RUI: Monte Carlo Simulations in Exploring Non-Equilibrium Systems

技术总结这个奖项是根据RUI的一项提议颁发的，旨在将非平衡统计力学、分子生物学和种群动力学的基本概念与蒙特卡洛模拟的实用技能相结合，以支持研究和教育。在探索具有相似物理基础的生物启发系统的总体主题下，这些项目旨在让学生接触前沿研究主题，这些主题展示了独创性、与他们的知识库的跨学科相关性，以及在物理系统研究的背景下磨练他们的编程技能的机会。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，将遗传信息从序列转化为功能蛋白质。然而，由于遗传密码的简并性，不同的mRNA序列可以产生相同的蛋白质，具有一定的序列依赖率。这个过程可以用一个格子气体模型来研究：完全不对称的简单排斥过程。完全不对称简单排斥过程是非平衡统计力学的范式之一，非常适合介绍给本科生，作为他们第一次接触这一领域。PI计划首先通过蒙特卡洛模拟来探索大肠杆菌中的4000多个基因序列及其蛋白质产量的极限。使用解析方法，PI将通过平均场理论来研究这些速率。智力上的优点包括但不限于：对非最佳序列的存在的见解；猝灭的随机性对完全不对称的简单排除过程的影响；以及指导实验者“微调”信使核糖核酸序列以获得最佳蛋白质生产。寄主-寄生虫动力学。与捕食者-食饵模型的普遍应用相反，宿主-寄生虫动力学模型较少系统地被探索，而且本质上是不同的。在一个简单的模型中，寄生虫在正方形格子上进行随机行走，只有在同一格子上遇到宿主时才会繁殖。寄生虫种群在系统中不是保守的。随着它们“找到”寄主的频率控制着它们的种群，寄生虫的空间和时间分布与寄主的分布错综复杂地联系在一起。PI计划以一种系统的方式研究宿主和寄生虫之间的关系。PI的一名学生的初步模拟表明，阐明从不稳定的寄生虫种群到稳定的寄生虫种群的不平凡的相变是可能的。其他研究途径包括对宿主-寄生虫类相互作用的全面描述和在流行病控制中的潜在应用。PI打算在一个以本科为主的机构建立一个高质量的研究项目。这个奖项支持八名本科生，并为他们创造了一个理想的背景，让他们学习一些传统物理课程所没有的学科，包括：细胞生物学、非平衡统计物理、数学模型的建立和高性能计算。非技术总结这个奖项是根据RUI的建议而设立的，支持在远离平衡、分子生物学和种群动力学的系统的统计力学界面上的理论研究和教育，同时整合蒙特卡罗计算机模拟的实践技能。在探索具有相似潜在物理的生物启发系统的总体主题下，这些项目旨在让学生接触前沿研究主题，这些主题展示了原创性、与他们的知识库的跨学科相关性以及在研究熟悉的物理系统的背景下磨练他们的计算机编程技能的机会。具体的项目使用统计物理的定量工具来探索：a)细菌中的蛋白质合成过程，例如，通过粒子传输模型的E.Coli，以及b)宿主-寄生虫的动态，使用蒙特卡洛模拟和分析方法，受到家用宠物中跳蚤侵扰的启发。这两个项目分别聚焦于生物学中微观和宏观系统的例子，都有一个共同的主题：每个项目都涉及研究一个由许多组件和丰富特征组成的复杂系统，这些系统可以通过应用统计物理工具来阐明。在这个过程中，提出了远离平衡的系统的统计力学理论。这样的理论将具有广泛的适用性，从生物系统到材料加工。前一个项目预计将为细菌中存在非最佳基因编码序列提供见解。后者旨在全面描述一些宿主-寄生虫的相互作用，并可能在流行病控制中有潜在的应用。PI打算在一个以本科为主的机构建立一个高质量的研究项目。该奖项支持八名本科生，并为他们提供了一个理想的背景，让他们学习传统物理课程中缺失的一些学科，包括：细胞生物学、非平衡统计物理、数学模型的建立和高性能计算。

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.