enzymatic digestion of circular vectors. Second, and evenly important, was the characterization of the novel bioorganic hybrid structures by a multitude of techniques, especially optical measurements. For studying DNA-dye conjugates methods like UV/Vis and photoluminescence spectroscopy as well as time resolved luminescence spectroscopy were utilized. While these measurements characterized the bulk behavior of an ensemble of DNA-dye hybrids it was necessary for a complete understanding of the systems to look at single structures. This was done by single-molecule fluorescence spectroscopy and fluorescence correlation spectroscopy. For complete analysis the optical experiments were complemented by direct visualization techniques, i.e. high resolution transmission electron microscopy and scanning force microscopy.

LIKELIHOOD ESTIMATION OF CONJUGACY RELATIONSHIPS IN LINEAR MODELS WITH APPLICATIONS TO HIGH-THROUGHPUT GENOMICS

In the simultaneous estimation of a large number of related quantities, multilevel models provide a formal mechanism for efficiently making use of the ensemble of information for deriving individual estimates. In this article we investigate the ability of the likelihood to identify the relationship between signal and noise in multilevel linear mixed models. Specifically, we consider the ability of the likelihood to diagnose conjugacy or independence between the signals and noises. Our work was motivated by the analysis of data from high-throughput experiments in genomics. The proposed model leads to a more flexible family. However, we further demonstrate that adequately capitalizing on the benefits of a well fitting fully-specified likelihood in the terms of gene ranking is difficult.

A BAYESIAN HIERARCHICAL FRAMEWORK FOR SPATIAL MODELING OF fMRI DATA

Functional neuroimaging techniques enable investigations into the neural basis of human cognition, emotions, and behaviors. In practice, applications of functional magnetic resonance imaging (fMRI) have provided novel insights into the neuropathophysiology of major psychiatric,neurological, and substance abuse disorders, as well as into the neural responses to their treatments. Modern activation studies often compare localized task-induced changes in brain activity between experimental groups. One may also extend voxel-level analyses by simultaneously considering the ensemble of voxels constituting an anatomically defined region of interest (ROI) or by considering means or quantiles of the ROI. In this work we present a Bayesian extension of voxel-level analyses that offers several notable benefits. First, it combines whole-brain voxel-by-voxel modeling and ROI analyses within a unified framework. Secondly, an unstructured variance/covariance for regional mean parameters allows for the study of inter-regional functional connectivity, provided enough subjects are available to allow for accurate estimation. Finally, an exchangeable correlation structure within regions allows for the consideration of intra-regional functional connectivity. We perform estimation for our model using Markov Chain Monte Carlo (MCMC) techniques implemented via Gibbs sampling which, despite the high throughput nature of the data, can be executed quickly (less than 30 minutes). We apply our Bayesian hierarchical model to two novel fMRI data sets: one considering inhibitory control in cocaine-dependent men and the second considering verbal memory in subjects at high risk for Alzheimer’s disease. The unifying hierarchical model presented in this manuscript is shown to enhance the interpretation content of these data sets.

Conformational preferences of natural and C3-modified epothilones in aqueous solution

The conformational properties of the microtubule-stabilizing agent epothilone A ( 1a) and its 3-deoxy and 3-deoxy-2,3-didehydro derivatives 2 and 3 have been investigated in aqueous solution by a combination of NMR spectroscopic methods, Monte Carlo conformational searches, and NAMFIS calculations. The tubulin-bound conformation of epothilone A ( 1a), as previously proposed on the basis of solution NMR data, was found to represent a significant fraction of the ensemble of conformations present for the free ligands in aqueous solution.

Impact of volcanic stratospheric aerosols on diurnal temperature range in Europe over the past 200 years: Observations versus model simulations

We analyze the impact of stratospheric volcanic aerosols on the diurnal temperature range (DTR) over Europe using long-term subdaily station records. We compare the results with a 28-member ensemble of European Centre/Hamburg version 5.4 (ECHAM5.4) general circulation model simulations. Eight stratospheric volcanic eruptions during the instrumental period are investigated. Seasonal all- and clear-sky DTR anomalies are compared with contemporary (approximately 20 year) reference periods. Clear sky is used to eliminate cloud effects and better estimate the signal from the direct radiative forcing of the volcanic aerosols. We do not find a consistent effect of stratospheric aerosols on all-sky DTR. For clear skies, we find average DTR anomalies of −0.08°C (−0.13°C) in the observations (in the model), with the largest effect in the second winter after the eruption. Although the clear-sky DTR anomalies from different stations, volcanic eruptions, and seasons show heterogeneous signals in terms of order of magnitude and sign, the significantly negative DTR anomalies (e.g., after the Tambora eruption) are qualitatively consistent with other studies. Referencing with clear-sky DTR anomalies to the radiative forcing from stratospheric volcanic eruptions, we find the resulting sensitivity to be of the same order of magnitude as previously published estimates for tropospheric aerosols during the so-called “global dimming” period (i.e., 1950s to 1980s). Analyzing cloud cover changes after volcanic eruptions reveals an increase in clear-sky days in both data sets. Quantifying the impact of stratospheric volcanic eruptions on clear-sky DTR over Europe provides valuable information for the study of the radiative effect of stratospheric aerosols and for geo-engineering purposes.

