Theoretical Condensed Matter Physics

9732083 Siggia该补助金由材料研究，物理学以及分子和细胞生物学部门共同资助。 在凝聚态物理学中发展的唯象方法将应用于从生物分子力学到细胞器形成的细胞生物学问题。 与细胞生物学家所采取的方法相反，对于选定的问题，物理理论可以在生物化学已知之前进行半定量预测，并以生物学家无法做到的方式将模型与实验联系起来。 定量力距离测量的DNA相互作用与凝聚剂（组蛋白和多胺）将建模，以提取结合剂，蛋白质-蛋白质相互作用和动力学的协会。 关于RNA折叠途径的一般问题及其机械延伸时的行为将通过二级结构的动力学蒙特卡罗代码进行研究，包括“伪结”。' 在减数分裂前期的染色体的经典研究强烈建议的聚合物刷的形态。 然后，聚合物理论解释了它们的一些性质，这些性质在其他方面是神秘的，并对力和张力进行了半定量的预测，这些预测可以通过实验进行验证。 在有丝分裂过程中导致拓扑异构酶II解析缠结的姐妹染色单体臂的偏差可以从多相聚合物共混物的角度来理解。 将继续与NIH的Lippincott-Schwartz实验室合作，包括光漂白实验的定量分析工作;测试药物诱导的高尔基体溶解的数据是否与细胞器间表面张力驱动的流动相容;以及开发和测试高尔基体组织和蛋白质分泌其他步骤的物理化学模型。 一个动力学蒙特卡罗或分子动力学代码将被开发用于由疏水和亲水单体组成的短聚合物，并将用于模拟双层膜中的动态过程，如融合和出芽。 通过这种方式可以获得实际的脂质数量和几乎合理的时间。 可以包括催化融合的蛋白质的类似的通用和粗粒度模型，然后模拟是一种启发式工具，从中可以开发一个简单的物理图片，以了解蛋白质如何使双层不稳定。 也将努力扩大被动标度平流的速度场的异常标度以前的计算。 目前还没有演绎理论来解释为什么速度波动随着尺度的增加而变得越来越非高斯。 该补助金由材料研究，物理学以及分子和细胞生物学部门共同资助。 在凝聚态物理学中发展的唯象方法将应用于从生物分子力学到细胞器形成的细胞生物学问题。 与细胞生物学家所采取的方法相反，对于选定的问题，物理理论可以在生物化学已知之前进行半定量预测，并以生物学家无法做到的方式将模型与实验联系起来。 ***

9732083 Siggia This grant is funded jointly by the Divisions of Materials Research, Physics, and Molecular and Cellular Biology. Phenomenological methods developed in condensed matter physics will be applied to problems in cell biology ranging from the mechanics of biomolecules to the formation of organelles. In contrast to approaches taken by cell biologists, for selected problems physical theory can make semiquantitative predictions before the biochemistry is known, and connect models to experiments in ways biologists cannot. Quantitative force-distance measurements of DNA interacting with condensing agents (histones and polyamines) will be modeled in order to extract binding agents, protein-protein interactions and the kinetics of association. General questions about folding pathways in RNA and its behavior when mechanically extended will be investigated by a kinetic Monte Carlo code for the secondary structure, including `pseudo-knots.' Classical studies of chromosomes in meiotic prophase strongly suggest the morphology of a polymer brush. Polymer theory then explains a number of their properties that were otherwise mysterious and makes semiquantitative predictions about forces and tensions which are feasible to check experimentally. The biases that cause topoisomerase II to resolve the engangled sister chromatid arms during mitosis may be understood in terms of a multiphase polymer blend. Collaborations will continue with the laboratory of Lippincott- Schwartz at NIH including work on the quantitative analysis of photobleach experiments; testing whether data for the drug induced dissolution of the Golgi is compatible with an interorganelle surface tension driven flow; and, develop and test physical-chemical models for the organization of the Golgi and other steps in protein secretion. A kinetic Monte Carlo or molecular dynamics code will be developed for short polymers consisting of hydrophobic and hydrophilic monomers and will be used to simul ate dynamical processes in bilayer membranes such as fusion and budding. Realistic numbers of lipids and almost reasonable times can be attained this way. Similar generic and coarse grained models for the proteins that catalyze fusion can be included, and the simulations then are a heuristic tool from which to develop a simple physical picture as to how proteins destabilize the bilayer. An effort will be made also to extend prior calculations of anomalous scaling in passive scaler advection to the velocity field. At present there are no deductive theories as to why velocity fluctuations become increasingly non-Gaussian as the scale size increases. %%% This grant is funded jointly by the Divisions of Materials Research, Physics, and Molecular and Cellular Biology. Phenomenological methods developed in condensed matter physics will be applied to problems in cell biology ranging from the mechanics of biomolecules to the formation of organelles. In contrast to approaches taken by cell biologists, for selected problems physical theory can make semiquantitative predictions before the biochemistry is known, and connect models to experiments in ways biologists cannot. ***