Lecture

Symmetry and Conservation in the Cell

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In course

BIO-692: Symmetry and Conservation in the Cell

This course shows students how the physical principles of conservation, symmetry, and locality influence the dynamics of living organisms at the molecular and cellular level. Computer simulations are used to explore examples of cellular dynamics and phase ...

Description

This lecture explores the concept of symmetry and conservation in cellular biology, focusing on the biophysics of cells. It covers topics such as the structure of cells, the importance of randomness in cellular functions, and the role of computer simulations in understanding cellular dynamics. The course delves into the principles of symmetry and conservation in cellular processes, emphasizing the significance of energy, entropy, shape, flexibility, and fluctuations. Through a series of lectures and simulations, students will gain insights into the fundamental principles governing cellular behavior and the computational modeling of cellular structures.

Instructor

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

Official source

Related concepts (32)

Randomness

In common usage, randomness is the apparent or actual lack of definite pattern or predictability in information. A random sequence of events, symbols or steps often has no order and does not follow an intelligible pattern or combination. Individual random events are, by definition, unpredictable, but if the probability distribution is known, the frequency of different outcomes over repeated events (or "trials") is predictable. For example, when throwing two dice, the outcome of any particular roll is unpredictable, but a sum of 7 will tend to occur twice as often as 4.

Randomness test

A randomness test (or test for randomness), in data evaluation, is a test used to analyze the distribution of a set of data to see whether it can be described as random (patternless). In stochastic modeling, as in some computer simulations, the hoped-for randomness of potential input data can be verified, by a formal test for randomness, to show that the data are valid for use in simulation runs. In some cases, data reveals an obvious non-random pattern, as with so-called "runs in the data" (such as expecting random 0–9 but finding "4 3 2 1 0 4 3 2 1.

Statistical randomness

A numeric sequence is said to be statistically random when it contains no recognizable patterns or regularities; sequences such as the results of an ideal dice roll or the digits of π exhibit statistical randomness. Statistical randomness does not necessarily imply "true" randomness, i.e., objective unpredictability. Pseudorandomness is sufficient for many uses, such as statistics, hence the name statistical randomness. Global randomness and local randomness are different.

Random number generation

Random number generation is a process by which, often by means of a random number generator (RNG), a sequence of numbers or symbols that cannot be reasonably predicted better than by random chance is generated. This means that the particular outcome sequence will contain some patterns detectable in hindsight but unpredictable to foresight. True random number generators can be hardware random-number generators (HRNGs), wherein each generation is a function of the current value of a physical environment's attribute that is constantly changing in a manner that is practically impossible to model.

Algorithmically random sequence

Intuitively, an algorithmically random sequence (or random sequence) is a sequence of binary digits that appears random to any algorithm running on a (prefix-free or not) universal Turing machine. The notion can be applied analogously to sequences on any finite alphabet (e.g. decimal digits). Random sequences are key objects of study in algorithmic information theory. As different types of algorithms are sometimes considered, ranging from algorithms with specific bounds on their running time to algorithms which may ask questions of an oracle machine, there are different notions of randomness.

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