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

人类和其他高等生物的发育创造了复杂的、精确定义的多细胞结构和模式。这些结构是存储在生物分子序列和浓度中的分子程序的结果，当分子通过化学反应相互作用和改变状态时，这些程序就会执行。这项提议的目标是了解生化系统如何可靠地编程，以形成具有多个组织层的不对称模式。这项提议是理解如何根据当地规则对全球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关键智力挑战。PI提出，复杂的、层次分明的化学模式可以由分子集体执行分子程序以形成模式的系统来形成。PI将开发非化学编程语言，在该语言中，通过逻辑运算将来自简单输入模式的信息整合在一起，以形成新的模式区域。然后，这些逻辑运算被系统地整合到更大的程序中，允许生成具有复杂的、多尺度结构的模式，类似于生物学中看到的模式。设计的合成DNA分子将一起充当电路元件，将用于实现这种语言。DNA分子是分子编程方法的理想底物，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项目紧密结合，该项目将开发一个教育项目，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 PIs propose that complex, hierarchical chemical patterns can be formedby systems in which the molecules collectively execute a molecularprogram for pattern formation. The PIs 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.