Development of novel computational tools and algorithms for realistic 3D visualization and modeling of non-membranous cellular organelles
Lead Research Organisation:
University of Edinburgh
Department Name: Sch of Biological Sciences
Abstract
Recently much effort has been invested in understanding the organization of cellular structures that are not delimited by membrane, very small (~100 nm) in size and formed by dense packing of dozens of protein types, such as kinetochores and centrioles. This recent interest is fuelled by the growing recognition that these structures play not only structural but also crucial signaling functions, for example, in the control of the spindle assembly checkpoint and mitotic exit network. Presently, biophysical understanding of these essentially semi-dense protein crystals is very rudimentary. To improve it, computational tools allowing 3D visualization and simulation are absolutely required.
This highly interdisciplinary project that is positioned on the interface of computer science, physics and biology has an ambitious goal to adapt and further develop tools that will allow both realistic 3D visualization and modeling. A student who is expected to possess background and experience in mathematics and programming will work with the open-source platform CellPack (www.cellpack.org) with the specific aim to develop realistic spatial models for the kinetochore and spindle pole body (fungal centrioles). The developed spatial static models will be used to interface with physical methods of dynamical simulation, such as molecular dynamics and Brownian particle dynamics. These methods have been burgeoning recently, and our collaborators at the U of E physics have a strong background in applying LAMMPS molecular dynamics platform to simpler and more conventional biological systems, such as lipid membranes and chromatin.
This project will provide a unique opportunity for a student with the background in mathematical sciences to develop novel skills and knowledge of modern cell biology. The project is expected to have strong synergy with the research contacted in the Wellcome Trust Center for Cell Biology in Edinburgh as well as with the research of our collaborators at the University of Dundee.
This highly interdisciplinary project that is positioned on the interface of computer science, physics and biology has an ambitious goal to adapt and further develop tools that will allow both realistic 3D visualization and modeling. A student who is expected to possess background and experience in mathematics and programming will work with the open-source platform CellPack (www.cellpack.org) with the specific aim to develop realistic spatial models for the kinetochore and spindle pole body (fungal centrioles). The developed spatial static models will be used to interface with physical methods of dynamical simulation, such as molecular dynamics and Brownian particle dynamics. These methods have been burgeoning recently, and our collaborators at the U of E physics have a strong background in applying LAMMPS molecular dynamics platform to simpler and more conventional biological systems, such as lipid membranes and chromatin.
This project will provide a unique opportunity for a student with the background in mathematical sciences to develop novel skills and knowledge of modern cell biology. The project is expected to have strong synergy with the research contacted in the Wellcome Trust Center for Cell Biology in Edinburgh as well as with the research of our collaborators at the University of Dundee.
Studentship Projects
Project Reference | Relationship | Related To | Start | End | Student Name |
---|---|---|---|---|---|
BB/M010996/1 | 01/10/2015 | 31/03/2024 | |||
1647540 | Studentship | BB/M010996/1 | 01/10/2015 | 30/09/2019 |
Description | That virtual reality can be useful for building molecular models based on noisy 3D data. |
Exploitation Route | My software is available freely and code can be added to it |
Sectors | Chemicals,Education,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
URL | https://youtu.be/pGWlklDohdk?t=1322 |
Description | Explorable Explanations in Newbattle school |
Geographic Reach | Local/Municipal/Regional |
Policy Influence Type | Participation in a guidance/advisory committee |
Impact | Worked with local council, local schools, and researchers at University (Judy Robertson and Kate Farrell) on educational software for learning data science in Scottish schools. Also involved advising school and local council on what educational software to use. |
Description | Innovation initiative grant |
Amount | £1,800 (GBP) |
Funding ID | GR002512 |
Organisation | University of Edinburgh |
Sector | Academic/University |
Country | United Kingdom |
Start | 05/2016 |
End | 07/2017 |
Description | "Conferencing" software for talking about proteins |
Organisation | Research Complex at Harwell |
Country | United Kingdom |
Sector | Public |
PI Contribution | Design and development of software. |
Collaborator Contribution | Contribution of server, specification of needs, experimentation with results. |
Impact | Experimentation with VR as a way of having meetings regarding pharmacology. |
Start Year | 2017 |
Description | "Virus, the Beauty of the Beast" |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | Created website for helping to understand mathematical virology. Website was visited by more than 20,000 unique people |
Year(s) Of Engagement Activity | 2016 |
URL | http://viruspatterns.com |
Description | Midlothian science festival demonstration |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | I made a virtual reality program which people could go into and have a sense of what it is like to be inside a leaf. They were holding a large molecule and could "scoop up" smaller molecules with it, which it would react with. It gave insight into how metabolism works in plants. |
Year(s) Of Engagement Activity | 2016 |