About This Project
Could you imagine if, having shaken a box of jigsaw puzzle pieces, you found the puzzle complete? Proteins perform similar miracles every day, but how? Statistical mechanics helped us develop the steam engine and computers. In this work, I apply statistical mechanics to predict how much time protein-like systems need to self-organize. This is basic research. It could lead to new methods of drug discovery/design, metabolic engineering, and more.Ask the Scientists
Join The DiscussionWhat is the context of this research?
To understand the importance of the paper, the reader may best be familiar with problems in condensed matter physics, including the problems of glasses (whether or not glasses are equilibrium states of matter, for example).
Readers familiar with questions about the physics of proteins and other biological molecules may also stand to gain much out of this work.
I am writing the paper to reach as broad an audience as possible. Although an understanding of statistical mechanics would be helpful, I don't think it is needed. I try to convey what is needed in the paper. I explain how the partition function is a sum of terms, each representing an arrangement of the particles, and I illustrate examples of such arrangements.
What is the significance of this project?
I recommend that anyone computationally simulating proteins read this work. I also think the work could be of significant interest to physicists studying glasses and other questions in basic statistical mechanics, such as Gibbs' paradox.
Although statistical mechanics has historically been useful for understanding the phases of pure substances and simple mixtures, I do not know that it has been applied as successfully to more complex systems. I have not seen the perhaps surprising conclusion about equilibration timescales in complex systems reported elsewhere.
Here are some biophysics questions I believe this research may help us answer:
How does a chaperone complex enable a protein to fold? Why do some proteins unfold irreversibly? How does molecular crowding affect protein structure?
What are the goals of the project?
I have a draft nearing completion.
The first step I'd like to do is rewrite the introduction.
I plan to send the paper to Nature, but before it's complete, I'd send a pre-submission inquiry to gauge their interest.
I'd like to proofread and revise the rest of the paper, including the mathematics, especially regarding systems of many specific and non-specific particles.
I might add some other work into the body of the paper or into the supplementary materials. Such additions I might take from my thesis.
With a little extra financial flexibility and time, I'd consider following up on some of the hypotheses this work lead me to. It may be possible to make sense of existing data in the literature using the theoretical approaches I outline. That could make a nice addition to the paper.
Budget
I would use the money to complete a draft of my theoretical physics paper and publish it.
I am (optimistically) trying to publish the paper via the Nature JPG. At their cost per colored figure, it could cost about $3000 for my 5 figures. I've heard that other journals would cost similarly.
Currently, I am on "wife support." I am taking in about $260 a week after taxes via unemployment insurance. I've been writing the article without salary over the last 6 months (b/t job hunting and playing entrepreneur), and it is almost ready for review (see abstract).
I intend to publish on the arXiv and in as high an impact peer-reviewed journal as possible. I believe peer-review will result in a better article, more readers, and a wider variety of backgrounds and interests.
The arXiv is free, but journals may charge open access fees. This article says the open access fee at PLoS One is $1300 but at Physical Review it is $2700.
Meet the Team
Team Bio
I recently completed my PhD in Applied Physics at Harvard University.Here's a link to my thesis, titled "Self-Assembly of Colloidal Spheres with Specific Interactions."
In my thesis experiments, I found that by carefully controlling the specificity of the interactions between microspheres, they self-assemble into otherwise unlikely or unstable structures. Here's an early description of that work, from well before I completed it.
I'm working on a theoretical physics paper about ideas related to my thesis experiments. The main result is that systems of many different components can take an unusually long time to reach their ground state compared to single- or few-component systems. I've signed up on experiment.com for financial help to complete and publish this work.
Jesse Collins
I believe when we're kids, we're all scientists. I loved observing plants and insects outdoors, and doing science projects such as measuring rainfall and versions of what I saw later in life as a Late Show with Letterman skit: “Will it float?"
I grew up in the '90s, a golden era for TV science, and I was more of a Beakman fan than a Bill Nye guy. My high school physics teacher was another great inspiration to me. He could weave history, physics and humor, perhaps most memorably in his lecture on Ptolemy's "Egocentric" theory of the sun's orbit around Earth.
My interests similarly spanned many topics. I took about as many classes in poetry at MIT as I did in physics.
I completed my PhD in Applied Physics at Harvard. Here's a link to my thesis, titled "Self-Assembly of Colloidal Spheres with Specific Interactions."
In my thesis experiments, I found that by carefully controlling the specificity of the interactions between microspheres, they self-assemble into otherwise unlikely or unstable structures. Here's an early description of that work, from well before I completed it.
I read so many journal articles that my PhD advisor, Vinny, put me on “probation" from reading any more. I worked more on my own ideas, leading to my reason for signing up on experiment.com. I am working on a theoretical physics paper related to my thesis experiments and am seeking funding to complete and publish it.
I'm also building a personal messaging app with some friends to help people share their initial reactions to each others' photo and video messages. Please see our landing page at www.faysee.com and find Faysee on the iOS app store.
Additional Information
See also, a similarly themed project: https://experiment.com/projects/toward-a-thermostatistics-for-complex-systemsProject Backers
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