Paweł Topa

A new approach to modeling of foraminiferal shells

Abstract The emergence of shell forms in the growth of foraminifera is an essential problem in the morphogenesis of these microorganisms. We present a model of foraminiferal shells that applies a moving-reference system. Previous models have referred to fixed-reference axes and have neglected apertures. Our model focuses on real morphologic characteristics and follows stepwise natural biological processes. It introduces apertures based on minimization of the local communication path and applies three parameters, which are either predetermined or selected at random from given ranges. Expression of stochastic parameters mimics phenotypic variability of a shell. We also present a detailed description of the method with examples of simulated shells and the first step toward analyses of the theoretical morphospace. The morphospace is divided into certain regions (phases) separated by transitional planes (phase transitions). Further prospects for foraminiferal modeling, which should focus on more in-depth models based on realistic intracellular dynamics, are also presented.

Dynamically Reorganising Vascular Networks Modelled Using Cellular Automata Approach

We present the model of tumour induced angiogenesis that apart from predominating phenomena, as influence of VEGF, includes newly discovered factors such as Dll4/Notch signalling and remodelling processes. The Cellular Automata approach is employed to model cellular and intracellular processes that occur in cancer tissue and surroundings. Vascular system is modelled by using the Graph of Cellular Automata, which combines graph theory with the Cellular Automata paradigm. Additionally, an outline of model verification method which uses graph descriptors is presented and exemplified.

A MULTISCALE CELLULAR AUTOMATA MODEL FOR SIMULATING COMPLEX TRANSPORTATION SYSTEMS

We present a new two-level numerical model describing the evolution of transportation network. Two separate but mutually interacting sub-systems are investigated: a starving environment and the network. We assume that the slow modes of the environment growth can be modeled with classical cellular automata (CA) approach. The fast modes representing the transportation network, we approximate by the graph of cellular automata (GCA). This allows the simulation of transportation systems over larger spatio-temporal scales and scrutinizing global interactions between the network and the environment. We show that the model can mimic the realistic evolution of complex river systems. We also demonstrate how the model can simulate a reverse situation. We conclude that the paradigm of this model can be extended further to a general framework, approximating many realistic multiscale transportation systems in diverse fields such as geology, biology and medicine.

Anastomosing Transportation Networks

Anastomosing network describes a blundering, irregular network composed of branches and divergent and convergent knots. Anastomosing river system is an example of such network in nature. We present concepts of numerical models of anastomosing river basing on cellular automata paradigm. Our first model is an extension of previously developed model of water flow, about the elements connected with phenomena characteristic for anastomosing river. Due to its limitations the another have been introduced, in which we enhance the utilization of cellular automata paradigm by defining a new structure: graph of cellular automata. We present the results obtained by using the both models.

Local Minimization Paradigm in Numerical Modeling of Foraminiferal Shells

We present a new approach to modelling of foraminiferal shells. Previous models referred to fixed reference axes and neglected apertures, which play a crucial role in morphogenesis of shells. Our 2D preliminary model applies the moving reference system based on introducing of apertures and minimization of the local communication path (LCP). LCP defines the position of every final aperture. A formal description of simple analytical methods with some elements of randomness is given in this paper. Selected examples of simulated shells are figured.

GPGPU implementation of cellular automata model of water flow

In this paper we present how Cellular Automata model can be implemented for processing on Graphics Processing Unit (GPU). Recently, graphics processors have gained a lot of interest as an efficient architecture for general-purpose computation. Cellular Automata algorithms that are inherently parallel give the opportunity to achieve very high efficiency when they are implemented on GPUs. We demonstrate how existing model of water flow can be ported to GPU environment with OpenCL programming framework. Sample simulation results and performance evaluations are included.

Towards a two-scale cellular automata model of tumour-induced angiogenesis

This paper presents a new framework for modelling tumour-induced angiogenesis Classical Cellular Automata approach is employed to model cellular and intracellular processes that occur in cancer tissue and neighbourhood Vascular system is modelled by using Graph of Cellular Automata, which combines graph theory with Cellular Automata paradigm A new model is proposed as a starting point for further investigations on multiscale model covering wide range of spatio-temporal scales including blood flow processes The basis of the model with the algorithms are presented Preliminary results with short discussion are also included.

Agent-oriented Foraminifera Habitat Simulation

An agent-oriented software solution for simulation of marine unicellular organisms called foraminifera is presented. Their simplified microhabitat interactions are described and implemented to run the model and verify its flexibility. This group of well fossilizable protists has been selected due to its excellent “in fossilio” record that should help to verify our future long-run evolutionary results. The introduced system is built utilizing PyAge platform and based on easily exchangeable components that may be replaced (also in runtime). Selected experiments considering substantial and technological efficiency were conducted and their results are presented and discussed. We show that our artificial life simulation follows realistic rules known from nature. The Lotka-Volterra predator-prey dynamics was simulated that proves the potential for extendability to more complex biological phenomena.

Cellular Automata Model Tuned for Efficient Computation on GPU with Global Memory Cache

Models based on Cellular Automata paradigm are inherently parallel and give the opportunity to achieve very high efficiency when they are implemented on GPUs. In previous works, the Author presented two versions of the CA model of water flow: one that uses only the global memory, and a second that uses local memory as a manually managed cache. In this paper, these two algorithms are tested on processors with Fermi architecture. The results of performance evaluations are presented and discussed.

Consuming Environment with Transportation Network Modelled Using Graph of Cellular Automata

We discuss the applications of new methods, derived from the cellular automata paradigm, for simulating dynamic feedback systems consisting of transportation network and consuming environment. The general framework of the model is introduced. We describe the application of the methods for modelling the anastomosing river system and root system of plants. The results of simulations are depicted and commented. We show that the methods mimicks well the realistic networking systems.