NOREC,a Monte Carlo code for simulating electron tracks in liquid water

The work reported here was originally motivated by a discussion of Monte Carlo computer codes for electron transport in water given in Report No. 130 by the National Council on Radiation Protection and Measurements (NCRP). It was pointed out (correctly) that a published depth-dose distribution calculated by the Oak Ridge electron transport code, OREC, for 800 keV electrons normally incident on a water slab was apparently in error, possibly due to inadequate treatment of elastic scattering. In this paper we describe the replacement of the original OREC elastic cross sections by current ones from the National Institute of Standards and Technology (NIST). This investigation led also to the critical examination and revision of some other parts of the program, as described here. The revised code, which we have renamed NOREC, represents the first substantial review and modification of the Oak Ridge code in a number of years. We also present some comparisons of results calculated with the old and new versions and discuss their implications with respect to earlier studies. We have also written a version of NOREC in C++ language, which is available to other investigators. This paper provides a record of a response to the NCRP published statement and documentation for the revised code, NOREC.     

Spatial distributions of inelastic events produced by electrons in gaseous and liquid water

The spatial distributions of ionizations and other inelastic events in charged-particle tracks are important quantities that influence the final outcome of radiation interaction. Calculations of such distributions are presented for the tracks of electrons in the energy range 100 eV to 10 keV in liquid water and water vapor, and the results are compared. The distributions include the frequency of nearest-neighbor distances for all inelastic events, the mean nearest-neighbor distances for ionizations and for all inelastic events as a function of electron energy, the frequency of distances between all ionizations and all inelastic events, and the farthest distances between all inelastic events in electron tracks. The physical differences between liquid water and water vapor are discussed in terms of the respective inverse mean free paths, the collision spectra, and the nonlocalization of energy losses that are likely to occur in the liquid.     

Co-ordination of vapour and liquid phase water transport properties in plants

The pathway for water movement from the soil through plants to the atmosphere can be represented by a series of liquid and vapour phase resistances. Stomatal regulation of vapour phase resistance balances transpiration with the efficiency of water supply to the leaves, avoiding leaf desiccation at one extreme, and unnecessary restriction of carbon dioxide uptake at the other. In addition to maintaining a long-term balance between vapour and liquid phase water transport resistances in plants, stomata are exquisitely sensitive to short-term, dynamic perturbations of liquid water transport. In balancing vapour and liquid phase water transport, stomata do not seem to distinguish among potential sources of variation in the apparent efficiency of delivery of water per guard cell complex. Therefore, an apparent soil-to-leaf hydraulic conductance based on relationships between liquid water fluxes and driving forces in situ seems to be the most versatile for interpretation of stomatal regulatory behaviour that achieves relative homeostasis of leaf water status in intact plants. Components of dynamic variation in apparent hydraulic conductance in intact plants include, exchange of water between the transpiration stream and internal storage compartments via capacitive discharge and recharge, cavitation and its reversal, temperature-induced changes in the viscosity of water, direct effects of xylem sap composition on xylem hydraulic properties, and endogenous and environmentally induced variation in the activity of membrane water channels in the hydraulic pathway. Stomatal responses to humidity must also be considered in interpreting co-ordination of vapour and liquid phase water transport because homeostasis of bulk leaf water status can only be achieved through regulation of the actual transpirational flux. Results of studies conducted with multiple species point to considerable convergence with regard to co-ordination of stomatal and hydraulic properties. Because stomata apparently sense and respond to integrated and dynamic soil-to-leaf water transport properties, studies involving intact plants under both natural and controlled conditions are likely to yield the most useful new insights concerning stomatal co-ordination of transpiration with soil and plant hydraulic properties.     

The effect of model approximations on single-collision distributions of low-energy electrons in liquid water

The development of cross sections for the inelastic interaction of low-energy electrons with condensed tissue-like media is best accomplished within the framework of the dielectric theory. In this work we investigate the degree to which various model approximations, used in the above methodology, influence electron single-collision distributions. These distributions are of major importance to Monte Carlo track structure codes, namely, the energy-loss spectrum, the inelastic inverse mean free path, and the ionization efficiency. In particular, we make quantitative assessment of the influence of (1) the optical data set, (2) the dispersion algorithm, and (3) the perturbation and exchange Born corrections. It is shown that, although the shape and position of the energy-loss spectrum remains almost fixed, its peak height may vary by up to a factor of 1.5. Discrepancies in the calculated inelastic inverse mean free path are largely within 20-30% above 100 eV; they increase drastically, though, at lower energies. Exchange and perturbation Born corrections increase gradually below 1 keV leading to a approximately 30 to 40% reduction of the inverse mean free path at 100 eV. The perturbation effect contributes more than the exchange effect to this reduction. Similar to the dispersion situation, the effect of Born corrections at lower energies is also unclear since the models examined disagree strongly below 100 eV. In comparison, the vapor data are higher than the liquid calculations by 20 to 50% as the energy decreases from 1 to 0.1 keV, respectively. The excitation contribution is the main cause of this difference, since the ionization efficiency in the liquid levels off at approximately 90%, whereas the plateau value for the vapor is approximately 70%. It is concluded that electron inelastic distributions for liquid water, although in some respects distinctively different from the vapor phase, have associated uncertainties that are comparable in magnitude to the phase differences. The situation below 100 eV is uncertain.     

