Particle Accelerators and Detectors for medical Diagnostics and Therapy

This Habilitationsschrift (Habilitation thesis) is focused on my research activities on medical applications of particle physics and was written in 2013 to obtain the Venia Docendi (Habilitation) in experimental physics at the University of Bern. It is based on selected publications, which represented at that time my major scientific contributions as an experimental physicist to the field of particle accelerators and detectors applied to medical diagnostics and therapy. The thesis is structured in two parts. In Part I, Chapter 1 presents an introduction to accelerators and detectors applied to medicine, with particular focus on cancer hadrontherapy and on the production of radioactive isotopes. In Chapter 2, my publications on medical particle accelerators are introduced and put into their perspective. In particular, high frequency linear accelerators for hadrontherapy are discussed together with the new Bern cyclotron laboratory. Chapter 3 is dedicated to particle detectors with particular emphasis on three instruments I contributed to propose and develop: segmented ionization chambers for hadrontherapy, a proton radiography apparatus with nuclear emulsion films, and a beam monitor detector for ion beams based on doped silica fibres. Selected research and review papers are contained in Part II. For copyright reasons, they are only listed and not reprinted in this on-line version. They are available on the websites of the journals.

Stereological estimation of particle shape and orientation from volume tensors

In the present paper, we describe new robust methods of estimating cell shape and orientation in 3D from sections. The descriptors of 3D cell shape and orientation are based on volume tensors which are used to construct an ellipsoid, the Miles ellipsoid, approximating the average cell shape and orientation in 3D. The estimators of volume tensors are based on observations in several optical planes through sampled cells. This type of geometric sampling design is known as the optical rotator. The statistical behaviour of the estimator of the Miles ellipsoid is studied under a flexible model for 3D cell shape and orientation. In a simulation study, the lengths of the axes of the Miles ellipsoid can be estimated with CVs of about 2% if 100 cells are sampled. Finally, we illustrate the use of the developed methods in an example, involving neurons in the medial prefrontal cortex of rat.

Species interactions and random dispersal rather than habitat filtering drive community assembly during early plant succession

Theory on plant succession predicts a temporal increase in the complexity of spatial community structure and of competitive interactions: initially random occurrences of early colonising species shift towards spatially and competitively structured plant associations in later successional stages. Here we use long-term data on early plant succession in a German post mining area to disentangle the importance of random colonisation, habitat filtering, and competition on the temporal and spatial development of plant community structure. We used species co-occurrence analysis and a recently developed method for assessing competitive strength and hierarchies (transitive versus intransitive competitive orders) in multispecies communities. We found that species turnover decreased through time within interaction neighbourhoods, but increased through time outside interaction neighbourhoods. Successional change did not lead to modular community structure. After accounting for species richness effects, the strength of competitive interactions and the proportion of transitive competitive hierarchies increased through time. Although effects of habitat filtering were weak, random colonization and subsequent competitive interactions had strong effects on community structure. Because competitive strength and transitivity were poorly correlated with soil characteristics, there was little evidence for context dependent competitive strength associated with intransitive competitive hierarchies.

Dual-Domain Filtering

We propose dual-domain filtering, an image processing paradigm that couples spatial domain with frequency domain filtering. Our dual-domain defined filter removes artifacts like residual noise of other image denoising methods and compression artifacts. Moreover, iterating the filter achieves state-of-the-art image denoising results, but with a much simpler algorithm than competing approaches. The simplicity and versatility of the dual-domain filter makes it an attractive tool for image processing.

Temporally Coherent Disparity Maps Using CRFs with Fast 4D Filtering

State of the art methods for disparity estimation achieve good results for single stereo frames, but temporal coherence in stereo videos is often neglected. In this paper we present a method to compute temporally coherent disparity maps. We define an energy over whole stereo sequences and optimize their Conditional Random Field (CRF) distributions using mean-field approximation. We introduce novel terms for smoothness and consistency between the left and right views, and perform CRF optimization by fast, iterative spatio-temporal filtering with linear complexity in the total number of pixels. Our results rank among the state of the art while having significantly less flickering artifacts in stereo sequences.

Observations of the Sensitivity of Beam Attenuation to Particle Size in a Coastal Bottom Boundary Layer

The goal of this study was to test the hypothesis that the aggregated state of natural marine particles constrains the sensitivity of optical beam attenuation to particle size. An instrumented bottom tripod was deployed at the 12-m node of the Martha's Vineyard Coastal Observatory to monitor particle size distributions, particle size-versus-settling-velocity relationships, and the beam attenuation coefficient (c(p)) in the bottom boundary layer in September 2007. An automated in situ filtration system on the tripod collected 24 direct estimates of suspended particulate mass (SPM) during each of five deployments. On a sampling interval of 5 min, data from a Sequoia Scientific LISST 100x Type B were merged with data from a digital floc camera to generate suspended particle volume size distributions spanning diameters from approximately 2 mu m to 4 cm. Diameter-dependent densities were calculated from size-versus-settling-velocity data, allowing conversion of the volume size distributions to mass distributions, which were used to estimate SPM every 5 min. Estimated SPM and measured c(p) from the LISST 100x were linearly correlated throughout the experiment, despite wide variations in particle size. The slope of the line, which is the ratio of c(p) to SPM, was 0.22 g m(-2). Individual estimates of c(p):SPM were between 0.2 and 0.4 g m(-2) for volumetric median particle diameters ranging from 10 to 150 mu m. The wide range of values in c(p):SPM in the literature likely results from three factors capable of producing factor-of-two variability in the ratio: particle size, particle composition, and the finite acceptance angle of commercial beam-transmissometers.

A Ladder Operator Solution to the Particle in a Box Problem

A ladder operator solution to the particle in a box problem of elementary quantum mechanics is presented, although the pedagogical use of this method for this problem is questioned.

Advance P. Chem. Problems (I) Populations, Partition Functions, Particle in Box, Harmonic Oscillators, Angular Momentum and Rigid Rotor

This is a set of P. Chem. problems posed at slightly higher than the normal text book level, for students who are continuing in the study of this subject.

Integrated Data Sets of the EU FP5 Research Project ORFOIS: Origin and fate of biogenic particle fluxes in the ocean and their interactions with atmospheric CO2 concentrations as well as the marine sediment

For a reliable simulation of the time and space dependent CO2 redistribution between ocean and atmosphere an appropriate time dependent simulation of particle dynamics processes is essential but has not been carried out so far. The major difficulties were the lack of suitable modules for particle dynamics and early diagenesis (in order to close the carbon and nutrient budget) in ocean general circulation models, and the lack of an understanding of biogeochemical processes, such as the partial dissolution of calcareous particles in oversaturated water. The main target of ORFOIS was to fill in this gap in our knowledge and prediction capability infrastructure. This goal has been achieved step by step. At first comprehensive data bases (already existing data) of observations of relevance for the three major types of biogenic particles, organic carbon (POC), calcium carbonate (CaCO3), and biogenic silica (BSi or opal), as well as for refractory particles of terrestrial origin were collated and made publicly available.