L-System model for the growth of arbuscular mycorrhizal fungi, both within and outside of their host roots.

Development of arbuscular mycorrhizal fungal colonization of roots and the surrounding soil is the central process of mycorrhizal symbiosis, important for ecosystem functioning and commercial inoculum applications. To improve mechanistic understanding of this highly spatially and temporarily dynamic process, we developed a three-dimensional model taking into account growth of the roots and hyphae. It is for the first time that infection within the root system is simulated dynamically and in a spatially resolved way. Comparison between data measured in a calibration experiment and simulated results showed a good fit. Our simulations showed that the position of the fungal inoculum affects the sensitivity of hyphal growth parameters. Variation in speed of secondary infection and hyphal lifetime had a different effect on root infection and hyphal length, respectively, depending on whether the inoculum was concentrated or dispersed. For other parameters (branching rate, distance between entry points), the relative effect was the same independent of inoculum placement. The model also indicated that maximum root colonization levels well below 100%, often observed experimentally, may be a result of differential spread of roots and hyphae, besides intrinsic plant control, particularly upon localized placement of inoculum and slow secondary infection.

Space-charge compensation measurements in electron cyclotron resonance ion source low energy beam transport lines with a retarding field analyzer.

In this paper we describe the first systematic measurement of beam neutralization (space charge compensation) in the ECR low energy transport line with a retarding field analyzer, which can be used to measure the potential of the beam. Expected trends for the space charge compensation levels such as increase with residual gas pressure, beam current, and beam density could be observed. However, the overall levels of neutralization are consistently low (<60%). The results and the processes involved for neutralizing ion beams are discussed for conditions typical for ECR injector beam lines. The results are compared to a simple theoretical beam plasma model as well as simulations.

First charge breeding of a rare-isotope beam with the electron-beam ion trap of the ReA post-accelerator at the National Superconducting Cyclotron Laboratory.

An electron-beam ion trap (EBIT) charge breeder is being brought into operation at the National Superconducting Cyclotron Laboratory at Michigan State University. The EBIT is part of the ReA post-accelerator for reacceleration of rare isotopes, which are thermalized in a gas "stopping" cell after being produced at high energy by projectile fragmentation. The ReA EBIT has a distinctive design; it is characterized by a high-current electron gun and a two-field superconducting magnet to optimize the capture and charge-breeding efficiency of continuously injected singly charged ion beams. Following a brief overview of the reaccelerator system and the ReA EBIT, this paper presents the latest commissioning results, particularly, charge breeding and reacceleration of the highly charged rare isotopes, (76)Ga(24 +, 25 +).

Coarse and fine root plants affect pore size distributions differently.

AIMS: Small scale root-pore interactions require validation of their impact on effective hydraulic processes at the field scale. Our objective was to develop an interpretative framework linking root effects on macroscopic pore parameters with knowledge at the rhizosphere scale. METHODS: A field experiment with twelve species from different families was conducted. Parameters of Kosugi's pore size distribution (PSD) model were determined inversely from tension infiltrometer data. Measured root traits were related to pore variables by regression analysis. A pore evolution model was used to analyze if observed pore dynamics followed a diffusion like process. RESULTS: Roots essentially conditioned soil properties at the field scale. Rooting densities higher than 0.5 % of pore space stabilized soil structure against pore loss. Coarse root systems increased macroporosity by 30 %. Species with dense fine root systems induced heterogenization of the pore space and higher micropore volume. We suggested particle re-orientation and aggregate coalescence as main underlying processes. The diffusion type pore evolution model could only partially capture the observed PSD dynamics. CONCLUSIONS: Root systems differing in axes morphology induced distinctive pore dynamics. Scaling between these effective hydraulic impacts and processes at the root-pore interface is essential for plant based management of soil structure.

Root induced changes of effective 1D hydraulic properties in a soil column.

