NANO: EMT: Revolutionary 3D Nanoarchitectures to Organize the Assembly of Computing Elements

计算能力的提高使得组件越来越小，以至于我们达到了当前自上而下制造方法的极限。 此外，目前采用的制造方法固有地限于部件的二维布置。 通过这项研究，我们计划解决这两个问题：我们将开发使用化学方法自下而上组装计算组件的方法。 此外，我们将把组装计算元素的能力从二维扩展到三维。我们计划如何实现这些雄心勃勃的目标？ 我们将使用自然界中发现的最有效和最有选择性的自组装系统- DNA。 我们都知道，DNA是从细菌到人类的生物体的遗传物质。 DNA的关键特征之一是双螺旋的两条链之间的互补性：如果螺旋的一侧包含一个称为A的单元，另一侧总是有另一个称为T的单元;同样，另外两个称为G和C的互补单元以相同的方式工作。 我们现在生活在一个非常容易合成带有特定序列的DNA链的时代，所以我们可以在一边编程给定的链，然后在另一边制造它的互补链。 此外，DNA是纳米级物体，宽度约为2 nm，螺旋重复约为3.5 nm。 此外，DNA是分子间相互作用最容易被编程的分子，从亲和力（哪些分子将与哪些分子结合）和结构（当它们联合收割机结合时会是什么样子）的角度来看。 这种分子间的编程是通过在每个分子的末端使用短的单链片段来完成的，这些片段被称为“粘性末端”。 大自然已经大量制造了线性DNA分子。 合成分子只是相对较短的物质“线”，那么它们有什么用呢？ 合成DNA分子的优点是它们可以被编程为分支分子，而不是线性分子。 因此，将一束线性DNA分子连接在一起可以导致更长的线，但是将分支分子连接在一起可以导致DNA的连接网络。 在过去，我们已经构建了各种具有特定模式的二维晶体阵列;为了做到这一点，我们设计了DNA链以形成二维图案，这些图案可以使用粘性末端进行自组装。 在该奖项下进行的研究中，我们将设计和自组装基序，这些基序将形成自组装产生三维阵列的基序，与传统晶体（如糖晶体）有关，除了它们的重复单元要大得多。 我们将使用检查三维物质的标准方法X射线晶体学来表征这些分子。三维DNA晶体的组装与革命性的计算有什么关系？ 我们刚刚讨论过DNA具有杰出的结构特性。 然而，它似乎并不适合作为计算组件。 相比之下，有许多新发现的纳米尺度系统，如碳纳米管或量子点，似乎是理想的计算目的，只要我们能把它们组织成电路为我们的目的。 一旦我们能够将DNA组装成三维结构，我们将着手利用其结构特征作为电子元件的三维支架。 因此，我们将联合收割机结合我们知道如何控制的DNA的杰出结构特性，与已展示的杰出电子元件形成三维电路。 这一成就最终将导致极其密集的存储单元和极其快速的计算。

Improvements in computational capability have entailed making the components smaller and smaller, to the point where we are reaching the limits of the current top-down fabrication methodologies. Furthermore, fabrication methods currently in place are inherently limited to two dimensional arrangements of components. With the research to be pursued under this award, we plan to address both of those problems: We will develop methods to assemble computing components from the bottom-up, using chemical methods. In addition, we will extend our ability to assemble computational elements from two dimensions to three dimensions.How do we plan to accomplish these ambitious goals? We will use the most effective and selective self-assembling system that is found in nature -- DNA. We are all aware that DNA serves as the genetic material of living organisms, from bacteria to humans. One of the key features of DNA that enables it to fulfill this role is complementarity between the two strands of the double helix: If one side of the helix contains a unit known as an A, the other side will always have another unit know as a T; likewise, two further complementary units known as G and C work in the same way. We now live in an era when it is very easy to synthesize DNA strands with particular sequences on them, so we can program a given strand on one side, and then make its complementary strand on the other side. Furthermore, DNA is a nanoscale object, with a width of about 2 nm, and a helical repeat of about 3.5 nm. In addition, DNA is the molecule whose intermolecular interactions are the most readily programmed, from the perspectives both of affinity (which molecules will bind to which others), and structure (what will they look like when they combine). This intermolecular programming is accomplished by using short single-stranded segments on the ends of each molecule, which are called 'sticky ends'.But wait. Nature already makes linear DNA molecules in profusion. Synthetic molecules would just be relatively short 'lines' of matter, so what use would they be? The advantage of synthetic DNA molecules is that they can be programmed to associate into branched, rather than linear molecules. Thus, joining a bunch of linear DNA molecules together can lead to longer lines, but joining branched molecules together can lead to connected networks of DNA. In the past, we have built a variety of two dimensional crystalline arrays with specific patterns; to do this we have designed DNA strands to form two dimensional motifs that could they self-assembled using sticky ends. In the research to be pursued under this award, we will design and self-assemble motifs that will form motifs that self-assemble to produce three dimensional arrays, related to conventional crystals, such as sugar crystals, except that their repeating units will be much larger. We will characterize these molecules using the standard method for examining three-dimensional matter, x-ray crystallography.How does the assembly of three dimensional DNA crystals relate to revolutionary computing? We have just discussed that DNA has outstanding architectural properties. However, it does not seem well-suited to serve as a computational component. By contrast, there are numerous newly discovered nanoscale-sized systems, such as carbon nanotubes or quantum dots that would seem to be ideal for computational purposes, if only we could organize them into circuitry for our purposes. Once we are able to assemble DNA into three-dimensional arrangements, we will undertake to use its architectural features to act as scaffolding in three dimensions for electronic components such as these. Thus, we will combine the outstanding architectural properties of DNA, which we know how to control, with demonstrated outstanding electronic components to form circuitry in three dimensions. This achievement ultimately will lead to extremely dense memory units and extremely rapid computation.