RUI: Monte Carlo Simulations in Exploring Non-Equilibrium Systems

RUI：探索非平衡系统中的蒙特卡罗模拟

• 批准号: 1248387
• 负责人: Jiajia Dong
• 金额: $ 11.83万
• 依托单位: Bucknell University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-06-05 至 2016-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1248387&HistoricalAwards=false
• 关键词: RUI; Monte; Carlo; Simulations; Exploring

TECHNICAL SUMMARYThis 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 SUMMARYThis 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.

技术摘要该奖项是根据 RUI 提案设立的，旨在支持旨在将非平衡统计力学、分子生物学和群体动力学的基本概念与蒙特卡罗模拟的实用技能相结合的研究和教育。在探索具有相似基础物理的受生物学启发的系统的总体主题下，这些项目旨在让学生接触前沿的研究主题，这些主题表现出原创性、与其知识库的跨学科相关性，以及在以下背景下磨练编程技能的机会：物理系统的研究。具体项目探索： 1.) 细菌中的蛋白质合成。在细菌的蛋白质合成过程中，当核糖体沿着 mRNA 模板移动时，就会形成一条氨基酸链，将遗传信息从序列翻译成功能性蛋白质。然而，由于遗传密码的简并性，相同的蛋白质可以由不同的 mRNA 序列以一系列序列依赖性速率产生。这个过程可以使用晶格气体模型来研究：完全不对称的简单排除过程。 完全不对称简单排除过程是非平衡统计力学的范式之一；它非常适合向本科生介绍，作为他们第一次接触该领域。 PI 计划首先通过蒙特卡罗模拟探索大肠杆菌中的 4000 多个基因序列及其蛋白质生产率的限制。 PI 将使用分析方法通过平均场理论研究这些速率。智力优点包括但不限于： 对非最优序列存在的见解；淬灭随机性对完全不对称简单排除过程的影响；并指导实验人员“微调”mRNA 序列以实现最佳蛋白质生产。2.) 宿主-寄生虫动力学。 与捕食者-被捕食者模型的普遍应用相反，宿主-寄生虫动力学模型的系统性探索较少，并且存在根本不同。在一个简单的模型中，寄生虫在方形格子上进行随机游走，并且仅在同一格子位置遇到宿主时才进行繁殖。寄生虫种群在系统中不保存。由于它们“发现”宿主的频率控制着它们的种群数量，寄生虫的空间和时间分布与宿主的空间和时间分布有着错综复杂的联系。 PI 计划有条不紊地研究宿主和寄生虫之间的关系。一名 PI 学生的初步模拟表明，阐明从不稳定状态到稳态寄生虫种群的重要相变是可能的。其他研究途径包括对宿主-寄生虫样相互作用的全面描述以及在流行病控制中的潜在应用。该项目负责人打算在一个主要是本科院校中建立一个高质量的研究项目。 该奖项支持八名本科生，并为他们学习许多科目创造了理想的背景，包括：细胞生物学、非平衡统计物理、数学模型的制定和高性能计算，这些都是传统物理课程中所缺少的。 -技术概要该奖项根据 RUI 提案颁发，支持远离平衡平衡、分子生物学和群体动力学的系统统计力学接口的理论研究和教育，同时整合蒙特卡罗计算机模拟的实践技能。在探索具有类似基础物理的受生物学启发的系统的总体主题下，这些项目旨在让学生接触前沿的研究主题，这些主题表现出原创性、与其知识库的跨学科相关性以及在该背景下磨练计算机编程技能的机会具体项目使用统计物理学的定量工具来探索：a）细菌（例如大肠杆菌）中的蛋白质合成过程，通过粒子传输模型，以及b）宿主-寄生虫动力学，灵感来自跳蚤侵扰在家庭宠物中，使用蒙特卡罗模拟和分析方法。这两个项目分别侧重于生物学中微观和宏观系统的例子，都有一个统一的主题：每个项目都涉及对由许多组成部分和丰富特征组成的复杂系统的研究，这些特征可以通过应用统计物理学工具来阐明。在此过程中，远离平衡态的系统的统计力学理论得到了发展。这样的理论将具有从生物系统到材料加工的广泛适用性。前一个项目预计将深入了解细菌中是否存在非最佳基因编码序列。后者旨在提供一些类似于宿主-寄生虫的相互作用的全面描述，并可能在流行病控制中具有潜在的应用。 PI 打算在一个主要是本科院校中建立一个高质量的研究项目。 该奖项支持八名本科生，并为他们学习许多科目创造了理想的背景，包括：细胞生物学、非平衡统计物理、数学模型的制定和高性能计算，这些都是传统物理课程中所缺少的。