Implementation of new physics models for low energy electrons in liquid water in Geant4-DNA

A new alternative set of elastic and inelastic cross sections has been added to the very low energy extension of the Geant4 Monte Carlo simulation toolkit, Geant4-DNA, for the simulation of electron interactions in liquid water. These cross sections have been obtained from the CPA100 Monte Carlo track structure code, which has been a reference in the microdosimetry community for many years. They are compared to the default Geant4-DNA cross sections and show better agreement with published data.In order to verify the correct implementation of the CPA100 cross section models in Geant4-DNA, simulations of the number of interactions and ranges were performed using Geant4-DNA with this new set of models, and the results were compared with corresponding results from the original CPA100 code. Good agreement is observed between the implementations, with relative differences lower than 1% regardless of the incident electron energy.Useful quantities related to the deposited energy at the scale of the cell or the organ of interest for internal dosimetry, like dose point kernels, are also calculated using these new physics models. They are compared with results obtained using the well-known Penelope Monte Carlo code.     

Formation of ionization clusters in nanometric structures of propane-based tissue-equivalent gas or liquid water by electrons and alpha-particles

Despite the importance of ionization yield formation in sub-cellular structures a few nanometres in size, with regard to radiation damage our present knowledge in this respect is almost exclusively based on Monte Carlo simulations which in turn are based on cross section sets for water vapour or liquid water. Experimental data, although urgently needed, are still missing because the direct measurement of ionization yields in sub-cellular structures or, at least, in nanometric volumes of liquid water, is not yet possible. The best feasible way to overcome this problem of measurement at present, is the use of highly sophisticated counters filled with gases at low operating pressure to simulate target volumes a few nanometres in diameter at unit density. An indispensable prerequisite of the reliability of such measurements is, however, a check of the equivalence of the ionization yield produced in a specified target gas and the yield to be expected in liquid water or biological material. For this purpose, the ionization yield formation by electrons and alpha-particles in liquid water was simulated using the Monte Carlo method and compared with that produced in propane-based tissue-equivalent gas (composition by volume 55% C3H8, 39.6% CO2, 5.4% N2). After a short summary of the most important physical aspects of ionization cluster formation, new results are presented and discussed from the point of view of radiation physics and radiation biology.     

Thermalization of subexcitation electrons in solid water

We present the results of our Monte Carlo simulations of the slowing down and thermalization of subexcitation (E less than 7.4 eV) electrons in solid water. The scattering cross sections used in the simulations were obtained in another study from the analysis of electron-impact experiments performed on thin ice films deposited on a metal substrate at 14 K. The procedure by which these cross sections were determined is tested with our simulation code and is shown to be satisfactory. We find an average electron thermalization distance of approximately 13 nm, which is larger than what is usually assumed (2-7 nm) in models describing the diffusion-controlled track reactions which occur after 10(-12) s in irradiated liquid water. As for our calculated average thermalization time, it is of the order of 10(-13) s, in good agreement with experimental observations. To show the progression of the thermalization process, we give the distributions of slowing-down distances and times obtained for different stages of this process. The possibility that the subexcitation electrons undergo a dissociative attachment to water molecules is considered and its consequences on the initial yield of various chemical species are discussed. In particular, this dissociative attachment could provide a new explanation for the origin of the unscavengeable initial yield of molecular hydrogen.     

Energy spectra of secondary electrons in water vapour

The purpose of this work is to present a method for the calculation of secondary electron spectra generated by photons in water vapour in the energy region from 10 eV to 10 MeV. The cross sections below and above 1 keV have been treated separately. Examples are given for secondary electron spectra for low-energy photons, <100 eV, in which all electrons are photoelectrons, and at higher energy regions, such as for ⁶⁰Co photons. The spectrum of the first generation of secondary electrons, produced by ⁶⁰Co photons, which are mainly due to incoherent scattering, was fitted with a set of polynomial functions which can be used as input for electron radiation action calculations.     

