Chapagain Prem P, Gerstman Bernard S, Bhandari Yuba R, Rimal Dipak
Department of Physics, Florida International University, Miami, Florida 33199, USA.
Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jun;83(6 Pt 1):061905. doi: 10.1103/PhysRevE.83.061905. Epub 2011 Jun 7.
Thermodynamic parameters such as free energies and heat capacities are important quantities for understanding processes involving structural transitions in complex molecules such as proteins. Computational investigations provide simulated data that can be used for calculating thermodynamic parameters. However, calculations give accurate results only if the simulations sample all of configuration space with the appropriate temperature-dependent Boltzmann equilibrium probabilities. For many systems, truly comprehensive sampling of configuration space is not computationally feasible. We present an approximation technique for the calculations that will give accurate values for thermodynamic parameters when the data is incomplete. Our work is applicable to systems in which there are two distinct, important regions of configuration space that must be sampled. Importantly, the results are also valid when the system is more complex than two-state systems. Transition pathways that involve intermediate configurations between two stable regions are allowed in this treatment, and therefore the results are valid for multistate systems.
诸如自由能和热容等热力学参数是理解涉及蛋白质等复杂分子结构转变过程的重要量。计算研究提供了可用于计算热力学参数的模拟数据。然而，只有当模拟以适当的温度依赖玻尔兹曼平衡概率对所有构型空间进行采样时，计算才能给出准确结果。对于许多系统而言，真正全面地采样构型空间在计算上是不可行的。我们提出了一种计算的近似技术，当数据不完整时，该技术将给出热力学参数的准确值。我们的工作适用于存在两个必须采样的不同且重要构型空间区域的系统。重要的是，当系统比双态系统更复杂时，结果仍然有效。在这种处理中允许涉及两个稳定区域之间中间构型的转变途径，因此结果对多态系统有效。
