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In a simulation, given a starting vector (list of the values of the variables), the progression of the system is calculated by solving the equations at each time-frame in small increments. In analysis, the properties of the equations are used to investigate the behavior of the system depending on the values of the parameters and variables.
Modelling biological systems is a significant task of systems biology and mathematical biology. [a] Computational systems biology [b] [1] aims to develop and use efficient algorithms, data structures, visualization and communication tools with the goal of computer modelling of biological systems.
For example, in a 1-dimensional cellular automaton like the examples below, the neighborhood of a cell x i t is {x i−1 t−1, x i t−1, x i+1 t−1}, where t is the time step (vertical), and i is the index (horizontal) in one generation.
At a more integrative level, it helps analyze and catalogue the biological pathways and networks that are an important part of systems biology. In structural biology, it aids in the simulation and modeling of DNA, [2] RNA, [2] [3] proteins [4] as well as biomolecular interactions. [5] [6] [7] [8]
A selection of simulated "swimbots" Artificial life (ALife or A-Life) is a field of study wherein researchers examine systems related to natural life, its processes, and its evolution, through the use of simulations with computer models, robotics, and biochemistry. [1]
The size of the simulation box must also be large enough to prevent periodic artifacts from occurring due to the unphysical topology of the simulation. In a box that is too small, a macromolecule may interact with its own image in a neighboring box, which is functionally equivalent to a molecule's "head" interacting with its own "tail".
VCell supports the following features: Within the "Physiology", models can be specified as reaction networks or reaction rules.[7]Simulations can be chosen to either resolve variations of concentrations over space (spatial simulations) or assume concentrations constant across compartments (compartmental simulations).
The term "theoretical biology" was first used as a monograph title by Johannes Reinke in 1901, and soon after by Jakob von Uexküll in 1920. One founding text is considered to be On Growth and Form (1917) by D'Arcy Thompson, [7] and other early pioneers include Ronald Fisher, Hans Leo Przibram, Vito Volterra, Nicolas Rashevsky and Conrad Hal ...