Lecture

Coarse-Grained Simulations: Basics and Applications

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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 introduces the concept of coarse-grained simulations, which simplify complex systems by grouping atoms into particles. It explains the advantages of coarse-graining, different coarse-graining schemes, and simulation types. The lecture covers the DPD algorithm, including non-bonded and bond forces, integration methods, and practical examples of coarse-graining lipid membranes. It also discusses the importance of setting interaction parameters in DPD simulations and determining time and length scales for lipid bilayers.

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 (17)

Simulation

A simulation is the imitation of the operation of a real-world process or system over time. Simulations require the use of models; the model represents the key characteristics or behaviors of the selected system or process, whereas the simulation represents the evolution of the model over time. Often, computers are used to execute the simulation. Simulation is used in many contexts, such as simulation of technology for performance tuning or optimizing, safety engineering, testing, training, education, and video games.

Simulation video game

Simulation video games are a diverse super-category of video games, generally designed to closely simulate real world activities. A simulation game attempts to copy various activities from real life in the form of a game for various purposes such as training, analysis, prediction, or entertainment. Usually there are no strictly defined goals in the game, and the player is allowed to control a character or environment freely. Well-known examples are war games, business games, and role play simulation.

Lipid raft

The plasma membranes of cells contain combinations of glycosphingolipids, cholesterol and protein receptors organised in glycolipoprotein lipid microdomains termed lipid rafts. Their existence in cellular membranes remains somewhat controversial. It has been proposed that they are specialized membrane microdomains which compartmentalize cellular processes by serving as organising centers for the assembly of signaling molecules, allowing a closer interaction of protein receptors and their effectors to promote kinetically favorable interactions necessary for the signal transduction.

Computer simulation

Computer simulation is the process of mathematical modelling, performed on a computer, which is designed to predict the behaviour of, or the outcome of, a real-world or physical system. The reliability of some mathematical models can be determined by comparing their results to the real-world outcomes they aim to predict. Computer simulations have become a useful tool for the mathematical modeling of many natural systems in physics (computational physics), astrophysics, climatology, chemistry, biology and manufacturing, as well as human systems in economics, psychology, social science, health care and engineering.

Cell membrane

The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates and protects the interior of a cell from the outside environment (the extracellular space). The cell membrane consists of a lipid bilayer, made up of two layers of phospholipids with cholesterols (a lipid component) interspersed between them, maintaining appropriate membrane fluidity at various temperatures.

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