| Unravelling Coherent Dynamics and Energy Dissipation in Photosynthetic Complexes by 2D Spectroscopy Biophysical Journal, Volume 94, Issue 9, 1 May 2008, Pages 3613-3619 Darius Abramavicius, Dmitri V. Voronine and Shaul Mukamel Abstract Spectroscopic studies of light harvesting and the subsequent energy conversion in photosynthesis can track quantum dynamics happening on the microscopic level. The Fenna-Matthews-Olson complex of the photosynthetic green sulfur bacteria is a prototype efficient light-harvesting antenna: it stores the captured photon energy in the form of excitons (collective excitations), which are subsequently converted to chemical energy with almost 100% efficiency. These excitons show an elaborate relaxation pattern involving coherent and incoherent pathways. We make use of the complex chirality and fundamental symmetries of multidimensional optical signals to design new sequences of ultrashort laser pulses that can distinguish between coherent quantum oscillations and incoherent energy dissipation during the exciton relaxation. The cooperative dynamical features, which reflect the coherent nature of excitations, are amplified. The extent of quantum oscillations and their timescales in photosynthesis can be readily extracted from the designed signals, showing that cooperativity is maintained during energy transport in the Fenna-Matthews-Olson complex. The proposed pulse sequences may also be applied to reveal information on the robustness of quantum states in the presence of fluctuating environments in other nanoscopic complexes and devices. Abstract | Full Text | PDF (1182 kb) |
| Spectral Signatures of Heterogeneous Protein Ensembles Revealed by MD Simulations of 2DIR Spectra Biophysical Journal, Volume 91, Issue 7, 1 October 2006, Pages 2636-2646 Ziad Ganim and Andrei Tokmakoff Abstract A model for the calculation of amide I FTIR and 2DIR spectra taking into account fluctuations in hydrogen bonding and structure from molecular dynamics (MD) simulations is tested on three systems. It is found that although the homogeneous lineshape approximation yields satisfactory FTIR spectra, 2DIR spectra are sensitive to the inhomogeneity naturally present in any solvated protein and the common approximations of a static structure and averaged-effect solvent are invalid. By building on the local amide Hamiltonian and incorporating site energy variation with electrostatic-based models and disorder from MD trajectories, good agreement is obtained between calculated and measured 2DIR spectra. The largest contribution to the observed inhomogeneity is found to be the fluctuating site energies, which in turn are most sensitive to the water solvent. With the ability to accurately predict 2DIR spectra from atomistic simulations, new opportunities to test force fields and mechanistic predictions from MD are revealed. Abstract | Full Text | PDF (2474 kb) |
| Use of the Covariance Matrix in Directly Fitting Kinetic Parameters: Application to GABAA Receptors Biophysical Journal, Volume 87, Issue 1, 1 July 2004, Pages 276-294 James J. Celentano and Alan G. Hawkes Abstract A new method of analysis is described that begins to explore the relationship between the phases of ion channel desensitization and the underlying states of the channel. The method, referred to as covariance fitting (CVF), couples -matrix calculations with a maximum likelihood algorithm to fit macroscopic desensitization data directly to kinetic models. Unlike conventional sum-of-squares minimization, CVF fits both the magnitude of the recorded current and the strength of the correlations between different time points. When applied to simulated data generated using various kinetic models with up to 11 free parameters, CVF leads to reasonable parameter estimates. Coupled with the likelihood ratio test, it accurately discriminates between models with different numbers of states, discriminates between most models with the same number but a different arrangement of states, and extracts meaningful information on the relationship between the desensitized states and the phases of macroscopic desensitization. When applied to GABA receptor traces (outside out patches, 122S, 1mM GABA, >2.5s), a model with two open states and three desensitized states is favored. When applied to simulated data generated using a consensus model, CVF leads to reasonable parameter estimates and accurately discriminates between this and other models. Abstract | Full Text | PDF (338 kb) |
Copyright © 1964 The Biophysical Society. All rights reserved.
Biophysical Journal, Volume 4, Issue 1, 69-75, 1 January 1964
doi:10.1016/S0006-3495(64)86769-2
Articles
John Z. Hearon
On the basis of its role in the analysis of mammillary compartmental systems, a matrix with non-zero elements in the first row, first column, and along the main diagonal and with zero elements elsewhere is called a mammillary matrix. It is pointed out that such matrices occur in a variety of biological problems including the linearized Hodgkin-Huxley equations (H-H). In considering whether such a linear system exhibits stability (all roots of the matrix with negative real parts) it is of interest to seek conditions, expressible in a simple manner in terms of the matrix elements, which lead to stability or instability. For the case when the diagonal elements, with the possible exception of the first, are negative (a condition physically guaranteed for the space-clamped axon) simple criteria for instability and stability are formulated in terms of the matrix elements. These criteria are derived by extending previous results from linear kinetics through appeal to a classical matrix theorem without recourse to the characteristic polynomial. The relation of these mathematical results to the work of Chandler, FitzHugh, and Cole on the space-clamped axon is discussed. The results are in no way restricted by the order of the matrix (which is four for the H-H equations) and other possible applications are noted.