SHF: Medium: Collaborative Research: From Molecules to Complex Shapes: Programming Pattern with DNA

人类和其他高等生物的发展创造了复杂的，精确定义的多细胞结构和模式。这些结构是分子程序的结果，这些程序存储在生物分子的序列和浓度中，当分子相互作用并通过化学反应改变状态时执行。这个提议的目标是了解生物化学系统如何被可靠地编程，以形成具有多层组织的不对称模式。这个建议是理解如何根据局部规则对全局行为和结构进行编程的总体目标的一部分，这是计算机科学许多领域的一个关键智力挑战。 PI的建议，复杂的，分层的化学模式可以形成的系统中，分子集体执行一个分子程序的模式形成。 PI将开发一种化学编程语言，在这种语言中，来自简单输入模式的信息通过逻辑运算被整合，形成新的模式区域。 这些逻辑操作然后被系统地集成到更大的程序中，允许生成具有复杂的多尺度结构的模式，类似于生物学中所看到的。设计的合成DNA分子一起充当电路元件将被用来实现这种语言。DNA分子是分子编程方法的理想基质，因为它们具有复杂的序列，具有可预测的行为和相互作用。这项研究与一个推广计划紧密结合，该计划将开发一个教育计划，致力于教授成功进行分子编程所必需的跨学科技能。

Development in humans and other higher organisms creates complex,precisely defined multicellular structures and patterns. Thesestructures are the result of molecular programs that are stored in thesequences and concentrations of biomolecules and are executed whenmolecules interact and change state through chemical reactions. Thegoal of this proposal is to understand how biochemical systems can bereliably programmed to form asymmetric patterns with multiple layersof organization. This proposal is part of a general goal to understandhow to program global behavior and structure based on local rules,which a key intellectual challenge in many areas of computer science. The PI's propose that complex, hierarchical chemical patterns can be formedby systems in which the molecules collectively execute a molecularprogram for pattern formation. The PI's will develop achemical programming language in which information from simple inputpatterns is integrated by logical operations to form new patternregions. These logical operations are then systematically integratedinto larger programs, allowing the generation of patterns withcomplex, multiscale structure similar to that seen inbiology. Designed synthetic DNA molecules that together act as circuitelements will be used to implement this language. DNA molecules areideal substrates for a molecular programming approach because theyhave complex sequences with predictable behaviors and interactions.This research is tightly integrated with an outreach program that will develop an educational program dedicated to teaching theinterdisciplinary skills that are necessary to be successful inmolecular programming.,