SGER: Design of a Biomolecular Distributed Operating Systems

生物分子分子计算（BMC）使用生化方法在分子水平上进行计算。本研究的目标是确定 BMC 的分布式操作系统 (BMC-OS) 所需的关键功能，包括：(i) 分布式控制流、(ii) 分布式消息传输和消息处理、(iii) 数据和文件的分发和检索、(iv) 局部性优化、(v) 数据完整性保证、(vi) 分布式 I/O。这项工作的重点是对 BMC-OS 设计影响最大的几个关键主题：(a) 完整性保证、减少 I/O 和错误恢复能力——计算机科学和生化技术的结合被用来进行数据指纹识别，并且将使用非常高的扇出数据分布方法（使用冗余编码）来提高数据错误恢复能力。 (b) BMC-OS的模型和仿真软件——参数化性能模型用于反映BMC-OS控制上的几何和其他约束（例如溶液和试剂浓度、DNA链的空间分布、温度、盐度等），包括应用MEM技术实现BMC自动化。

Biomolecular molecular computation (BMC) uses biochemical methods to do computation at the molecular level. The goal of this research is to determine key required capabilities of a distributed operating system (BMC-OS) for BMC, including: (i) distributed flow of control,(ii) distributed message transmission and message handling, (iii) distribution and retrieval of data and files,(iv) locality optimizations, (v) data integrity assurance, an(vi)distributed I/O. The effort is focusing on a few key topics which have the most impact on the design of a BMC-OS :(a) Integrity Assurance, Decreased I/O and Error Resiliency--a combination of computer science and biochemical techniques are being used to do data fingerprinting and a very high fan-out data distribution method (using redundant coding) will be used to increase data error resiliency. (b) Models and Simulation Software for BMC-OS--Parameterized performance models are used to reflect the geometric and other constraints (e.g., solution and reagent concentration, spatial distribution of DNA strands, temperature, salinity, etc.) on the BMC-OS control, including the application of MEMs technology to automate BMC.