Center for Theoretical Biological Physics

理论生物物理中心

• 批准号: 2019745
• 负责人: Jose Onuchic
• 金额: $ 1290万
• 依托单位: William Marsh Rice University
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2025-08-31
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2019745&HistoricalAwards=false
• 关键词: Center; Theoretical; Biological; Physics

Theoretical physics has become increasingly important in understanding complex living systems and plays a key role in addressing phenomena and behavior on the cellular and multicellular level. This Physics Frontiers Centers award to the Center for Theoretical Biological Physics (CTBP) builds on the extensive research, education, and outreach successes achieved during previous awards to both expand the reach and accelerate the rate of scientific progress on critical issues in biological physics, and extend the scope of training and outreach activities. The goal of the work is to further our understanding of : (1) living systems by combining soft matter approaches with molecular biophysics, (2) information rich network-based computations with stochastic nonlinear dynamics, and (3) self-organization with design through Darwinian evolution. Topics to be studied include: the structure and function of the genome; phenotypic decision-making via nonlinear information processing in biological networks; and the physical architecture of the cell and its control by incoming signals. Collaborations with many contacts at the Texas Medical Center and a new association with faculty at the Harvard Medical School will continue CTBP's training of students and postdoctoral fellows in the information rich areas of theoretical biological physics. The CTBP outreach includes a pioneering program that brings undergraduates from underrepresented groups to the Center for intensive summer experiences and provides them with mentoring research and career guidance, following up through the academic year. This effort will be expanded and also extended to a new remote CTBP site at Northeastern University.The research program includes four main research areas: 1) Developing a theory-based strategy to create quantitatively predictive models of genome structural ensembles applicable to a broad range of cell types and states of the cell cycle; 2) Creating a new set of experimental and analytic tools for obtaining and interpreting data regarding genome structure and dynamics; 3) Utilizing tools from statistical physics, soft condensed matter physics, polymeric materials, and non-linear dynamical systems to further understanding of regulatory networks involving genomic transcriptional regulation; and 4) Studying the structure of the living cell, the active cytoskeleton, which determines basic cellular architecture and also serves as a conduit of signals running between different subcellular regions. The planned research utilizes the unique scientific capability provided by the Physics Frontier Center. Crucially, it continues the strategy of both developing and using concepts and techniques from physics and applied mathematics to tackle otherwise intractable problems in the science of living matter and conversely to use biological problems to motivate new concepts of broad applicability throughout physics. This Physics Frontiers Centers award is co-funded by the Division of Physics and the Division of Materials Research within the Directorate of Mathematical and Physical Sciences, and the Division of Molecular and Cellular Biosciences and the Division of Integrative Organismal Systems within the Directorate for Biological Sciences.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.

理论物理学在理解复杂的生命系统方面变得越来越重要，并在解决细胞和多细胞水平上的现象和行为方面发挥着关键作用。 这个物理前沿中心奖给理论生物物理中心（CTBP）建立在广泛的研究，教育和推广的成功，在以前的奖项，既扩大了覆盖面，加快了生物物理学中的关键问题的科学进步的速度，并扩大了培训和推广活动的范围。这项工作的目标是进一步了解：（1）通过将软物质方法与分子生物物理学相结合来实现生命系统，（2）基于随机非线性动力学的信息丰富的网络计算，以及（3）通过达尔文进化论设计的自组织。将研究的主题包括：基因组的结构和功能;通过生物网络中的非线性信息处理进行表型决策;细胞的物理结构及其受输入信号的控制。与德克萨斯医学中心的许多联系人以及与哈佛医学院教师的新协会的合作将继续CTBP在理论生物物理学的信息丰富领域对学生和博士后研究员的培训。CTBP外展包括一个开创性的计划，将来自代表性不足的群体的本科生带到中心进行密集的夏季体验，并为他们提供指导研究和职业指导，并在整个学年中跟进。该研究计划包括四个主要研究领域：1）发展基于理论的策略，建立适用于广泛细胞类型和细胞周期状态的基因组结构集合的定量预测模型; 2）创建一套新的实验和分析工具，用于获取和解释有关基因组结构和动态的数据; 3）利用统计物理、软凝聚态物理、聚合物材料和非线性动力学系统等工具，进一步理解涉及基因组转录调控的调控网络; 4）研究活细胞的结构，即活性细胞骨架，它决定了基本的细胞结构，也是不同亚细胞区域之间信号传递的管道。 计划中的研究利用了物理前沿中心提供的独特科学能力。至关重要的是，它继续发展和使用物理学和应用数学的概念和技术的战略，以解决生命物质科学中的其他棘手问题，并反过来使用生物学问题来激发整个物理学中广泛适用的新概念。该物理前沿中心奖由数学和物理科学理事会内的物理学部和材料研究部共同资助，该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的知识产权进行评估来支持。优点和更广泛的影响审查标准。

项目成果

Mean-field model for nematic alignment of self-propelled rods

自驱动棒向列排列的平均场模型

• DOI: 10.1103/physreve.106.034613
• 发表时间: 2022
• 期刊: Physical Review E
• 影响因子: 2.4
• 作者: Perepelitsa, Misha;Timofeyev, Ilya;Murphy, Patrick;Igoshin, Oleg A.
• 通讯作者: Igoshin, Oleg A.

BAP1 is a novel regulator of HIF-1α.

BAP1 是 HIF-1α 的新型调节剂。

• DOI: 10.1073/pnas.2217840120
• 发表时间: 2023-01-24
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Bononi, Angela;Wang, Qian;Zolondick, Alicia A.;Bai, Fang;Steele-Tanji, Mika;Suarez, Joelle S.;Pastorino, Sandra;Sipes, Abigail;Signorato, Valentina;Ferro, Angelica;Novelli, Flavia;Kim, Jin-Hee;Minaai, Michael;Takinishi, Yasutaka;Pellegrini, Laura;Napolitano, Andrea;Xu, Ronghui;Farrar, Christine;Goparaju, Chandra;Bassi, Cristian;Negrini, Massimo;Pagano, Ian;Sakamoto, Greg;Gaudino, Giovanni;Pass, Harvey I.;Onuchic, Jose N.;Yang, Haining;Carbone, Michele
• 通讯作者: Carbone, Michele

A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of "Genetic Purging" and Genomic Stability.

• DOI: 10.3390/genes13071270
• 发表时间: 2022-07-18
• 期刊: Genes
• 影响因子: 3.5

Investigating human chromosome organization by whole-genome simulations

通过全基因组模拟研究人类染色体组织

• DOI: 10.1016/j.bpj.2022.11.1728
• 发表时间: 2023
• 期刊: Biophysical Journal
• 影响因子: 3.4
• 作者: Mello, Matheus F.;Dodero-Rojas, Esteban;Oliveira Jr, Antonio B.;Contessoto, Vinicius;Onuchic, José N.
• 通讯作者: Onuchic, José N.

Dynamics of chemical reactions on single nanocatalysts with heterogeneous active sites

具有异质活性位点的单一纳米催化剂上的化学反应动力学

• DOI: 10.1063/5.0137751
• 发表时间: 2023
• 期刊: The Journal of Chemical Physics
• 作者: Chaudhury, Srabanti;Jangid, Pankaj;Kolomeisky, Anatoly B.
• 通讯作者: Kolomeisky, Anatoly B.