1,720,970 research outputs found
On the description of the environment polarization response to electronic transitions
No full textThis paper addresses the issue of accurately describing the structures and properties of electronically
excited systems embedded in an environment, through multiscale approaches combining
quantum-mechanical (QM) and polarizable classical representations of the system and
environment, respectively. Such approaches represent an efficient strategy and allow to effectively
study the excited states of molecular systems in the condensed phase, still maintaining
the computational efficiency and the physical reliability of the ground-state calculations. The
most important theoretical and computational aspects of the coupling between the QM system
and the polarizable environment are presented and discussed. Even if these approaches already
reached an evident degree of maturity, they can still be subject to further development, in order
to achieve their full potential. This perspective presents an overview of the state of the art of
these strategies, showing the fields of applicability and indicating the current limitations, which
need to be overcome in future developments
Control of Coherences and Optical Responses of Pigment-Protein Complexes by Plasmonic Nanoantennae
No full textThe key for light-harvesting in pigment-protein complexes are molecular excitons, delocalized excited states comprising a superposition of excitations at different molecular sites. There is experimental evidence that the optical response due to such excitons can be largely affected by plasmonic nanoantennae. Here we employ a multiscale approach combining time-dependent density functional theory and polarizable classical models to study the optical behavior of the LH2 complex present in bacteria when interacting with a gold nanorod. The simulation not only reproduces the experiments but also explains their molecular origin. By tuning the chromophoric unit and selectively switching on/off the excitonic interactions, as well as by exploring different setups, we clearly show that the dramatic enhancement in the optical response, unexpectedly, is not accompanied by changes in the coherences. Instead polarization effects are dominant. These results can be used to design an optimal control of the light-harvesting process through plasmonic nanoantennae
Theoretical description of protein field effects on electronic excitations of biological chromophores
Full text linkPhotoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems
Can triphasic spiral CT provide data for the histologic characterization of liver masses?
No full textSpiral Computed Tomography (CT) has rapidly gained acceptance as the preferred CT technique for routine liver evaluation because it provides image acquisition at peak enhancement of the liver parenchyma during single breath hold. In this study, we evaluated a wide range of non cystic liver lesions with triphasic spiral CT technique, that allows imaging of the entire liver in arterial, portal and equilibrium phases. In particularly we focused on hemangioma, adenoma, focal nodular hyperplasia, hepatocarcinoma and metastases
CT-scanning and virtual reproduction of the Saccopastore Neandertal crania
No full textThe two early Neanderthal crania from Saccopastore (Rome, Italy) have been CT-scanned and virtually reproduced using computer-assisted techniques. The matrix, still pervading many internal volumes, was partially removed in order to identify and isolate endocranial structures and internal features. Saccopastore 1 shows high degree of mineralisation. In addition, calcareous inclusions permeates the deeper layers of the bone, involving some degree of overflow and difficulties to clearly identify part of the anatomical structures of the basicranium. Anyhow, the endocast (never described so far) is almost entirely reproduced, as well as features of dental roots, maxillary sinuses, and inner ear elements. Saccopastore 2 shows also a high level of fossilisation, but with less problems for the scan process (given also the smaller volume of the anatomical districts preserved); even in this case, dental roots, maxillary and frontal sinuses, and inner ear elements can be identified. These two important specimens, dated to a crucial (Eemian) stage along the Neanderthal evolutionary lineage, are now available for CT-based analyses and comparisons
Può la TAC spirale trifasica fornire elementi per la caratterizzazione istologica delle masse epatiche?
No full textCoupling Real-Time Time-Dependent Density Functional Theory with Polarizable Force Field
No full textReal-time time-dependent density functional theory (RT-TDDFT) is a powerful tool for obtaining spectroscopic observables and understanding complex, time-dependent properties. Currently, performing RT-TDDFT calculations on large, fully quantum mechanical systems is not computationally feasible. Previously, polarizable mixed quantum mechanical and molecular mechanical (QM/MMPol) models have been successful in providing accurate, yet efficient, approximations to a fully quantum mechanical system. Here we develop a coupling scheme between induced dipole based QM/MMPol and RT-TDDFT. Our approach is validated by comparing calculated spectra with both real-time and linear-response TDDFT calculations. The model developed within provides an accurate method for performing RT-TDDFT calculations on extended systems while accounting for mutual polarization between the quantum mechanical and molecular mechanical regions
Coupling to Charge Transfer States is the Key to Modulate the Optical Bands for Efficient Light Harvesting in Purple Bacteria
No full textThe photosynthetic apparatus of purple bacteria uses exciton delocalization and static disorder to modulate the position and broadening of its absorption bands, leading to efficient light harvesting. Its main antenna complex, LH2, contains two rings of identical bacteriochlorophyll pigments, B800 and B850, absorbing at 800 and 850 nm, respectively. It has been an unsolved problem why static disorder of the strongly coupled B850 ring is several times larger than that of the B800 ring. Here we show that mixing between excitons and charge transfer states in the B850 ring is responsible for the effect. The linear absorption spectrum of the LH2 system is simulated by using a multiscale approach with an exciton Hamiltonian generalized to include the charge transfer states that involve adjacent pigment pairs, with static disorder modeled microscopically by molecular dynamics simulations. Our results show that sufficient inhomogeneous broadening of the B850 band, needed for efficient light harvesting, is only obtained by utilizing static disorder in the coupling between local excited and interpigment charge transfer states
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
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