MRI/RUI: 32-processor Beowulf cluster for the application of ab initio and density functional methods to Quantitative Structure Thermodynamic Relationships

在David Magers博士的指导下，密西西比学院(MC)获得了一笔赠款，用于购买32处理器的Beowulf集群和集成的并行计算化学软件，用于计算一系列具有生物意义的分子的构象能量学和分子参数。所有的生化反应都需要分子参与者之间形成稳定的络合物。彻底了解蛋白质和核酸靶标识别小分子的物理基础需要详细了解分子结构和描述结合作用强度的热力学。众所周知，反应物和溶剂的结构决定了这些结合能。然而，仍然不可能准确地预测小分子与其同源蛋白质或核酸靶标的结合亲和力。随着多处理机并行运行的发展，现在可以用密度泛函理论和从头算方法严格地处理小分子。具体地说，通过赠款获得的Beowulf集群和集成软件将用于研究专门识别三螺旋DNA结构的新型萘喹啉小库的结构和结合热力学之间的定量关系。这些结构，如H-DNA，目前被认为有助于调节基因的表达，因为它们被发现存在于一些哺乳动物基因的启动子区域。高水平的量子力学计算将被用来预测这些萘基喹啉的分子性质，然后将它们与实验确定的结合能相关联。美国化学学会专业培训委员会为认可的本科生化学课程制定了指导方针，最近公布了更新的指导方针，承认计算机在化学中越来越重要。在MC的几门课程中已经增加了计算实验室作业，物理化学第三学期的课程完全围绕理论和计算化学设计。新的计算机将对这些课程中的计算机作业产生直接影响，从而允许研究更大的和生物相关的系统。最后，Beowulf集群将增加MC的整体研究基础设施，并扩大与附近学院和大学合作的可能性。

A grant has been awarded to Mississippi College (MC) under the direction of Dr. David Magers for the acquisition of a 32-processor Beowulf cluster and integrated parallel computational chemistry software for the calculation of conformational energetics and molecular parameters of a series of biologically significant molecules. All biochemical reactions require the formation of stable complexes between the molecular participants. Thoroughly understanding the physical basis for the recognition of small molecules by protein and nucleic acid targets requires a detailed knowledge of both molecular structure as well as the thermodynamics which describe the strength of the binding interactions. It is well recognized that the structures of the reactants and the solvent dictate these binding energetics. However, it is still not possible to predict precisely the binding affinity of small molecules to their cognate protein or nucleic acid targets. With the advance of multi-processor computers running in parallel, it is now possible to treat small molecules rigorously by density functional theory and ab initio methods. Specifically, the Beowulf cluster and integrated software acquired through the grant will be used to examine the quantitative relationships that exist between the structure and the binding thermodynamics of a small library of novel naphthylquinolines that specifically recognize triple helical DNA structures. These structures such as H-DNA are currently thought to help regulate gene expression since they have been found to occur in the promoter regions of some mammalian genes. High level quantum mechanical calculations will be used to predict the molecular properties of these naphthylquinolines and then to correlate them to experimentally determined binding energetics.The Committee on Professional Training of the American Chemical Society, which sets the guidelines for accredited undergraduate chemistry programs recently announced updated guidelines recognizing the increasing importance of computers in chemistry. Computational laboratory assignments have already been added to several courses at MC, and the third semester course in Physical Chemistry is designed exclusively around theoretical and computational chemistry. The new computer will have a direct impact on the computer assignments in these courses allowing larger and biologically relevant systems to be investigated. Finally, the Beowulf cluster will increase MC's overall research infrastructure and broaden the possibilities for collaboration with nearby colleges and universities.