Role of aquaporin water channels in airway fluid transport, humidification, and surface liquid hydration

Several aquaporin-type water channels are expressed in mammalian airways and lung: AQP1 in microvascular endothelia, AQP3 in upper airway epithelia, AQP4 in upper and lower airway epithelia, and AQP5 in alveolar epithelia. Novel quantitative methods were developed to compare airway fluid transport-related functions in wild-type mice and knockout mice deficient in these aquaporins. Lower airway humidification, measured from the moisture content of expired air during mechanical ventilation with dry air through a tracheotomy, was 54-56% efficient in wild-type mice, and reduced by only 3-4% in AQP1/AQP5 or AQP3/AQP4 double knockout mice. Upper airway humidification, measured from the moisture gained by dry air passed through the upper airways in mice breathing through a tracheotomy, decreased from 91 to 50% with increasing ventilation from 20 to 220 ml/min, and reduced by 3-5% in AQP3/AQP4 knockout mice. The depth and salt concentration of the airway surface liquid in trachea was measured in vivo using fluorescent probes and confocal and ratio imaging microscopy. Airway surface liquid depth was 45 +/- 5 microm and [Na(+)] was 115 +/- 4 mM in wild-type mice, and not significantly different in AQP3/AQP4 knockout mice. Osmotic water permeability in upper airways, measured by an in vivo instillation/sample method, was reduced by approximately 40% by AQP3/AQP4 deletion. In doing these measurements, we discovered a novel amiloride-sensitive isosmolar fluid absorption process in upper airways (13% in 5 min) that was not affected by aquaporin deletion. These results establish the fluid transporting properties of mouse airways, and indicate that aquaporins play at most a minor role in airway humidification, ASL hydration, and isosmolar fluid absorption.     

Exact Multiple Comparisons of Three or More Regression Lines: Pairwise Comparisons and Comparisons with a Control

The problem of finding exact simultaneous confidence bounds for differences in regression models for k groups via the union‐intersection method is considered. The error terms are taken to be iid normal random variables. Under an assumption slightly more general than having identical design matrices for each of the k groups, it is shown that an existing probability point for the multivariate studentized range can be used to find the necessary probability point for pairwise comparisons of regression models. The resulting methods can be used with simple or multiple regression. Under a weaker assumption on the k design matrices that allows more observations to be taken from the control group than from the k‐1 treatment groups, a method is developed for computing exact probability points for comparing the simple linear regression models of the k‐1 groups to that of the control. Within a class of designs, the optimal design for comparisons with a control takes the square root of (k‐1) times as many observations from the control than from each treatment group. The simultaneous confidence bounds for all pairwise differences and for comparisons with a control are much narrower than Spurrier's intervals for all contrasts of k regression lines.     

In situ separation of root hydraulic redistribution of soil water from liquid and vapor transport

Nocturnal increases in water potential (ψ) and water content (θ) in the upper soil profile are often attributed to root water efflux, a process termed hydraulic redistribution (HR). However, unsaturated liquid or vapor flux of water between soil layers independent of roots also contributes to the daily recovery in θ (Δθ), confounding efforts to determine the actual magnitude of HR. We estimated liquid (J _l) and vapor (J _v) soil water fluxes and their impacts on quantifying HR in a seasonally dry ponderosa pine (Pinus ponderosa) forest by applying existing datasets of ψ, θ and temperature (T) to soil water transport equations. As soil drying progressed, unsaturated hydraulic conductivity declined rapidly such that J _l was irrelevant (<2E−05 mm h⁻¹ at 0–60 cm depths) to total water flux by early August. Vapor flux was estimated to be the highest in upper soil (0–15 cm), driven by large T fluctuations, and confounded the role of HR, if any, in nocturnal θ dynamics. Within the 15–35 cm layer, J _v contributed up to 40% of hourly increases in nocturnal soil moisture. While both HR and net soil water flux between adjacent layers contribute to θ in the 15–65 cm soil layer, HR was the dominant process and accounted for at least 80% of the daily recovery in θ. The absolute magnitude of HR is not easily quantified, yet total diurnal fluctuations in upper soil water content can be quantified and modeled, and remain highly applicable for establishing the magnitude and temporal dynamics of total ecosystem water flux.     

Ion transport and energy transduction of P-type ATPases: Implications from electrostatic calculations

This paper summarizes our present electrostatic calculations on P-type ATPases and their contribution to understand the molecular details of the reaction mechanisms. One focus was set on analyzing the proton countertransport of the sarcoplasmic reticulum Ca²⁺-ATPase (SERCA1a). Protonation of acidic residues was calculated in dependence of pH for different enzyme states in the reaction cycle of the Ca²⁺-ATPase. We proposed that the acidic Ca²⁺ ligands Glu 771, Asp 800 and Glu 908 participate in the proton countertransport whereas Glu 309 is more likely to serve as a proton shuttle between binding site I and the cytoplasm. Complementary to infrared measurements, we assigned infrared bands to specific Ca²⁺ ligands that are hydrogen bonded. Ion pathways were proposed based on the calculations and structural data. Another focus was set on analyzing the energy transduction mechanism of P-type ATPases. In accordance to electrophysiological experiments, we simulated an electric field across the membrane. The impact of the electric field was studied by an accumulated number of residue conformational and ionization changes on specific transmembrane helices. Our calculations on the Ca²⁺-ATPase and the Na⁺/K⁺-ATPase indicated that the highly conserved transmembrane helix M5 is one structural element that is likely to act as energy transduction element in P-type ATPases. Perspectives and limitations of the electrostatic calculations for future computational studies are pointed out.     

