PRAC - Hierarchical molecular dynamics sampling for assessing pathways and free energies of RNA catalysis, ligand binding, and conformational change

该奖项促进了使用IBM正在开发的名为Blue Waters的大型新计算资源的科学研究，该资源计划于2011年部署在伊利诺伊大学。它提供差旅资金，以支持主要调查人员、Blue Waters项目团队和供应商技术团队之间的技术协调。一支经验丰富的琥珀生物分子模拟软件开发团队，其专业知识包括QM/MM方法、增强的采样方法、代码优化和并行化以及生物分子模拟，旨在增强Amber软件，以在Blue Waters机器上实现最佳功能。计划的应用领域涉及RNA，主要目标是分层紧密地耦合一系列优化的分子动力学引擎，以更好地绘制出RNA的构象、能量和化学景观。模拟引擎将在超级节点级别进行优化，并将耦合在一起并交换信息，以更好地采样和解释自由能源格局。更广泛的影响和意义最终集中在更好地了解RNA和蛋白质的结构、动力学和功能，以及生物分子模拟技术的发展、探索和集成，以更好地了解和探索生物分子的结构、化学和能量景观。后一种影响将转化为其他应用领域和新兴的计算机硬件。

This award facilitates scientific research using the large, new, computational resource named Blue Waters being developed by IBM and scheduled to be deployed at the University of Illinois in 2011. It provides travel funds to support technical coordination between the principal investigators, the Blue Waters project team and the vendor technical team.An experienced team of AMBER biomolecular simulation software developers with expertise ranging from QM/MM methods, enhanced sampling methods, code optimization and parallelization, and biomolecular simulation aim to enhance the AMBER software for optimal function on the Blue Waters machine. The intended application area involves RNA and the main goals are to hierarchically and tightly couple a series of optimized molecular dynamics engines to better map out the conformational, energetic and chemical landscape of RNA. The simulation engines will be optimized at the supernode level and will be coupled together and exchange information to better sample and interpret the free energy landscape. Broader impact and significance centers on ultimately providing a better understanding of RNA and protein structure, dynamics and function and the development, exploration, and integration of biomolecular simulation technologies to better understand and explore the structural, chemical and energetic landscapes of biomolecules. The latter impacts will translate to other application areas and emerging computer hardware.