Computer simulation of polymers in confined and crowded environments

受限和拥挤环境中聚合物的计算机模拟

• 批准号: RGPIN-2016-04955
• 负责人: Polson, James
• 金额: $ 1.97万
• 依托单位: University of Prince Edward Island
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2017
• 资助国家: 加拿大
• 起止时间: 2017-01-01 至 2018-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=633594
• 关键词: Computer; simulation; polymers; confined; crowded

Polymers are chain-like molecules composed of a sequence of repeating chemical units called monomers. DNA is a biologically significant example of a polymer, one whose monomeric units are called nucleotides. It is the sequence of the nucleotides that comprises the genetic information of an organism. In recent years, there has been intense research activity devoted to the development of novel technologies for manipulating and analyzing DNA. Many of these technologies involve the transport of DNA through very compact regions of of space. The confinement of polymers in such regions is known to affect their physical properties. For example, the flexibility of polymers means that they will sample many different molecular shapes, or conformations, and confinement reduces the number of accessible conformations. Thus, the conformational "entropy" (a measure of the number of such conformations) decreases. Another quantity called "free energy" tends to increase as the entropy decreases. A basic understanding of the relationship between the free energy and the nature of the confinement of polymers is essential for interpreting the results of experiments involving confined DNA and thus for developing techniques for DNA analysis. In addition, this information is useful for understanding natural processes. One example is the segregation of replicated chromosomes (which are comprised of DNA) in bacteria. It is thought that the process may be driven in part by the natural tendency for the conformational free energy to decrease, and this is affected by the confinement inside the bacterium. In addition to confinement, the effects of "crowding" due to large proteins and other cellular components can also influence the dynamics of other processes involving DNA and other biopolymers.

聚合物是由一系列被称为单体的重复化学单元组成的链状分子。DNA是一种具有重要生物学意义的聚合物，其单体单位称为核苷酸。它是构成生物体遗传信息的核苷酸序列。近年来，有大量的研究活动致力于开发操纵和分析DNA的新技术。这些技术中有许多涉及DNA在空间非常紧凑区域的运输。已知聚合物在这些区域的限制会影响它们的物理性质。例如，聚合物的灵活性意味着它们可以对许多不同的分子形状或构象进行采样，而限制则减少了可访问构象的数量。因此，构象“熵”（这类构象的数量的度量）减少了。另一个被称为“自由能”的量随着熵的减少而增加。对自由能与聚合物约束性质之间关系的基本理解，对于解释涉及约束DNA的实验结果，从而开发DNA分析技术是必不可少的。此外，这些信息对于理解自然过程是有用的。一个例子是细菌中复制染色体（由DNA组成）的分离。据认为，这一过程可能部分是由构象自由能减少的自然趋势所驱动的，而这种趋势受到细菌内部限制的影响。除了限制外，由于大蛋白质和其他细胞成分造成的“拥挤”效应也可以影响涉及DNA和其他生物聚合物的其他过程的动力学。