Lecture

Cellular Scale Modeling

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In course

BIOENG-455: Computational cell biology

Computer modeling is used to study dynamic phenomena in cell biology. This course shows how to identify mathematical features of cell biology mechanisms and use numerical algorithms to model their behavior. ...

Description

This lecture discusses the challenges of applying Newton's laws at the cellular scale, emphasizing the complexity of cellular systems compared to billiard balls. It covers the concept of degrees of freedom, the importance of relevant coordinates in cell biology, and the significance of scales in a cell. The lecture also explores the units and dimensions relevant to cell biology, significant ratios, organelle descriptions, and the process of building mathematical models in computational cell biology.

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)

Synthetic biology

Synthetic biology (SynBio) is a multidisciplinary field of science that focuses on living systems and organisms, and it applies engineering principles to develop new biological parts, devices, and systems or to redesign existing systems found in nature. It is a branch of science that encompasses a broad range of methodologies from various disciplines, such as biotechnology, biomaterials, material science/engineering, genetic engineering, molecular biology, molecular engineering, systems biology, membrane science, biophysics, chemical and biological engineering, electrical and computer engineering, control engineering and evolutionary biology.

Degrees of freedom (physics and chemistry)

In physics and chemistry, a degree of freedom is an independent physical parameter in the formal description of the state of a physical system. The set of all states of a system is known as the system's phase space, and the degrees of freedom of the system are the dimensions of the phase space. The location of a particle in three-dimensional space requires three position coordinates. Similarly, the direction and speed at which a particle moves can be described in terms of three velocity components, each in reference to the three dimensions of space.

Organelle

In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name organelle comes from the idea that these structures are parts of cells, as organs are to the body, hence organelle, the suffix -elle being a diminutive. Organelles are either separately enclosed within their own lipid bilayers (also called membrane-bound organelles) or are spatially distinct functional units without a surrounding lipid bilayer (non-membrane bound organelles).

Equipartition theorem

In classical statistical mechanics, the equipartition theorem relates the temperature of a system to its average energies. The equipartition theorem is also known as the law of equipartition, equipartition of energy, or simply equipartition. The original idea of equipartition was that, in thermal equilibrium, energy is shared equally among all of its various forms; for example, the average kinetic energy per degree of freedom in translational motion of a molecule should equal that in rotational motion.

Ideal gas

An ideal gas is a theoretical gas composed of many randomly moving point particles that are not subject to interparticle interactions. The ideal gas concept is useful because it obeys the ideal gas law, a simplified equation of state, and is amenable to analysis under statistical mechanics. The requirement of zero interaction can often be relaxed if, for example, the interaction is perfectly elastic or regarded as point-like collisions.

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