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Lecture

Dynamic Systems: Model Building and Trajectories Representation

In course

BIO-341: Dynamical systems in biology

Life is non-linear. This course introduces dynamical systems as a technique for modelling simple biological processes. The emphasis is on the qualitative and numerical analysis of non-linear dynamical models. Examples are taken from biology and population ...

Description

This lecture covers the necessary steps to build a model for a switch, including understanding the phenomenology and interpreting results. It also discusses drawing trajectories as a function of time and key concepts from Kuramoto's model.

Instructors (2)

Felix Naef

Felix Naef studied theoretical physics at the ETHZ and obtained his PhD from the EPFL in 2000. He then received postdoctoral training at the Center for Studies in Physics and Biology at the Rockefeller University (NYC) under the guidance of Prof. Magnasco. His research focuses on the modeling and interpretation of high-throughput functional data and the study of biomolecular oscillators. He joined ISREC as an associate scientist in early 2004 and is currently Associate Professor in the Institute of Bioengineering (IBI).

Julian Charles Shillcock

Julian received his PhD at Simon Fraser University in Canada for work on Monte Carlo simulations of liquid crystal phase transitions and the elastic properties of fluid and polymerized membranes. He was a Group Leader at the Max Planck Institute of Colloids and Interfaces, Germany for five years applying coarse-grained simulation techniques - principally Dissipative Particle Dynamics (DPD) and Brownian Dynamics - to equilibrium and dynamic properties of fluid lipid membranes. A major target of this research was to reveal the molecular rearrangements that occur during vesicle fusion. During this time, he developed a commercially-available, parallel DPD code that is being used by several universities. He was an Associate Professor at MEMPHYS in the Department of Physics and Chemistry, University of Southern Denmark. He has also worked in industry, designing and writing software for communication satellite simulations (British Aerospace, 1986-1990), and fluid simulation software (Accelrys, Inc., 1998-1999). He joined the Blue Brain Project in 2011, and uses mesoscale simulation techniques, together with theoretical analysis and collaborations with experimentalists, to study the dynamics of cellular processes. Current projects include simulating the formation of the post-synaptic density in dendritic spines and developing theoretical models of the supramolecular organisation of synapses. He also teaches Master's and PhD courses in computational cell biology and biophysics. He wrote and maintains an open source dissipative particle dynamics simulation code: https://github.com/Osprey-DPD/osprey-dpd Orcid: orcid.org/0000-0002-7885-735X

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Related concepts (8)

Parabolic trajectory

In astrodynamics or celestial mechanics a parabolic trajectory is a Kepler orbit with the eccentricity equal to 1 and is an unbound orbit that is exactly on the border between elliptical and hyperbolic. When moving away from the source it is called an escape orbit, otherwise a capture orbit. It is also sometimes referred to as a C3 = 0 orbit (see Characteristic energy). Under standard assumptions a body traveling along an escape orbit will coast along a parabolic trajectory to infinity, with velocity relative to the central body tending to zero, and therefore will never return.

Dynamical system

In mathematics, a dynamical system is a system in which a function describes the time dependence of a point in an ambient space, such as in a parametric curve. Examples include the mathematical models that describe the swinging of a clock pendulum, the flow of water in a pipe, the random motion of particles in the air, and the number of fish each springtime in a lake. The most general definition unifies several concepts in mathematics such as ordinary differential equations and ergodic theory by allowing different choices of the space and how time is measured.

Hyperbolic trajectory

In astrodynamics or celestial mechanics, a hyperbolic trajectory or hyperbolic orbit is the trajectory of any object around a central body with more than enough speed to escape the central object's gravitational pull. The name derives from the fact that according to Newtonian theory such an orbit has the shape of a hyperbola. In more technical terms this can be expressed by the condition that the orbital eccentricity is greater than one.

Radial trajectory

In astrodynamics and celestial mechanics a radial trajectory is a Kepler orbit with zero angular momentum. Two objects in a radial trajectory move directly towards or away from each other in a straight line. There are three types of radial trajectories (orbits). Radial elliptic trajectory: an orbit corresponding to the part of a degenerate ellipse from the moment the bodies touch each other and move away from each other until they touch each other again. The relative speed of the two objects is less than the escape velocity.

Dynamical systems theory

Dynamical systems theory is an area of mathematics used to describe the behavior of complex dynamical systems, usually by employing differential equations or difference equations. When differential equations are employed, the theory is called continuous dynamical systems. From a physical point of view, continuous dynamical systems is a generalization of classical mechanics, a generalization where the equations of motion are postulated directly and are not constrained to be Euler–Lagrange equations of a least action principle.

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