A robust simulator for physiologically structured population models.

A framework to simulate physiologically structured population (PSP) models on high performance compute (HPC) infrastructure is built. Based on the model of a single cell, billions of cells can be simulated in an efficient way, allowing fast simulation of the interaction of an entire organ with other body parts. Trough combination of three state-of-the-art algorithms, the simulation time is decreased with multiple orders of magnitude. First: PSP modelling exploits the fact that a lot of the cells act the same at the same time which results in multiple orders of magnitude speed-up. Secondly, speed-up is achieved by using an unconditionally stable, partial differential equation solver which allows to trade speed for precision and allows big time stepping. Third speed-up is due to the fact that the framework is designed with HPC cluster use in mind. The PSP simulator is mathematically derived to have maximal stability.Simulation results are validated and simulation speed and accuracy are measured.

Localized auxin peaks in concentration-based transport models of the shoot apical meristem.

We study the formation of auxin peaks in a generic class of concentration-based auxin transport models, posed on static plant tissues. Using standard asymptotic analysis, we prove that, on bounded domains, auxin peaks are not formed via a Turing instability in the active transport parameter, but via simple corrections to the homogeneous steady state. When the active transport is small, the geometry of the tissue encodes the peaks' amplitude and location: peaks arise where cells have fewer neighbours, that is, at the boundary of the domain. We test our theory and perform numerical bifurcation analysis on two models that are known to generate auxin patterns for biologically plausible parameter values. In the same parameter regimes, we find that realistic tissues are capable of generating a multitude of stationary patterns, with a variable number of auxin peaks, that can be selected by different initial conditions or by quasi-static changes in the active transport parameter. The competition between active transport and production rate determines whether peaks remain localized or cover the entire domain. In particular, changes in the auxin production that are fast with respect to the cellular life cycle affect the auxin peak distribution, switching from localized spots to fully patterned states. We relate the occurrence of localized patterns to a snaking bifurcation structure, which is known to arise in a wide variety of nonlinear media, but has not yet been reported in plant models.

Numerical bifurcation analysis of the pattern formation in a cell based auxin transport model.

Transport models of growth hormones can be used to reproduce the hormone accumulations that occur in plant organs. Mostly, these accumulation patterns are calculated using time step methods, even though only the resulting steady state patterns of the model are of interest. We examine the steady state solutions of the hormone transport model of Smith et al. (Proc Natl Acad Sci USA 103(5):1301-1306, 2006) for a one-dimensional row of plant cells. We search for the steady state solutions as a function of three of the model parameters by using numerical continuation methods and bifurcation analysis. These methods are more adequate for solving steady state problems than time step methods. We discuss a trivial solution where the concentrations of hormones are equal in all cells and examine its stability region. We identify two generic bifurcation scenarios through which the trivial solution loses its stability. The trivial solution becomes either a steady state pattern with regular spaced peaks or a pattern where the concentration is periodic in time.

Towards mechanistic models of plant organ growth.

Modelling and simulation are increasingly used as tools in the study of plant growth and developmental processes. By formulating experimentally obtained knowledge as a system of interacting mathematical equations, it becomes feasible for biologists to gain a mechanistic understanding of the complex behaviour of biological systems. In this review, the modelling tools that are currently available and the progress that has been made to model plant development, based on experimental knowledge, are described. In terms of implementation, it is argued that, for the modelling of plant organ growth, the cellular level should form the cornerstone. It integrates the output of molecular regulatory networks to two processes, cell division and cell expansion, that drive growth and development of the organ. In turn, these cellular processes are controlled at the molecular level by hormone signalling. Therefore, combining a cellular modelling framework with regulatory modules for the regulation of cell division, expansion, and hormone signalling could form the basis of a functional organ growth simulation model. The current state of progress towards this aim is that the regulation of the cell cycle and hormone transport have been modelled extensively and these modules could be integrated. However, much less progress has been made on the modelling of cell expansion, which urgently needs to be addressed. A limitation of the current generation models is that they are largely qualitative. The possibilities to characterize existing and future models more quantitatively will be discussed. Together with experimental methods to measure crucial model parameters, these modelling techniques provide a basis to develop a Systems Biology approach to gain a fundamental insight into the relationship between gene function and whole organ behaviour.

Complete photo-induced breakup of the H2 molecule as a probe of molecular electron correlation.

Despite decades of progress in quantum mechanics, electron correlation effects are still only partially understood. Experiments in which both electrons are ejected from an oriented hydrogen molecule by absorption of a single photon have recently demonstrated a puzzling phenomenon: The ejection pattern of the electrons depends sensitively on the bond distance between the two nuclei as they vibrate in their ground state. Here, we report a complete numerical solution of the Schrödinger equation for the double photoionization of H2. The results suggest that the distribution of photoelectrons emitted from aligned molecules reflects electron correlation effects that are purely molecular in origin.

Threshold vibrational excitation of CO2 by slow electrons.

Threshold structures, reminiscent of those seen in the polar hydrogen halides, have recently been observed in the cross sections for electron impact excitation of certain vibrational levels of the nonpolar CO2 molecule. These structures occur at energies outside the range where shape resonances dominate the dynamics. We propose a virtual state model that describes the multidimensional nuclear dynamics during the collision and explains quantitatively the selectivity observed in the excitation of the Fermi dyad, as well as the pattern of threshold peaks and oscillations seen in the upper levels of the higher polyads.

Modified J-matrix method for scattering.

We modify the J-matrix technique for scattering so that problems with long-range interactions are easily solved. This is done by introducing additional terms in the asymptotic three-term recurrence relation that take into account asymptotic effects of the potential. The solutions of this modified recurrence relation are a very good approximation of the exact scattering solution. Only a small number of residual coefficients need to be calculated. As a result, the numerical effort to solve the scattering problem is seriously reduced. The technique is illustrated with a Yukawa potential.