A global historical ozone data set and prominent features of stratospheric variability prior to 1979

We present a vertically resolved zonal mean monthly mean global ozone data set spanning the period 1901 to 2007, called HISTOZ.1.0. It is based on a new approach that combines information from an ensemble of chemistry climate model (CCM) simulations with historical total column ozone information. The CCM simulations incorporate important external drivers of stratospheric chemistry and dynamics (in particular solar and volcanic effects, greenhouse gases and ozone depleting substances, sea surface temperatures, and the quasi-biennial oscillation). The historical total column ozone observations include ground-based measurements from the 1920s onward and satellite observations from 1970 to 1976. An off-line data assimilation approach is used to combine model simulations, observations, and information on the observation error. The period starting in 1979 was used for validation with existing ozone data sets and therefore only ground-based measurements were assimilated. Results demonstrate considerable skill from the CCM simulations alone. Assimilating observations provides additional skill for total column ozone. With respect to the vertical ozone distribution, assimilating observations increases on average the correlation with a reference data set, but does not decrease the mean squared error. Analyses of HISTOZ.1.0 with respect to the effects of El Niño–Southern Oscillation (ENSO) and of the 11 yr solar cycle on stratospheric ozone from 1934 to 1979 qualitatively confirm previous studies that focussed on the post-1979 period. The ENSO signature exhibits a much clearer imprint of a change in strength of the Brewer–Dobson circulation compared to the post-1979 period. The imprint of the 11 yr solar cycle is slightly weaker in the earlier period. Furthermore, the total column ozone increase from the 1950s to around 1970 at northern mid-latitudes is briefly discussed. Indications for contributions of a tropospheric ozone increase, greenhouse gases, and changes in atmospheric circulation are found. Finally, the paper points at several possible future improvements of HISTOZ.1.0.

The importance of glacier and forest change in hydrological climate-impact studies

Changes in land cover alter the water balance components of a catchment, due to strong interactions between soils, vegetation and the atmosphere. Therefore, hydrological climate impact studies should also integrate scenarios of associated land cover change. To reflect two severe climate-induced changes in land cover, we applied scenarios of glacier retreat and forest cover increase that were derived from the temperature signals of the climate scenarios used in this study. The climate scenarios were derived from ten regional climate models from the ENSEMBLES project. Their respective temperature and precipitation changes between the scenario period (2074–2095) and the control period (1984–2005) were used to run a hydrological model. The relative importance of each of the three types of scenarios (climate, glacier, forest) was assessed through an analysis of variance (ANOVA). Altogether, 15 mountainous catchments in Switzerland were analysed, exhibiting different degrees of glaciation during the control period (0–51%) and different degrees of forest cover increase under scenarios of change (12–55% of the catchment area). The results show that even an extreme change in forest cover is negligible with respect to changes in runoff, but it is crucial as soon as changes in evaporation or soil moisture are concerned. For the latter two variables, the relative impact of forest change is proportional to the magnitude of its change. For changes that concern 35% of the catchment area or more, the effect of forest change on summer evapotranspiration is equally or even more important than the climate signal. For catchments with a glaciation of 10% or more in the control period, the glacier retreat significantly determines summer and annual runoff. The most important source of uncertainty in this study, though, is the climate scenario and it is highly recommended to apply an ensemble of climate scenarios in the impact studies. The results presented here are valid for the climatic region they were tested for, i.e., a humid, mid-latitude mountainous environment. They might be different for regions where the evaporation is a major component of the water balance, for example. Nevertheless, a hydrological climate-impact study that assesses the additional impacts of forest and glacier change is new so far and provides insight into the question whether or not it is necessary to account for land cover changes as part of climate change impacts on hydrological systems.

Seasonality and magnitude of floods in Switzerland under future climate change

The flood seasonality of catchments in Switzerland is likely to change under climate change because of anticipated alterations of precipitation as well as snow accumulation and melt. Information on this change is crucial for flood protection policies, for example, or regional flood frequency analysis. We analysed projected changes in mean annual and maximum floods of a 22-year period for 189 catchments in Switzerland and two scenario periods in the 21st century based on an ensemble of climate scenarios. The flood seasonality was analysed with directional statistics that allow assessing both changes in the mean date a flood occurs as well as changes in the strength of the seasonality. We found that the simulated change in flood seasonality is a function of the change in flow regime type. If snow accumulation and melt is important in a catchment during the control period, then the anticipated change in flood seasonality is most pronounced. Decreasing summer precipitation in the scenarios additionally affects the flood seasonality (mean date of flood occurrence) and leads to a decreasing strength of seasonality, that is a higher temporal variability in most cases. The magnitudes of mean annual floods and more clearly of maximum floods (in a 22-year period) are expected to increase in the future because of changes in flood-generating processes and scaled extreme precipitation. Southern alpine catchments show a different signal, though: the simulated mean annual floods decrease in the far future, that is at the end of the 21st century. Copyright © 2013 John Wiley & Sons, Ltd.

