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Multiphoton Absorption of Myoglobin–Nitric Oxide Complex: Relaxation by D-NEMD of a Stationary State
Full text linkABSTRACT:
The photodissociation and geminate recombination of nitric oxide in
myoglobin, under continuous illumination, is modeled computationally. The
relaxation of the photon energy into the protein matrix is also considered in a
single simulation scheme that mimics a complete experimental setup. The dynamic
approach to non-equilibrium molecular dynamics is used, starting from a steady
state, to compute its relaxation to equilibrium. Simulations are conducted for the
native form of sperm whale myoglobin and for two other mutants, V68W and L29F,
illustrating a fair diversity of spatial and temporal geminate recombination processes.
Energy flow to the heme and immediate protein environment provide hints to
allostery. In particular, a pathway of energy flow between the heme and the FG loop
is illustrated. Although the simulations were conducted for myoglobin only, the thermal fluctuations of the FG corner are in
agreement with the large structural shifts of FG during the allosteric transition of tetrameric hemoglobin
Computational Modeling of Geminate Recombination and Energy Relaxation of Nitric Oxide in Myoglobin under Constant Illumination,
No full text
Multiphoton Absorption of Myoglobin–Nitric Oxide Complex: Relaxation by D-NEMD of a Stationary State
No full textThe photodissociation and geminate recombination of nitric oxide in myoglobin, under continuous illumination, is modeled computationally. The relaxation of the photon energy into the protein matrix is also considered in a single simulation scheme that mimics a complete experimental setup. The dynamic approach to non-equilibrium molecular dynamics is used, starting from a steady state, to compute its relaxation to equilibrium. Simulations are conducted for the native form of sperm whale myoglobin and for two other mutants, V68W and L29F, illustrating a fair diversity of spatial and temporal geminate recombination processes. Energy flow to the heme and immediate protein environment provide hints to allostery. In particular, a pathway of energy flow between the heme and the FG loop is illustrated. Although the simulations were conducted for myoglobin only, the thermal fluctuations of the FG corner are in agreement with the large structural shifts of FG during the allosteric transition of tetrameric hemoglobin
Computational modeling of geminate recombination and energy relaxation of nitric oxide in myoglobin under constant illumination.
No full textA new boundary driven NEMD scheme for heat and particle diffusion in binary mixtures
Full text linkA new method for Boundary Driven Non-Equilibrium Molecular Dynamics (BD-NEMD) simulation is presented. It allows the simultaneous imposition of both a constant temperature and concentration gradient. By varying the strength of the imposed gradients and obtaining stationary values of the mass and energy flux, this new technique can be used to extract the Onsager transport coefficients directly. We demonstrate the setup and measure explicitly the Soret and Dufour effects for a binary mixture of Argon and Krypton. We compare the Soret coefficient computed using this new scheme against the experimentally inspired protocol where the system has no mass current. However, this method is limited to only an estimate of the Soret coefficient rendered inefficient due to the poor signal-to-noise ratio and cannot give the transport coefficients explicitly. The new technique allows for accurate measurements of non-zero flux values and, if run in the linear response domain, the full set of transport coefficients can be extracted directly. We also speculate about how this scheme could be applied to more complex systems with applications for polymer separations and biological activities
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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