Grant: Research Tools and Instruments - Category 1 (<$150,000)
University of Calgary
$150,000.00
Data infrastructure for biomolecular simulation - Steacie Supplement
FY 2008-09
Summary
Biomolecules, such as proteins, DNA, lipids, and carbohydrates, exist in a microscopic universe with time and length scales 6-12 orders of magnitude smaller than the meters and seconds in which we measure length and time. They move rapidly on a time scale of nanoseconds and interact with individual water molecules. The size of most biomolecules is very small compared to the wavelength of visible light, which means they cannot be seen with ordinary microscopes, although there are many sophisticated experimental methods to measure aspects of the behaviour, shape, and interactions of biomolecules. Computer simulations of models that describe atoms and their interactions have become a powerful and widely used method to study matter at the level of electrons, atoms, and molecules. Many of these models are applicable to a broad range of materials, including biomolecules.
Using powerful computers and a description of how atoms interact with each other, it is possible to calculate in atomic detail how lipids, water and proteins move in time. In recent years, this molecular dynamics simulation method has been a very powerful method to solve problems in the area of lipids and proteins. It is very computationally intensive. Simulations are run on local, regional, and national supercomputer facilities, but the data the simulations generate have to be analyzed and processed locally by students and postdoctoral fellows. For this we need large-scale data storage and backup capabilities. This proposal requests disk storage and tape backup for the development of a new model for coarse-grained biomolecular simulations in a related operating grant proposal. This project focuses specifically on improving the accuracy of our description of peptides and proteins. If we are successful, we will be able in the future to understand the molecular basis of new antimicrobial agents, the aggregation of proteins and peptides and their interactions with cell membranes and other biomolecules, and perhaps design new biocompatible materials for bioengineering purposes.
Program
Research Tools and Instruments - Category 1 (<$150,000)
Recipient
Location
Alberta, Canada
Recipient Type
Academia
Type
Grant
Source
NSERC's Awards Data
As published
Application id
372880-2009
Name nom
Tieleman, Peter
Department département
Biological Sciences
Organization id
11
Institution établissement
University of Calgary
Province en
Alberta
Province fr
Alberta
Country en
CANADA
Country fr
CANADA
Fiscal year exercice financier
2008
Competition year année de concours
2009
Award amount
150000
Program id
EQPEQ
Program nane en
Research Tools and Instruments - Category 1 (<$150,000)
Program name fr
Outils et instruments de recherche - catégorie 1 (<150 000$)
Group en
Discovery grants programs
Group fr
Programmes de subventions à la découverte
Committee code
104
Committee name en
Steacie Fellowship Sel Cttee
Committee name fr
Cté de sél des bourses Steacie
Area of application code
1202
Area of application group en
Advancement of knowledge
Area of application group fr
Avancement des connaissances
Area of application en
Physical sciences
Area of application fr
Sciences physiques
Research subject code
3404
Research subject group en
Physical chemistry
Research subject group fr
Chimie physique
Research subject en
Biophysical chemistry
Research subject fr
Chimie biophysique
Partie
1
Nb partie
1
Application title
Data infrastructure for biomolecular simulation - Steacie Supplement
Keyword
NA
Application summary
Biomolecules, such as proteins, DNA, lipids, and carbohydrates, exist in a microscopic universe with time and length scales 6-12 orders of magnitude smaller than the meters and seconds in which we measure length and time. They move rapidly on a time scale of nanoseconds and interact with individual water molecules. The size of most biomolecules is very small compared to the wavelength of visible light, which means they cannot be seen with ordinary microscopes, although there are many sophisticated experimental methods to measure aspects of the behaviour, shape, and interactions of biomolecules. Computer simulations of models that describe atoms and their interactions have become a powerful and widely used method to study matter at the level of electrons, atoms, and molecules. Many of these models are applicable to a broad range of materials, including biomolecules.
Using powerful computers and a description of how atoms interact with each other, it is possible to calculate in atomic detail how lipids, water and proteins move in time. In recent years, this molecular dynamics simulation method has been a very powerful method to solve problems in the area of lipids and proteins. It is very computationally intensive. Simulations are run on local, regional, and national supercomputer facilities, but the data the simulations generate have to be analyzed and processed locally by students and postdoctoral fellows. For this we need large-scale data storage and backup capabilities. This proposal requests disk storage and tape backup for the development of a new model for coarse-grained biomolecular simulations in a related operating grant proposal. This project focuses specifically on improving the accuracy of our description of peptides and proteins. If we are successful, we will be able in the future to understand the molecular basis of new antimicrobial agents, the aggregation of proteins and peptides and their interactions with cell membranes and other biomolecules, and perhaps design new biocompatible materials for bioengineering purposes.