Large-scale temperature response to external forcing in simulations and reconstructions of the last millennium

Understanding natural climate variability and its driving factors is crucial to assessing future climate change. Therefore, comparing proxy-based climate reconstructions with forcing factors as well as comparing these with paleoclimate model simulations is key to gaining insights into the relative roles of internal versus forced variability. A review of the state of modelling of the climate of the last millennium prior to the CMIP5–PMIP3 (Coupled Model Intercomparison Project Phase 5–Paleoclimate Modelling Intercomparison Project Phase 3) coordinated effort is presented and compared to the available temperature reconstructions. Simulations and reconstructions broadly agree on reproducing the major temperature changes and suggest an overall linear response to external forcing on multidecadal or longer timescales. Internal variability is found to have an important influence at hemispheric and global scales. The spatial distribution of simulated temperature changes during the transition from the Medieval Climate Anomaly to the Little Ice Age disagrees with that found in the reconstructions. Thus, either internal variability is a possible major player in shaping temperature changes through the millennium or the model simulations have problems realistically representing the response pattern to external forcing. A last millennium transient climate response (LMTCR) is defined to provide a quantitative framework for analysing the consistency between simulated and reconstructed climate. Beyond an overall agreement between simulated and reconstructed LMTCR ranges, this analysis is able to single out specific discrepancies between some reconstructions and the ensemble of simulations. The disagreement is found in the cases where the reconstructions show reduced covariability with external forcings or when they present high rates of temperature change.

Amplified inception of European Little Ice Age by sea ice-ocean-atmosphere feedbacks

The inception of the Little Ice Age (~1400–1700 AD) is believed to have been driven by an interplay of external forcing and climate system internal variability. While the hemispheric signal seems to have been dominated by solar irradiance and volcanic eruptions, the understanding of mechanisms shaping the climate on a continental scale is less robust. In an ensemble of transient model simulations and a new type of sensitivity experiments with artificial sea ice growth, the authors identify a sea ice–ocean–atmosphere feedback mechanism that amplifies the Little Ice Age cooling in the North Atlantic–European region and produces the temperature pattern suggested by paleoclimatic reconstructions. Initiated by increasing negative forcing, the Arctic sea ice substantially expands at the beginning of the Little Ice Age. The excess of sea ice is exported to the subpolar North Atlantic, where it melts, thereby weakening convection of the ocean. Consequently, northward ocean heat transport is reduced, reinforcing the expansion of the sea ice and the cooling of the Northern Hemisphere. In the Nordic Seas, sea surface height anomalies cause the oceanic recirculation to strengthen at the expense of the warm Barents Sea inflow, thereby further reinforcing sea ice growth. The absent ocean–atmosphere heat flux in the Barents Sea results in an amplified cooling over Northern Europe. The positive nature of this feedback mechanism enables sea ice to remain in an expanded state for decades up to a century, favoring sustained cold periods over Europe such as the Little Ice Age. Support for the feedback mechanism comes from recent proxy reconstructions around the Nordic Seas.

Cryo-electron tomography of Kaposi's sarcoma-associated herpesvirus capsids reveals dynamic scaffolding structures essential to capsid assembly and maturation.

Kaposi's sarcoma-associated herpesvirus (KSHV) is a recently discovered DNA tumor virus that belongs to the gamma-herpesvirus subfamily. Though numerous studies on KSHV and other herpesviruses, in general, have revealed much about their multilayered organization and capsid structure, the herpesvirus capsid assembly and maturation pathway remains poorly understood. Structural variability or irregularity of the capsid internal scaffolding core and the lack of adequate tools to study such structures have presented major hurdles to earlier investigations employing more traditional cryo-electron microscopy (cryoEM) single particle reconstruction. In this study, we used cryo-electron tomography (cryoET) to obtain 3D reconstructions of individual KSHV capsids, allowing direct visualization of the capsid internal structures and systematic comparison of the scaffolding cores for the first time. We show that B-capsids are not a structurally homogenous group; rather, they represent an ensemble of "B-capsid-like" particles whose inner scaffolding is highly variable, possibly representing different intermediates existing during the KSHV capsid assembly and maturation. This information, taken together with previous observations, has allowed us to propose a detailed pathway of herpesvirus capsid assembly and maturation.

