| NSF Org: |
DMR Division Of Materials Research |
| Recipient: |
|
| Initial Amendment Date: | October 24, 2012 |
| Latest Amendment Date: | May 30, 2013 |
| Award Number: | 1248387 |
| Award Instrument: | Continuing Grant |
| Program Manager: |
Daryl Hess
dhess@nsf.gov (703)292-4942 DMR Division Of Materials Research MPS Directorate for Mathematical and Physical Sciences |
| Start Date: | June 5, 2012 |
| End Date: | August 31, 2016 (Estimated) |
| Total Intended Award Amount: | $118,311.00 |
| Total Awarded Amount to Date: | $118,311.00 |
| Funds Obligated to Date: |
FY 2013 = $39,964.00 |
| History of Investigator: |
|
| Recipient Sponsored Research Office: |
1 DENT DR LEWISBURG PA US 17837-2005 (570)577-3510 |
| Sponsor Congressional District: |
|
| Primary Place of Performance: |
7TH & MOORE AVE LEWISBURG PA US 17837-2111 |
| Primary Place of
Performance Congressional District: |
|
| Unique Entity Identifier (UEI): |
|
| Parent UEI: |
|
| NSF Program(s): | CONDENSED MATTER & MAT THEORY |
| Primary Program Source: |
01001314DB NSF RESEARCH & RELATED ACTIVIT |
| Program Reference Code(s): |
|
| Program Element Code(s): |
|
| Award Agency Code: | 4900 |
| Fund Agency Code: | 4900 |
| Assistance Listing Number(s): | 47.049 |
ABSTRACT
TECHNICAL SUMMARY
This award made on an RUI proposal supports research and education aimed at integrating fundamental concepts in non-equilibrium statistical mechanics, molecular biology and population dynamics with the practical skills of Monte Carlo simulations. Under the overarching theme of exploring biology-inspired systems with similar underlying physics, the projects are designed to bring students in contact with cutting edge research topics which exhibit originality, interdisciplinary relevance to their knowledge base and opportunities to hone their programming skills in the context of the study of physical systems.
The specific projects explore:
1.) Protein synthesis in bacteria. During protein synthesis in bacteria, a chain of amino acids is formed when ribosomes move along the mRNA template, translating genetic information from the sequence to functioning proteins. Due to the degeneracy in the genetic code, however, the same protein can be produced by different mRNA sequences with a range of sequence-dependent rates. This process can be studied using a lattice gas model: The totally asymmetric simple exclusion process. The totally asymmetric simple exclusion process is one of the paradigms in nonequilibrium statistical mechanics; it is well suited to be introduced to undergraduate students as their first exposure to this field. The PI plans to explore over 4000 gene sequences in E. coli and the limits on their protein production rates first through Monte Carlo simulations. Using analytic methods, the PI will investigate these rates by mean field theory. The intellectual merits include but are not limited to: Insights on the existence of non-optimal sequences; effects of quenched randomness on the totally asymmetric simple exclusion process; and guidance to experimentalists on "fine-tuning" mRNA sequence for optimal protein production.
2.) Host-parasite dynamics. Contrary to the ubiquitous applications of the predator-prey model, the host-parasite dynamics model is less systematically explored and fundamentally different. In a simple model, parasites conduct a random walk on a square lattice and reproduce only when encountering a host at the same lattice site. The parasite population is not conserved in the system. As the frequency at which they "find" the host controls their population, the spatial and temporal distributions of the parasites are intricately connected to that of the host. The PI plans to study the relation between host and parasites in a methodical manner. Preliminary simulations by one of the PI's students suggest that elucidating a non-trivial phase transition from unstable to steady state parasite population may be possible. The other avenues of study include a comprehensive description on the host-parasite-like interactions and potential applications in epidemics control.
The PI intends to establish a quality research program in a primarily undergraduate institution. This award supports eight undergraduate students and creates an ideal backdrop for them to learn a number of subjects, including: cell biology, non-equilibrium statistical physics, formulation of mathematical models, and high performance computation, that are absent from traditional physics curricula.
NON-TECHNICAL SUMMARY
This award made on an RUI proposal supports theoretical research and education at the interface of the statistical mechanics of systems that are far from the balance of equilibrium, molecular biology and population dynamics while integrating the practical skills of Monte Carlo computer simulations. Under the overarching theme of exploring biology-inspired systems with similar underlying physics, the projects are designed to bring students in contact with cutting edge research topics which exhibit originality, interdisciplinary relevance to their knowledge base and opportunities to hone their computer programming skills in the context of the study of familiar physical systems.