AIMS: Roots are essential drivers of soil structure and pore formation. This study aimed at quantifying root induced changes of the pore size distribution (PSD). The focus was on the extent of clogging vs. formation of pores during active root growth. METHODS: Parameters of Kosugi's lognormal PSD model were determined by inverse estimation in a column experiment with two cover crops (mustard, rye) and an unplanted control. Pore dynamics were described using a convection-dispersion like pore evolution model. RESULTS: Rooted treatments showed a wider range of pore radii with increasing volumes of large macropores >500 µm and micropores <2.5 µm, while fine macropores, mesopores and larger micropores decreased. The non-rooted control showed narrowing of the PSD and reduced porosity over all radius classes. The pore evolution model accurately described root induced changes, while structure degradation in the non-rooted control was not captured properly. Our study demonstrated significant short term root effects with heterogenization of the pore system as dominant process of root induced structure formation. CONCLUSIONS: Pore clogging is suggested as a partial cause for reduced pore volume. The important change in micro- and large macropores however indicates that multiple mechanic and biochemical processes are involved in root-pore interactions.

HDR syndrome: a follow-up genotype-phenotype analysis of a de novo missense Thr272Ile mutation in exon 4 of GATA3.

Hypoparathyroidism, sensorineural deafness and renal dysplasia (HDR) syndrome (MIM 146255) is a rare autosomal dominant disorder caused by mutations in the gene encoding GATA3, a dual zinc-finger transcription factor involved in vertebrate embryonic development. In this clinical case study we report on a follow-up of a phenotype associated with a GATA3 mutation. HDR syndrome was clinically diagnosed at age of 1.5 years in a boy with a de novo heterozygous missense (c.815C→T) mutation, Thr272Ile, in exon 4 of the GATA3 gene. Both parents were negative for Thr272Ile.At age of 17 months, the patient had a weight of 10.7, a body length of 78 cm, and a head circumference of 47.5 cm. By the age of 7 years, growth is age-appropriate, severe bilateral hearing loss (dB 60) was corrected by hearing aids. However, cognitive development (auditory sensory me-mory and language abilities) is at the lower ends of the test scores.In conclusion, a mildly impaired clinical course was achieved by the age of 7 years in a patient with HDR syndrome; this report adds to the body of data on genotype-phenotype analysis in HDR syndrome. ·

Initial commissioning results with the NSCL Electron Beam Ion Trap.

The ReA reaccelerator is being added to the National Superconducting Cyclotron Laboratory (NSCL) fragmentation facility in order to provide exotic rare-isotope beams, not available at the Isotope Separation On-Line facilities, in the several-MeV/u energy range. The first stage of the NSCL reaccelerator complex, consisting of an EBIT charge breeder, a room-temperature radiofrequency quadrupole (RFQ) accelerator, and superconducting linear accelerator modules, has been completed and is being put into operation. Commissioning of the EBIT has started by extracting charge-bred residual gas ions, ions created from a Ne gas jet directed across the EBIT's electron beam and ions captured from an external test ion source. Charge-bred ions from the Ne gas jet have been extracted as a pulse and accelerated through the RFQ and the two cryomodules.

Low energy beam transport for facility for rare isotope beams driver linear particle accelerator.

The driver linac for the facility for rare isotope beams (FRIB) will provide a wide range of primary ion beams for nuclear physics research. The linac will be capable of accelerating a uranium beam to an energy of up to 200 Mev∕u and delivering it to a fragmentation target with a maximum power of 400 kW. Stable ion beams will be produced by a high performance electron cyclotron resonance ion source operating at 28 GHz. The ion source will be located on a high voltage platform to reach an initial beam energy of 12 keV∕u. After extraction, the ion beam will be transported vertically down to the linac tunnel in a low energy beam transport (LEBT) system and injected into a radio frequency quadrupole (RFQ) operating at a frequency of 80.5 MHz. To meet the beam power requirements, simultaneous acceleration of two-charge states will be used for heavier ions (≥Xe). This paper presents the layout of the FRIB LEBT and the beam dynamics in the LEBT. In particular, simulation and design of the beam line section before charge state selection will be detailed. The need to use an achromatic design for the charge state selection system and the advantage of an ion beam collimation system to limit the emittance of the beam injected into the RFQ will be discussed in this paper.

