1,720,963 research outputs found
Linear response and electron transfer in complex biomolecular systems and a reaction center protein
No full textThis paper is focused on the dielectric linear response in the context of electron-transfer reactions in complex biomolecules with and without explicit electronic polarization. Molecular dynamics simulation is used for a detailed investigation of two systems: a bacteriochlorophyll molecule in a homogeneous environment (liquid water) and a reaction center protein of bacterial photosynthesis in amphophilic solution. The limits of the linear approximation and the size of its deviation from the results, in principle exact, obtained from thermodynamic integration are pinpointed. Our findings will be of crucial importance in further investigations of electron transfer in complex biomolecules making use of linear response, still the easiest and least time- consuming approach
Dynamics of hydration in Hen Egg white lysozime
No full textWe investigate the hydration dynamics of a small globular protein, hen egg-white lysozyme. Extensive simulations (two trajectories of 9 ns each) were carried out to identify the time-scales and mechanism of water attachment to this protein. The location of the surface and integral water molecules in lysozyme was also investigated. Three peculiar temporal scales of the hydration dynamics can be discerned: two among these, with sub-nanosecond mean residence time, tau (w), are characteristic of surface hydration water; the slower time-scale (tau (w) similar to 2/3 ns) is associated with buried water molecules in hydrophilic pores and in superficial clefts. The computed tau (w) values in the two independent runs fall in a similar range and are consistent with each other, thus adding extra weight to our result. The tau (w) of surface water obtained from the two independent trajectories is 20 and 24 ps. In both simulations only three water molecules are bound to lysozyme for the entire length of the trajectories, in agreement with nuclear magnetic relaxation dispersion estimates. Locations other than those identified in the protein crystal are found to be possible for these long-residing water molecules. The dynamics of the hydration water molecules observed in our simulations implies that each water molecule visits a multitude of residues during the lifetime of its bound with the protein. The number of residues seen by a single water molecule increases with the time-scale of its residence time and, on average, is equal to one only for the water molecules with shorter residence time. Thus, tau (w) values obtained from inelastic neutron scattering and based on jump-diffusion models are likely not to account for the contribution of water molecules with longer residence time
water rotational relaxation and diffusion in hydrated lysozyme
No full textThis paper is concerned with the dynamics of water around a small globular protein. Dipolar second-rank relaxation time and diffusion properties of surface water were computed by extensive molecular dynamics simulations of lysozyme in water which lasted a total of 28 ns. Our results indicate that the rotational relaxation of water in the vicinity of lysozyme is 3-7 times slower than that in the bulk depending on how the hydration shell is defined in the calculation. We have also verified that the dynamics of water translational diffusion in the vicinity of lysozyme have retardations similar to rotational relaxation. This is a common assumption in nuclear magnetic relaxation dispersion (NMRD) studies to derive residence times. In contrast to bulk water dynamics, surface water is in a dispersive diffusion regime or subdiffusion. Very good agreement of dipolar second-rank relaxation time with NMRD estimates is obtained by using appropriate dimensions of the hydration shell. Although our computed second-rank dipolar retardations are independent of the water model, SPC/E describes more realistically the time scale of the water dynamics around lysozyme than does TIP3P
Pressure-induced core packing and interfacial dehydration in nonionic C12E6 micelle in aqueous solution
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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
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Coherent Excitation Transfer Driven by Torsional Dynamics : a Model Hamiltonian for PPV Type Systems
No full textA model Hamiltonian is proposed for systems of poly-phenylene-vinylene (PPV) type, which describes excitation energy transfer (EET) in the presence of torsional and bond-length-alternation coordinates that couple neighboring fragments. This model is employed to describe coherent EET, starting from a partially delocalized exciton state which is initially separated from the rest of the chain by a defect due to a pronounced torsional displacement at one of the inter-fragment junctions. EET is found to be driven by the restoring force of the torsions towards the planar geometry. Quantum dynamical calculations are carried out for a minimal five-site model, using the multiconfiguration time-dependent Hartree (MCTDH) method
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