Computational Molecular Biophysics and Modern Dynamics

计算分子生物物理学和现代动力学

• 批准号: 6007-2006
• 负责人: Gray, Christopher
• 金额: $ 2.52万
• 依托单位: University of Guelph
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2007
• 资助国家: 加拿大
• 起止时间: 2007-01-01 至 2008-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=361733
• 关键词: Computational; Molecular; Biophysics; Modern; Dynamics

Computational Molecular Biophysics:  We are simulating at the atomic scale the conductance and selectivity of potassium ion channels (eg. KcsA), by applying an electric field across the channel and measuring the ion flux.  Our pioneering first calculations will now be improved using more realistic models for the electrolyte solutions and membrane, and unfreezing the motions of the whole ion channel protein.  The water permeability of KcsA will also be simulated and compared to the value recently measured experimentally, thus providing an additional test of the KcsA molecular model and force field.  We are initiating a simulation of the GLUT1 transporter protein, which is responsible for transporting glucose into the red blood cell and other cells.  Initially we shall focus on the equilibrium binding constant, related to the free energy of binding of the glucose molecule to the GLUT1 protein. Modern Dynamics:  We are continuing to apply the new variational (action) principles discovered by our group to systems of interst, both classical and semiclassical.  In particular we are applying our new semiclassical variational principle to estimate the energy levels of multidimensional nonintegrable (chaotic) systems.  For such systems our method is much simpler than other methods currently used, such as the Gutzwiller trace formula.  We are examining an action criterion for trajectory stability to see if it can be employed as an action criterion for trajectory chaos.

计算分子生物物理学：我们正在原子尺度上模拟钾离子通道的电导和选择性（例如，KcsA），通过在通道上施加电场并测量离子通量。我们开创性的第一次计算现在将使用更真实的电解质溶液和膜模型进行改进，并解冻整个离子通道蛋白的运动。KcsA的水渗透性也将被模拟并与最近实验测量的值进行比较，因此提供了KcsA分子模型和力场的额外测试。我们正在启动GLUT 1转运蛋白的模拟，该转运蛋白负责将葡萄糖转运到红细胞和其他细胞中。最初，我们将关注平衡结合常数，与葡萄糖分子与GLUT 1蛋白结合的自由能有关。现代动力：我们继续将我们小组发现的新的变分原理应用于感兴趣的经典和半经典系统，特别是我们将新的半经典变分原理应用于估计多维不可积（混沌）系统的能级，对于这样的系统，我们的方法比目前使用的其他方法简单得多，如Gutzwiller轨迹公式。我们正在研究一个行动准则的轨道稳定性，看看它是否可以作为一个行动准则的轨道混沌。