Abdiravuf A. Dzhurakhalov

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.

Virtual Plant Tissue: Building Blocks for Next-Generation Plant Growth Simulation

Motivation: Computational modeling of plant developmental processes is becoming increasingly important. Cellular resolution plant tissue simulators have been developed, yet they are typically describing physiological processes in an isolated way, strongly delimited in space and time. Results: With plant systems biology moving toward an integrative perspective on development we have built the Virtual Plant Tissue (VPTissue) package to couple functional modules or models in the same framework and across different frameworks. Multiple levels of model integration and coordination enable combining existing and new models from different sources, with diverse options in terms of input/output. Besides the core simulator the toolset also comprises a tissue editor for manipulating tissue geometry and cell, wall, and node attributes in an interactive manner. A parameter exploration tool is available to study parameter dependence of simulation results by distributing calculations over multiple systems. Availability: Virtual Plant Tissue is available as open source (EUPL license) on Bitbucket (https://bitbucket.org/vptissue/vptissue). The project has a website https://vptissue.bitbucket.io.

Monte Carlo parameterization in the VirtualLeaf framework

The recently developed simulation framework VirtualLeaf uses Metropolis Monte Carlo dynamics for studying plant tissue morphogenesis. Minimizing the energy of the tissue is done by an energy evaluation-only method. We developed a more robust criterion for the energy minimization method for the multivariable and complex systems where the use of a gradient norm is impossible. The proposed criterion is based on checking energy changes in a sliding window of successive energy steps against a threshold value. The advantages of the sliding window criterion are discussed and results obtained by this method are presented. The impact of the choice threshold value on the energy minimization has been studied.

Ion Bombardment-Induced Surface Effects in Materials

This chapter deals with the experimental research and computer simulation of lowand medium-energy (E 0 = 1-30 keV) ion collisions on the surface of a solid and of the accompanying effects, namely scattering, sputtering, and surface implantation. Experimental and computer simulation studies of low-energy (Е 0 = 80–500 eV) Cs+ ions scattering on Ta, W, Re target surfaces and K+ ions scattering on Ti, V, Cr target surfaces have been performed for more accurate definition of mechanism of scattering, with a purpose of evaluation of use of slow ions scattering as a tool for surface layer analy‐ sis. The peculiarities of the process of correlated small angle scattering of 5–15 keV He, Ne, Ar, Kr, Xe, and Rn ions by the Cu(100), Ni(100), and V(100) single-crystal surfaces have been investigated by computer simulation. It has been shown that under these conditions the inelastic energy losses become predominant over the elastic ones. The anomalous energy losses observed experimentally at the grazing ion scattering by the single-crystal surface were explained. It has been shown by computer simulation that the peculiarities of the chain effect at direct and reverse relation of masses of colliding particles and rainbow effect at quasi-single and quasi-double scattering of ions, heavier than adatoms, lead to the appearance of characteristic peaks in the energy and angular distributions of scattered ions. Analysis of these peaks and comparison with experi‐ ment give an opportunity to control the initial stages of adsorption and identification of adsorption structures with the help of low-energy ion scattering. It has been shown that from the correlation of the experimental and calculated energy distributions of the scattered particles, one may determine a spatial extension of the isolated atomic steps on the single-crystal surface damaged by the ion bombardment. Results obtained can be also used to study short-range order in alloys undergoing ordering. Grazing ionsputtering processes of Si(001), SiC(001), and Cu3Au(001) surfaces at 0.5–5 keV Ne+ bombardment have been studied by computer simulations. A preferential emission of Cu atoms in the case of Cu3Au (001) surface sputtering is observed. It was shown that in the case of grazing ion bombardment, the layer-by-layer sputtering is possible, and its optimum is observed within the small angle range of the glancing angles near the threshold sputtering angle. The peculiarities of trajectories, ranges, and energy losses of low-energy different-mass ions channeling in thin single crystals of metals and semiconductors have been thoroughly studied by computer simulation. It has been

Computer simulation of the interaction of ringlike carbon clusters with nanographene

Various cases of interaction of ringlike carbon clusters C7, C12 and C13 with a rectangular nanographene consisting of 272 atoms were studied and presented. It was found that this interaction results in the structural change in these clusters and in the local part of nanographene. The cohesive energies of these clusters in the isolated (free) state and their binding energies with nanographene have been calculated. The results show that despite this interaction the atoms of cluster are hold together as a single cluster thanks to the significantly higher cohesive energy of cluster the its binding energy with nanographene.

Computer modeling of scattering carbon atoms with graphene

Collision processes of carbon atoms with a kinetic energy of 10 and 100 eV with graphene at certain points of this graphene have been studied by computer simulation.