Lecture

Cell Biology: Thermodynamics

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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 covers the importance of reversibility in cells to minimize energy dissipation, the concept of entropy in isolated systems, the second law of thermodynamics, and the different types of free energies related to boundary conditions. It also discusses phase transitions, entropic springs in biological molecules, and the phase transition of entropic springs. The lecture concludes with a detailed analysis of the collapse of an entropic spring and the force-extension curve, highlighting the relationship between free energy, temperature, and polymer contour length.

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

Ontological neighbourhood

Physics

Thermodynamics: Statistical mechanics

Related concepts (31)

Second law of thermodynamics

The second law of thermodynamics is a physical law based on universal experience concerning heat and energy interconversions. One simple statement of the law is that heat always moves from hotter objects to colder objects (or "downhill"), unless energy in some form is supplied to reverse the direction of heat flow. Another definition is: "Not all heat energy can be converted into work in a cyclic process." The second law of thermodynamics in other versions establishes the concept of entropy as a physical property of a thermodynamic system.

Laws of thermodynamics

The laws of thermodynamics are a set of scientific laws which define a group of physical quantities, such as temperature, energy, and entropy, that characterize thermodynamic systems in thermodynamic equilibrium. The laws also use various parameters for thermodynamic processes, such as thermodynamic work and heat, and establish relationships between them. They state empirical facts that form a basis of precluding the possibility of certain phenomena, such as perpetual motion.

Thermodynamics

Thermodynamics is a branch of physics that deals with heat, work, and temperature, and their relation to energy, entropy, and the physical properties of matter and radiation. The behavior of these quantities is governed by the four laws of thermodynamics which convey a quantitative description using measurable macroscopic physical quantities, but may be explained in terms of microscopic constituents by statistical mechanics.

Chemical thermodynamics

Chemical thermodynamics is the study of the interrelation of heat and work with chemical reactions or with physical changes of state within the confines of the laws of thermodynamics. Chemical thermodynamics involves not only laboratory measurements of various thermodynamic properties, but also the application of mathematical methods to the study of chemical questions and the spontaneity of processes. The structure of chemical thermodynamics is based on the first two laws of thermodynamics.

Entropy (information theory)

In information theory, the entropy of a random variable is the average level of "information", "surprise", or "uncertainty" inherent to the variable's possible outcomes. Given a discrete random variable , which takes values in the alphabet and is distributed according to : where denotes the sum over the variable's possible values. The choice of base for , the logarithm, varies for different applications. Base 2 gives the unit of bits (or "shannons"), while base e gives "natural units" nat, and base 10 gives units of "dits", "bans", or "hartleys".

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