The future of physics-based simulation

Structure generated by NAST, RNA modeling toolAlthough my research is only tangentially related to physics-based simulation, I work in a building that houses a National Center and many of my colleagues work in the field. A topic that came up a few weeks ago concerned the future of physics-based simulation, specifically, the following open-ended questions:

  • What are high impact biomedical arenas that offer exciting challenges for physics-based simulation?
  • What are new areas of computational research in physics-based simulation that will have a major impact on biology?

There were a number of good ideas regarding the computational side, including development on GPUs (graphical processing units like your Playstation 3) and better integration of modeling at multiple scales – whether they be time scales or physical scales – but it seemed that fewer people had a good idea of what biomedical areas would present new opportunities for simulation.

One idea that popped into my head and was brought up near the end of the discussion was systems biology. It’s a concept that has been thrown around rather indiscriminately since its emergence and sometimes dismissed as too broad or ambitious, for it carries a sense of the “holy grail” of biology: to understand how molecular systems work in part but more importantly as a whole. An important aspect of systems are their dynamics, which in cells translates into the concentrations of molecules and the rates of change, which affect the state of the system.

Where simulation connects to this is in determining the conditions under which change occurs. Many events in the cell happen due to interactions between structures such as proteins and DNA, and their interaction partners. Physics-based simulation is often used to study these types of interactions. One could imagine an experimental framework where molecular simulations model the interaction between proteins and their ligands, which when favorable lead to downstream interactions (which can also be modeled) which overall inform the dynamics of the system. Such an endeavor is far in the future but it would provide an unprecedented level of detail and provide testable hypotheses. It would be really cool to get to a place where you could ask “how does mutation X in protein Y affect process Z?” (and beyond) and be able to get a complete picture, from molecular dynamics to protein levels to the overall influence on a process, organ system, or organism.

These are still open questions and I’m sure the people I work with would be interested in more ideas, so feel free to suggest other possible answers!

(Image: structure generated by NAST – Nucleic Acid Simulation Tool, available at


3 Responses to The future of physics-based simulation

  1. This idea of simulations thought multiple scales has been on my mind for some time now. It sounds like the main objective of biological research to me. How does genetic variation change the components (DNA, RNA, proteins, genome structure), systems (interactions, metabolic flux,etc) and phenotypes (cycles, memory, migration). Up until now we have mostly simulated each particular scale separately but it will be exciting to start putting them together.

  2. Pingback: The future of simulation : business|bytes|genes|molecules

  3. melvin goldstein says:

    Science and technology does have its limitation. There are Physics Foibles. See Godel Incompleteness.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s