The specific projects use the quantitative tools of statistical physics to explore: a) the protein synthesis process in bacteria, for example E.Coli, through a particle transport model, and b) the host-parasite dynamics, inspired by flea infestation in household pets, using Monte Carlo simulations and analytical approaches. Focused on examples of microscopic and macroscopic systems in biology respectively, both projects share a unifying theme: each involves the study of a complex system of many components and rich features that may be illuminated by applying the tools of statistical physics. In the process, the theory of statistical mechanics for systems far from the balance of equilibrium is advance. Such a theory will have wide applicability from biological systems to materials processing. The former project is expected to provide insights into the existence of non-optimal gene coding sequences in bacteria. The latter is intended to provide a comprehensive description of some host-parasite-like interactions and may have potential applications in epidemics control.
The PI intends to establish a quality research program in a primarily undergraduate institution. This award supports eight undergraduate students and creates an ideal backdrop for them to learn a number of subjects, including: cell biology, non-equilibrium statistical physics, formulation of mathematical models, and high performance computation, that are absent from traditional physics curricula.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Note:
When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external
site maintained by the publisher. Some full text articles may not yet be available without a
charge during the embargo (administrative interval).
Some links on this page may take you to non-federal websites. Their policies may differ from
this site.
PROJECT OUTCOMES REPORT
Disclaimer
This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.
Aiming at integrating fundamental concepts in non-equilibrium statistical mechanics (NESM), molecular biology and population dynamics with the practical skills of Monte Carlo simulations to explore the dynamics in complex systems, our group set out to investigate two systems: 1) protein synthesis process in bacteria during which ribosomes translocate along a genetic template; and 2) host-parasite dynamics resembling flea reproduction in household pets.
The processes of transcribing DNA into messenger RNA and then translating into proteins in bacteria provide an active field and ideal starting point for modeling a complex non-equilibrium system. Our investigation of this critical process is motivated by the experimental observation that active transcribing RNA polymerases – the “workhorses” of transcription of genetic information – interact with one another and can result in the “cooperative speed-up.” To quantify this effect, we used a combination of Monte Carlo simulation and theoretical analysis.
Our model, reminiscent of Newton’s cradle, consists of a one-dimensional lattice along which particles can hop when the neighboring site is empty and triggers an additional particle to hop if (a) the first particle arrives at the rear end of another cluster particles; (b) the cluster size is less than the maximal interaction length (lmax), shown in upper right. We study an accelerated exclusion process (AEP) and extract quantitative insights on the relationship between particle density (ρ) and steady state flux (J).
The study revealed new phases in the model, in which the active RNA polymerases can either be in a “solid” phase, clustering together and moving in concert with unit velocity (UV), or a “liquid” phase with an augmented current (AC). Consequently, we observed new J-ρ relation beyond the paradigmatic TASEP (totally asymmetric simple exclusion process).
Turning to the other front of investigation, we look at the parasite-host (PH) interaction. Much less studied and fundamentally different from the predator-prey system, parasites and hosts interact only during the process of reproduction. We explored the PH model with the new dynamics and observed several novel phenomena arising from it, such as a non-trivial parasite survival-extinction transition, Yukawa-like spatial distribution of parasites, and non-monotonic parasite total population as a function of birth rate. Formulating this system on a discrete lattice, we solved this problem analytically, with results that agree well with simulations. We also considered the continuum and thermodynamic limits to gain further intuitive physical insights.
This grant supported a total of six undergraduates, including one from under-represented groups, for their work on the above projects. Together with the PI, the students developed algorithms and refined the models. The different contexts of the projects enabled the students to see how similar physics principles govern rather complex and different physical systems. They were able to explore such complexity via computer simulation and modeling. The students also presented (oral presentations and posters) the research outcomes at national and regional conferences, gaining the invaluable experience of disseminating results to the broader scientific community.
The student-engagement in the sponsored research also inspired the PI to think deeply on invigorating the existing computational physics curriculum. The PI developed and has been refining a set of computational assignments using Python and integrated them in her undergraduate-level Modern Physics course.
Last Modified: 09/08/2016
Modified by: Jiajia Dong
Please report errors in award information by writing to: awardsearch@nsf.gov.
