Paper Citing NAMD - Abstract
Falvo, Cyril; Debnath, Arunangshu; Meier, Christoph
Vibrational ladder climbing in carboxy-hemoglobin: Effects of the protein environment
JOURNAL OF CHEMICAL PHYSICS, 138 Art. No. 145101, APR 14 2013
We present simulations on vibrational ladder climbing in carboxy-hemoglobin. Motivated by recent experiments, we study the influence of different realistic pump probe parameters. To allow for a direct comparison with experimental results, transient absorption spectra obtained by a weak probe pulse following the strong, shaped pump pulse are calculated. The influence of the protein fluctuations is taken into account using a recently developed microscopic model. This model consists of a quantum Hamiltonian describing the CO vibration in carboxy-hemoglobin, together with a fluctuating potential, which is obtained by electronic structure calculation based on a large number of protein configurations. Using realistic pulse parameters, vibrational excitations to very high-lying states are possible, in qualitative agreement with experimental observations. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4799271]