Progress towards the development of a realistic electron cyclotron resonance ion source extraction model.

In this paper, an ongoing effort to provide a simulation and design tool for electron cyclotron resonance ion source extraction and low energy beam transport is described and benchmarked against experimental results. Utilizing the particle-in-cell code WARP, a set of scripts has been developed: A semiempirical method of generating initial conditions, a 2D-3D hybrid method of plasma extraction and a simple beam transport deck. Measured emittances and beam profiles of uranium and helium beams are shown and the influence of the sextupole part of the plasma confinement field is investigated. The results are compared to simulations carried out using the methods described above. The results show that the simulation model (with some additional refinements) represents highly charged, well-confined ions well, but that the model is less applicable for less confined, singly charged ions.

DNA methylation studies on imprinted loci in a male monozygotic twin pair discordant for Beckwith-Wiedemann syndrome.

Beckwith­Wiedemann syndrome (BWS) is one of the most prevalent congenital disorders predominantly caused by epigenetic alterations. Here we present an extensive case study of a monozygotic monochorionic male twin pair discordant for BWS. Our analysis allows to correlate BWS symptoms, like a protruding tongue, indented ears and transient neonatal hypoglycaemia, to an abnormal methylation at the KvDMR1. DNAs extracted from peripheral blood, skin fibroblasts, saliva and buccal swab of both twins, their sister and parents were analysed at 11 differentially methylated regions (DMRs) including all four relevant DMRs of the BWS region. The KvDMR1 was exclusively found to be hypomethylated in all cell types of the affected BWS twin, while the unaffected twin and the relatives showed normal methylation in fibroblasts, buccal swab and saliva DNA. Interestingly, the twins share a common blood-specific hypomethylation phenotype most probably caused by a feto-fetal transfusion between both twins. Because microsatellite analysis furthermore revealed a normal biparental karyotype for chromosome 11, our results point to an exclusive correlation of the observed BWS symptoms to locally restricted epimutations at the KvDMR1 of the maternal chromosome.

The third generation superconducting 28 GHz electron cyclotron resonance ion source VENUS (invited).

VENUS is a third generation electron cyclotron resonance (ECR) ion source, which incorporates a high field superconducting NbTi magnet structure, a 28 GHz gryotron microwave source and a state of the art closed cycle cryosystem. During the decade from initial concept to regular operation, it has demonstrated both the feasibility and the performance levels of this new generation of ECR ion sources and required innovation on magnet construction, plasma chamber design, and beam transport. In this paper, the development, performance, and major innovations are described as well as a look to the potential to construct a fourth generation ECR ion source.

The effect of rf pulse pattern on bremsstrahlung and ion current time evolution of an ECRIS.

Time-resolved helium ion production and bremsstrahlung emission from JYFL 14 GHz ECRIS is presented with different radio frequency pulse lengths. rf on times are varied from 5 to 50 ms and rf off times from 10 to 1000 ms between different measurement sets. It is observed that the plasma breakdown occurs a few milliseconds after launching the rf power into the plasma chamber, and in the beginning of the rf pulses a preglow transient is seen. During this transient the ion beam currents are increased by several factors compared to a steady state situation. By adjusting the rf pulse separation the maximum ion beam currents can be maintained during the so-called preglow regime while the amount of bremsstrahlung radiation is significantly decreased.

Measurement of radial and axial high energy x-ray spectra in electron cyclotron resonance ion source plasmas.

Radial and axial x-ray measurements of electron cyclotron resonance ion sources operating at microwave frequencies of 6.4 and 14 GHz are presented. Results indicate a greater detected photon energy in the radial direction than the axial direction for both the 6.4 GHz source and the 14 GHz source. It is also seen that the 14 GHz source produces x-rays with higher energies, when compared to the 6.4 GHz source, in both radial and axial directions.

Nb3Sn superconducting magnets for electron cyclotron resonance ion sources.