On the reduced sensitivity of the Atlantic overturning to Greenland ice sheet melting in projections: a multi-model assessment

Large uncertainties exist concerning the impact of Greenland ice sheet melting on the Atlantic meridional overturning circulation (AMOC) in the future, partly due to different sensitivity of the AMOC to freshwater input in the North Atlantic among climate models. Here we analyse five projections from different coupled ocean–atmosphere models with an additional 0.1 Sv (1 Sv = 10 6 m3/s) of freshwater released around Greenland between 2050 and 2089. We find on average a further weakening of the AMOC at 26°N of 1.1 ± 0.6 Sv representing a 27 ± 14% supplementary weakening in 2080–2089, as compared to the weakening relative to 2006–2015 due to the effect of the external forcing only. This weakening is lower than what has been found with the same ensemble of models in an identical experimen - tal set-up but under recent historical climate conditions. This lower sensitivity in a warmer world is explained by two main factors. First, a tendency of decoupling is detected between the surface and the deep ocean caused by an increased thermal stratification in the North Atlantic under the effect of global warming. This induces a shoaling of ocean deep ventilation through convection hence ventilating only intermediate levels. The second important effect concerns the so-called Canary Current freshwater leakage; a process by which additionally released fresh water in the North Atlantic leaks along the Canary Current and escapes the convection zones towards the subtropical area. This leakage is increasing in a warming climate, which is a consequence of decreasing gyres asymmetry due to changes in Ekman rumping. We suggest that these modifications are related with the northward shift of the jet stream in a warmer world. For these two reasons the AMOC is less susceptible to freshwater perturbations (near the deep water formation sides) in the North Atlantic as compared to the recent historical climate conditions. Finally, we propose a bilinear model that accounts for the two former processes to give a conceptual explanation about the decreasing AMOC sensitivity due to freshwater input. Within the limit of this bilinear model, we find that 62 ± 8% of the reduction in sensitivity is related with the changes in gyre asymmetry and freshwater leakage and 38 ± 8% is due to the reduction in deep ocean ventilation associated with the increased stratification in the North Atlantic.

The dominant role of semi-arid ecosystems in the trend and variability of the land CO2 sink

The growth rate of atmospheric carbondioxide(CO2) concentrations since industrialization is characterized by large interannual variability, mostly resulting from variability in CO 2 uptake by terrestrial ecosystems (typically termed carbon sink). However, the contributions of regional ecosystems to that variability are not well known. Using an ensemble of ecosystem and land-surface models and an empirical observation-based product of global gross primary production, we show that the mean sink, trend, and interannual variability in CO2 uptake by terrestrial ecosystems are dominated by distinct biogeographic regions. Whereas the mean sink is dominated by highly productive lands (mainly tropical forests), the trend and interannual variability of the sink are dominated by semi-arid ecosystems whose carbon balance is strongly associated with circulation-driven variations in both precipitation and temperature.

Transient Earth system responses to cumulative carbon dioxide emissions: linearities, uncertainties, and probabilities in an observation-constrained model ensemble

Information on the relationship between cumulative fossil CO2 emissions and multiple climate targets is essential to design emission mitigation and climate adaptation strategies. In this study, the transient response of a climate or environmental variable per trillion tonnes of CO2 emissions, termed TRE, is quantified for a set of impact-relevant climate variables and from a large set of multi-forcing scenarios extended to year 2300 towards stabilization. An  ∼ 1000-member ensemble of the Bern3D-LPJ carbon–climate model is applied and model outcomes are constrained by 26 physical and biogeochemical observational data sets in a Bayesian, Monte Carlo-type framework. Uncertainties in TRE estimates include both scenario uncertainty and model response uncertainty. Cumulative fossil emissions of 1000 Gt C result in a global mean surface air temperature change of 1.9 °C (68 % confidence interval (c.i.): 1.3 to 2.7 °C), a decrease in surface ocean pH of 0.19 (0.18 to 0.22), and a steric sea level rise of 20 cm (13 to 27 cm until 2300). Linearity between cumulative emissions and transient response is high for pH and reasonably high for surface air and sea surface temperatures, but less pronounced for changes in Atlantic meridional overturning, Southern Ocean and tropical surface water saturation with respect to biogenic structures of calcium carbonate, and carbon stocks in soils. The constrained model ensemble is also applied to determine the response to a pulse-like emission and in idealized CO2-only simulations. The transient climate response is constrained, primarily by long-term ocean heat observations, to 1.7 °C (68 % c.i.: 1.3 to 2.2 °C) and the equilibrium climate sensitivity to 2.9 °C (2.0 to 4.2 °C). This is consistent with results by CMIP5 models but inconsistent with recent studies that relied on short-term air temperature data affected by natural climate variability.