Comparisons between warm and cold water swim stress in mice

The following experiments evaluated the effects of warm- or cold-water swim stress on tail-flick latencies (TFL) in mice. To first determine the appropriete control group, the TFL's of dry-vs-dunked mice were compared. Dry mice had significantly shorter TFL's than dunked mice, implying that the dampness of the mouse's tail contributed to the increase in the TFL. Therefore, dunked mice were used as the relevant control for the swum mice. Cold water swimming (2°C) produced a significant increase in the TFL; this was not blocked by the opiate antagonist naloxone (3 mg/kg sc) or potentiated by the enkephalinase inhibitor thiorphan (100 mg/kg sc). Warm water swimming (32°C) up to 3 min produced an inconsistent effect on TFL's, implying that the effects were at the threshold of detectability. Naloxone attenuated and thiorphan modestly potentiated the effects of warm water swimming on TFL's. This suggests that warm water swim stress-induced increases in mouse TFL's may involve opioid pathways, whereas cold water swim stress-induced changes in mice TFL's appear not to be opioid mediated.     

Stopping power and CSDA range calculations for incident electrons and positrons in breast and brain tissues

The stopping power in some biological compounds for electrons and positrons was calculated over the energy range from 100 eV to 1 GeV. Total stopping power was obtained by summing the electronic (collisional) and radiative stopping power of the target materials and then employing the continuous slowing down approximation (CSDA) to calculate the path length of incident particles in the target. An effective charge approximation was used for the calculation of collisional stopping power, and an analytical expression for the radiation length was applied to obtain the radiative stopping power. Calculations of stopping power and CSDA range were based mostly on analytical expressions, to allow for an easy calculation of these parameters. The results were tabulated and compared with available data.     

Osmotic water transport with glucose in GLUT2 and SGLT

Carrier-mediated water cotransport is currently a favored explanation for water movement against an osmotic gradient. The vestibule within the central pore of Na⁺-dependent cotransporters or GLUT2 provides the necessary precondition for an osmotic mechanism, explaining this phenomenon without carriers. Simulating equilibrative glucose inflow via the narrow external orifice of GLUT2 raises vestibular tonicity relative to the external solution. Vestibular hypertonicity causes osmotic water inflow, which raises vestibular hydrostatic pressure and forces water, salt, and glucose into the outer cytosolic layer via its wide endofacial exit. Glucose uptake via GLUT2 also raises oocyte tonicity. Glucose exit from preloaded cells depletes the vestibule of glucose, making it hypotonic and thereby inducing water efflux. Inhibiting glucose exit with phloretin reestablishes vestibular hypertonicity, as it reequilibrates with the cytosolic glucose and net water inflow recommences. Simulated Na⁺-glucose cotransport demonstrates that active glucose accumulation within the vestibule generates water flows simultaneously with the onset of glucose flow and before any flow external to the transporter caused by hypertonicity in the outer cytosolic layers. The molar ratio of water/glucose flow is seen now to relate to the ratio of hydraulic and glucose permeability rather than to water storage capacity of putative water carriers.     

Quantification of water transport in plants with NMR imaging

A new nuclear magnetic resonance imaging (NMRi) method is described to calculate the characteristics of water transport in plant stems. Here, dynamic NMRi is used as a non-invasive technique to record the distribution of displacements of protons for each pixel in the NMR image. Using the NMR-signal of the stationary water in a reference tube for calibration, the following characteristics can be calculated per pixel without advance knowledge of the flow-profile in that pixel: the amount of stationary water, the amount of flowing water, the cross-sectional area of flow, the average linear flow velocity of the flowing water, and the volume flow. The accuracy of the method is demonstrated with a stem segment of a chrysanthemum flower by comparing the volume flow, measured with NMR, with the actual volumetric uptake, measured with a balance. NMR measurements corresponded to the balance uptake measurements with a rms error of 0.11 mg s(-1) in a range of 0 to 1.8 mg s(-1). Local changes in flow characteristics of individual voxels of a sample (e.g. intact plant) can be studied as a function of time and of any conceivable changes the sample experiences on a time-scale, longer than the measurement time of a complete set of pixel-propagators (17 min).     

Modeling soil-root water transport with non-uniform water supply and heterogeneous root distribution

Plant and Soil - A 2D physically based framework is proposed to analyze the effect of a non-uniform water supply at the soil surface generated by rainfall interception and stemflow on soil-root...