Electron cyclotron resonance (ECR) ion sources are an essential component of heavy-ion accelerators. Over the past few decades advances in magnet technology and an improved understanding of the ECR ion source plasma physics have led to remarkable performance improvements of ECR ion sources. Currently third generation high field superconducting ECR ion sources operating at frequencies around 28 GHz are the state of the art ion injectors and several devices are either under commissioning or under design around the world. At the same time, the demand for increased intensities of highly charged heavy ions continues to grow, which makes the development of even higher performance ECR ion sources a necessity. To extend ECR ion sources to frequencies well above 28 GHz, new magnet technology will be needed in order to operate at higher field and force levels. The superconducting magnet program at LBNL has been developing high field superconducting magnets for particle accelerators based on Nb(3)Sn superconducting technology for several years. At the moment, Nb(3)Sn is the only practical conductor capable of operating at the 15 T field level in the relevant configurations. Recent design studies have been focused on the possibility of using Nb(3)Sn in the next generation of ECR ion sources. In the past, LBNL has worked on the VENUS ECR, a 28 GHz source with solenoids and a sextupole made with NbTi operating at fields of 6-7 T. VENUS has now been operating since 2004. We present in this paper the design of a Nb(3)Sn ECR ion source optimized to operate at an rf frequency of 56 GHz with conductor peak fields of 13-15 T. Because of the brittleness and strain sensitivity of Nb(3)Sn, particular care is required in the design of the magnet support structure, which must be capable of providing support to the coils without overstressing the conductor. In this paper, we present the main features of the support structure, featuring an external aluminum shell pretensioned with water-pressurized bladders, and we analyze the expected coil stresses with a two-dimensional finite element mechanical model.

Development of a pepper-pot device to determine the emittance of an ion beam generated by electron cyclotron resonance ion sources.

This paper describes the recent development and commissioning of a pepper-pot emittance meter at the Lawrence Berkeley National Laboratory (LBNL). It is based on a potassium bromide (KBr) scintillator screen in combination with a charged coupled device camera. Pepper-pot scanners record the full four-dimensional transverse phase space emittances which are particularly interesting for electron cyclotron resonance ion sources. The strengths and limitations of evaluating emittances using optical pepper-pot scanners are described and systematic errors induced by the optical data acquisition system will be presented. Light yield tests of KBr exposed to different ion species and first emittance measurement data using ion beams extracted from the 6.4 GHz LBNL electron cyclotron resonance ion source are presented and discussed.

A dynamic model of nutrient uptake by root hairs.

Root hairs are known to be important in the uptake of sparingly soluble nutrients by plants, but quantitative understanding of their role in this is weak. This limits, for example, the breeding of more nutrient-efficient crop genotypes. We developed a mathematical model of nutrient transport and uptake in the root hair zone of single roots growing in soil or solution culture. Accounting for root hair geometry explicitly, we derived effective equations for the cumulative effect of root hair surfaces on uptake using the method of homogenization. Analysis of the model shows that, depending on the morphological and physiological properties of the root hairs, one of three different effective models applies. They describe situations where: (1) a concentration gradient dynamically develops within the root hair zone; (2) the effect of root hair uptake is negligibly small; or (3) phosphate in the root hair zone is taken up instantaneously. Furthermore, we show that the influence of root hairs on rates of phosphate uptake is one order of magnitude greater in soil than solution culture. The model provides a basis for quantifying the importance of root hair morphological and physiological properties in overall uptake, in order to design and interpret experiments in different circumstances.

Measurement of the high energy component of the x-ray spectra in the VENUS electron cyclotron resonance ion source.

