Theoretical and computational investigations of single biomolecule and multicellular morphogenetic processes

在这个提议中，我们从物理学的角度，使用分析和计算工具来研究生物学中的基本现象。我们主要关注三个研究领域。一个是生物启发优化问题。通常，进化通过改变形状、运动或分子来优化有机体的适应性。在某些情况下，这种优化可以在数学上理解，在其他情况下，通过计算机算法来理解。我们特别关注一个重要的问题，以了解蛋白质如何折叠到其生物功能结构，这涉及到推广的距离的概念，通常采取点之间，以更高的维度的对象。另一个优化问题与系统发育树（生命之树）有关，涉及到构建最小长度的高维网络，以表明现存物种的密切关系，以及它们的共同祖先可能是什么样子。我们有兴趣构建这样的网络，并了解它们的普遍性质。

In this proposal, we investigate fundamental phenomena in biology from the viewpoint of physics, using analytical and computational tools. We are interested primarily in 3 research areas. One is in biologically inspired optimization problems. Often evolution seeks to optimize the fitness of an organism by modifying shape, motion, or molecules. In some cases such optimization may be understood mathematically, in others, through computer algorithms. We focus specifically on a problem important to understanding how a protein folds to its biologically functional structure, which involves generalizing the notion of distance, normally taken between points, to objects of higher dimension. Another optimization problem is related to phylogenetic trees, the tree of life, and involves the construction of high-dimensional networks of minimal length indicating how closely related living species are, as well as what their common ancestors may have looked like. We are interested in constructing such networks and understanding their universal properties.