RUI: Study of parasite-host model and its biological applications: simulations and theory

RUI：寄生虫-宿主模型及其生物学应用的研究：模拟和理论

• 批准号: 1702321
• 负责人: Jiajia Dong
• 金额: $ 14.98万
• 依托单位: Bucknell University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-05-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1702321&HistoricalAwards=false
• 关键词: RUI; Study; parasite; host; model

NONTECHNICAL SUMMARYThis award supports theoretical and computational research and education to investigate problems at the interface between soft matter and biology and to advance fundamental understanding of systems far from the familiar tranquil but robust state of equilibrium. These systems span from materials synthesis and growth to living things. Different species of living systems exhibit rich dynamical behaviors such as coexistence, competition, and symbiosis. The quantitative understanding of these phenomena requires a combination of different methods, such as modeling and computer simulations, as well as an integrated perspective from fundamental physical laws applied to living systems. This project focuses on the parasite-host type interaction in the context of plasmids - small DNA molecules - transforming bacteria from susceptible to resistant to antibiotic treatments. In the model, the spread of antibiotic resistance depends on the physical contact between the plasmid and the bacteria cells, as well as the susceptible and the resistance cells. By tuning the physically relevant parameters, such as the bacteria reproduction rate, plasmid diffusion rate, and the interactions amongst cells, the research team aims to gain insight into the rapid emergence of antibiotic resistance in a population, and spark further interest in interdisciplinary collaborations with biologists.Furthermore, this project will involve six undergraduate students, who will hone their computational skills through solving a real-world problem. They will also advance their understanding of complex systems and topics on stochastic processes through this project. These help broaden the research horizon of the students and bridge the transition from a learner to a scientist.TECHNICAL SUMMARYThis award supports theoretical and computational research and education to investigate problems at the interface between soft matter and biology and to advance fundamental understanding of systems far from equilibrium. Different species of living systems exhibit rich dynamical behaviors such as coexistence, competition, and symbiosis. The quantitative understanding of these phenomena is facilitated by the theoretical framework established in non-equilibrium statistical mechanics and modeling aided by computer simulations. In this project, the aims to integrate fundamental concepts in non-equilibrium statistical mechanics, population dynamics and cell biology with Monte Carlo simulations to explore a focused class of complex systems: the parasite-host (PH) model and its biological implications.The PH dynamics is less systematically explored, fundamentally different, and immensely important in life sciences. This project focuses on the parasite-host type interaction in the context of plasmids - small DNA molecules - transforming bacteria from susceptible to resistant to antibiotic treatments. The emergence of a resistant population comes from two mechanisms: plasmid-transformation and cell-cell conjugation. Both the dynamics, such as birth and death, and the spatial structure of the bacterial populations will be investigated. Casting this problem in the language of reaction-diffusion systems and using the theoretical results as a foundation, the research team plans to develop tools for probing the steady state properties and the dynamics of the PH system both in a well-mixed scenario and one with spatial structure. In this way, the PI aims to identify defining characteristics to curb the growth of a resistant population. Furthermore, the team plans to provide a more general description of the class of PH-like models and potential applications in the control of epidemics and the evolution of drug resistance in bacteria.The research team will involve six undergraduate students over three years. They will hone their computational skills through solving a real-world problem. They will also advance their understanding of complex system and topics on stochastic processes through this project. These help broaden the research horizon of students and bridge the transition from a learner to a scientist.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

非技术摘要这一奖项支持理论和计算研究和教育，以调查软物质与生物学之间界面的问题，并促进对系统远离熟悉的宁静但强大的平衡状态的基本理解。这些系统从材料合成和生长到生物。不同种类的生活系统表现出丰富的动力学行为，例如共存，竞争和共生。对这些现象的定量理解需要不同方法的组合，例如建模和计算机模拟，以及适用于生活系统的基本物理定律的综合观点。该项目着重于质粒 - 小型DNA分子的背景下的寄生虫 - 宿主类型相互作用 - 将细菌从易感到抗生素处理转化为抗生素处理。在模型中，抗生素耐药性的扩散取决于质粒和细菌细胞以及易感细胞和耐药细胞之间的物理接触。通过调整与物理相关的参数，例如细菌的繁殖率，质粒扩散率和细胞之间的相互作用，研究团队旨在深入了解人群中抗生素耐药性的快速出现，并激发人们对跨学科的兴趣的兴趣。他们还将通过该项目提高对随机过程的复杂系统和主题的理解。这些有助于扩大学生的研究范围，并弥合从学习者到科学家的过渡。技术摘要奖支持理论和计算研究和教育，以调查软物质与生物学之间的界面问题，并提高对远离平衡系统的系统的基本了解。不同种类的生活系统表现出丰富的动力学行为，例如共存，竞争和共生。在非平衡统计力学中建立的理论框架并在计算机模拟的帮助下，对这些现象的定量理解促进了对这些现象的促进。在该项目中，旨在将非平衡统计学机制，种群动力学和细胞生物学与蒙特卡洛模拟中的基本概念整合在一起，以探索重点的复杂系统类别：寄生虫宿主（pH）模型及其生物学含义。pH动力学在根本上探索了pH动力学，在根本上是不同的，在根本上是不同的，并且在生命中很重要。该项目着重于质粒 - 小型DNA分子的背景下的寄生虫 - 宿主类型相互作用 - 将细菌从易感到抗生素处理转化为抗生素处理。抗性种群的出现来自两种机制：质粒转化和细胞 - 细胞结合。将研究动态，例如出生和死亡，以及细菌种群的空间结构。研究小组计划在反应扩散系统的语言中施放这个问题，并以理论结果为基础，计划在良好的场景中开发用于探测稳态属性和pH系统动态的工具，并且具有空间结构。通过这种方式，PI旨在确定定义特征以遏制抵抗人群的生长。此外，该团队计划对类似pH的模型和潜在的应用程序进行更一般的描述，并在流行病的控制中使用潜在的应用以及细菌中耐药性的演变。研究团队将在三年内涉及六名本科生。他们将通过解决现实世界中的问题来磨练计算技能。他们还将通过该项目提高对复杂系统和随机过程的主题的理解。这些有助于扩大学生的研究视野，并弥合从学习者到科学家的过渡。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子优点和更广泛影响的评论标准来评估值得支持的。

项目成果

Population dynamics model and analysis for bacteria transformation and conjugation

• DOI: 10.1088/2399-6528/abb8be
• 发表时间: 2020-09-01
• 期刊: JOURNAL OF PHYSICS COMMUNICATIONS
• 影响因子: 1.2
• 作者: Dong, J. J.;Russo, J. D.;Sampson, K.
• 通讯作者: Sampson, K.