High performance electron cyclotron resonance (ECR) ion sources, such as VENUS (Versatile ECR for NUclear Science), produce large amounts of x-rays. By studying their energy spectra, conclusions can be drawn about the electron heating process and the electron confinement. In addition, the bremsstrahlung from the plasma chamber is partly absorbed by the cold mass of the superconducting magnet, adding an extra heat load to the cryostat. Germanium or NaI detectors are generally used for x-ray measurements. Due to the high x-ray flux from the source, the experimental setup to measure bremsstrahlung spectra from ECR ion sources is somewhat different from that for the traditional nuclear physics measurements these detectors are generally used for. In particular, the collimation and background shielding can be problematic. In this paper, we will discuss the experimental setup for such a measurement, the energy calibration and background reduction, the shielding of the detector, and collimation of the x-ray flux. We will present x-ray energy spectra and cryostat heating rates depending on various ion source parameters, such as confinement fields, minimum B-field, rf power, and heating frequency.

Long-range influence of carbohydrates on the solvation dynamics of water--answers from terahertz absorption measurements and molecular modeling simulations.

We present new terahertz (THz) spectroscopic measurements of solvated sugars and compare the effect of two disaccharides (trehalose and lactose) and one monosaccharide (glucose) with respect to the solute-induced changes in the sub-picosecond network dynamics of the hydration water. We found that the solute affects the fast collective network motions of the solvent, even beyond the first solvation layer. For all three carbohydrates, we find an increase of 2-4% in the THz absorption coefficient of the hydration water in comparison to bulk water. Concentration-dependent changes in the THz absorption between 2.1 and 2.8 THz of the solute-water mixture were measured with a precision better than 1% and were used to deduce a dynamical hydration shell, which extends from the surface up to 5.7 +/- 0.4 and 6.5 +/- 0.9 A for the disaccharides lactose and trehalose, respectively, and 3.7 +/- 0.9 A for the glucose. This exceeds the values for the static hydration shell as determined, for example, by scattering, where the long-range structure was found to be not significantly affected by the solute beyond the first hydration shell. When comparing all three carbohydrates, we found that the solute-induced change in the THz absorption depends on the product of molar concentration of the solute and the number of hydrogen bonds between the carbohydrate and water molecules. We can conclude that the long-range influence on the sub-picosecond collective water network motions of the hydration water is directly correlated with the average number of hydrogen bonds between the molecule and adjacent water molecules for carbohydrates. This implies that monosaccharides have a smaller influence on the surrounding water molecules than disaccharides. This could explain the bioprotection mechanism of sugar-water mixtures, which has been found to be more effective for disaccharides than for monosaccharides.

Fourth generation electron cyclotron resonance ion sources.

The concepts and technical challenges related to developing a fourth generation electron cyclotron resonance (ECR) ion source with a rf frequency greater than 40 GHz and magnetic confinement fields greater than twice B(ECR) will be explored in this article. Based on the semiempirical frequency scaling of ECR plasma density with the square of operating frequency, there should be significant gains in performance over current third generation ECR ion sources, which operate at rf frequencies between 20 and 30 GHz. While the third generation ECR ion sources use NbTi superconducting solenoid and sextupole coils, the new sources will need to use different superconducting materials, such as Nb(3)Sn, to reach the required magnetic confinement, which scales linearly with rf frequency. Additional technical challenges include increased bremsstrahlung production, which may increase faster than the plasma density, bremsstrahlung heating of the cold mass, and the availability of high power continuous wave microwave sources at these frequencies. With each generation of ECR ion sources, there are new challenges to be mastered, but the potential for higher performance and reduced cost of the associated accelerator continues to make this a promising avenue for development.

High intensity production of high and medium charge state uranium and other heavy ion beams with VENUS.

The next generation, superconducting electron cyclotron resonance (ECR) ion source VENUS (versatile ECR ion source for nuclear science) started operation with 28 GHz microwave heating in 2004. Since then it has produced world record ion beam intensities. For example, 2850 e microA of O(6+), 200 e microA of U(33+) or U(34+), and in respect to high charge state ions, 1 e microA of Ar(18+), 270 e microA of Ar(16+), 28 e microA of Xe(35+), and 4.9 e microA of U(47+) have been produced. A brief overview of the latest developments leading to these record intensities is given and the production of high intensity uranium beams is discussed in more detail.