Theoretical description of protein field effects on electronic excitations of biological chromophores

Photoinitiated 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

Theoretical S1 \u2192S0 Absorption Energies of the Anionic Forms of Oxyluciferin by Variational Monte Carlo and Many-Body Green's Function Theory

The structures of three negatively charged forms (anionic keto-1 and enol-1 and dianionic enol-2) of oxyluciferin (OxyLuc), which are the most probable emitters responsible for the firefly bioluminescence, have been fully relaxed at the variational Monte Carlo (VMC) level. Absorption energies of the S1 \u2190 S0 vertical transition have been computed using different levels of theory, such as TDDFT, CC2, and many-body Green\u2019s function theory (MBGFT). The use of MBGFT, by means of the Bethe\u2013Salpeter (BS) formalism, on VMC structures provides results in excellent agreement with the value (2.26(8) eV) obtained by action spectroscopy experiments for the keto-1 form (2.32 eV). To unravel the role of the quality of the optimized ground-state geometry, BS excitation energies have also been computed on CASSCF geometries, inducing a non-negligible blue shift (0.08 and 0.07 eV for keto-1 and enol-1 forms, respectively) with respect to the VMC ones. Structural effects have been analyzed in terms of over- or undercorrelation along the conjugated bonds of OxyLuc by using different methods for the ground-state optimization. The relative stability of the S1 state for the keto-1 and enol-1 forms depends on the method chosen for the excited-state calculation, thus representing a fundamental caveat for any theoretical study on these systems. Finally, Kohn\u2013Sham HOMO and LUMO orbitals of enol-2 are (nearly) bound only when the dianion is embedded into a solvent (water and toluene in the present work); excited-state calculations are therefore meaningful only in the presence of a dielectric medium which localizes the electronic density. The combination of VMC for the ground-state geometry and BS formalism for the absorption spectra clearly outperforms standard TDDFT and quantum chemistry approaches

Demand side management analysis of a supermarket integrated HVAC, refrigeration and water loop heat pump system

Supermarkets are intensive energy consumers because of a high electricity demand, mainly due to refrigeration utilities. Thus, in this work a supermarket integrated HVAC, refrigeration and water loop heat pump (WLHP) system was analyzed according to a demand side management approach, adopting a demand response strategy coupled with real-time pricing predictive rule based controls. The system was modeled with TRNSYS and several DR strategies were applied to both the space heating/cooling and the WLHP to determine the plant configuration with the most effective electricity cost saving. It was found that two setups guarantee the highest economic savings. The first consists of a predictive rule based control applied to the space heating/cooling only, which is basically inexpensive and allows an annual cost saving of 4.06% respect to the baseline configuration. The second, instead, combines predictive rule based controls applied to both the space heating/cooling and the WLHP auxiliary heater, and shows the best performance with the adoption of a 200\u202fm3 water-based thermal energy storage. Respect to the baseline, this configuration provides an annual cost saving of 4.67%

Demand Side Management analysis of a commercial Water Loop Heat Pump system

Demand side management (DSM) can be defined as a set of measures adopted to modify customers\u2019 energy demand with the aim of improving the efficiency of the overall energy system. Indeed, DSM strategies can be used to reduce customers\u2019 demand at peak times, reduce energy consumption seasonally/yearly, change the timing of end-use consumption from high to low-cost periods, and increase consumption during off-peak periods. DSM strategies can be implemented by using the energy flexibility available in the final users\u2019 applications, e.g. the thermal inertia of the building mass, the presence of additional energy storage systems enabling load shaping or the use of control systems to turn on/off end-users\u2019 devices when required. Being intensive energy consumers because of a high electric energy demand (mainly for refrigeration, which accounts for about 40 % of the yearly energy consumption), supermarkets are ideal candidates for energy use optimizations obtained through a DSM approach. This work shows the results of a DSM analysis carried out for a refrigeration and HVAC plant in a supermarket coupled with a Water Loop Heat Pump (WLHP) system. The water loop is used as a heat source/sink for the refrigeration unit supplying the cooling capacity required by food preservation and for several heat pumps that provide heating/cooling inside the supermarket building. The system is modelled in TRNSYS and the role of the water loop and its thermal inertia to provide energy flexibility is investigated. The system design and control strategy are modified in order to reduce the electricity costs in presence of demand response programs based on real-time price mechanisms

Testing Theories of Gravity with a Spherical Gravitational Wave Detector

We consider the possibility of discriminating different theories of gravity using a recently proposed gravitational wave detector of spherical shape. We argue that the spin content of different theories can be extracted relating the measurements of the excited spheroidal vibrational eigenmodes to the Newman-Penrose parameters. The sphere toroidal modes cannot be excited by any metric GW and can be thus used as a veto.Comment: latex file, 16 pages, 1 figur

Laparoscopic Gastric Sleeve and Micronutrients Supplementation: Our Experience

Background. Laparoscopic gastric sleeve (LGS) has been recently introduced as a stand-alone, restrictive bariatric surgery. Theoretically, LGS attenuates micronutrients deficiencies and associated complications that were typically observed following malabsorptive procedures. The aim of this study was to assess some micronutrients and mineral deficiencies in patients undergoing LGS. Methods. In the period between July 2008 and April 2010, 138 obese patients (110 females and 28 males) with mean BMI 44.4 kg/m2 ± 6.5, mean age 43.9 ± 10.9 years were enrolled and underwent LGS. Patients were followed up with routine laboratory tests and anthropometric measurements and assessed for nutritional status, as regards vitamin B12, folic acid, iron, hemoglobin, calcium, and vitamin D, every three months throughout 12 months. Results. 12 months after sleeve, patients did not show iron deficiency and/or anemia; plasma calcium levels were in the normal range without supplementation from the sixth month after the operation. Vitamin B12 and folic acid were adequately supplemented for all the follow-up period. Vitamin D was in suboptimal levels, despite daily multivitamin supplementation. Conclusion. In this study, we showed that LGS is an effective surgery for the management of morbid obesity. An adequate supplementation is important to avoid micronutrients deficiencies and greater weight loss does not require higher dosage of multivitamins

Detectability of gravitational wave events by spherical resonant-mass antennas

We have calculated signal-to-noise ratios for eight spherical resonant-mass antennas interacting with gravitational radiation from inspiralling and coalescing binary neutron stars and from the dynamical and secular bar-mode instability of a rapidly rotating star. We find that by using technology that could be available in the next several years, spherical antennas can detect neutron star inspiral and coalescence at a distance of 15 Mpc and the dynamical bar-mode instability at a distance of 2 Mpc.Comment: 39 pages, 4 EPS Figures, some additional SNRs for secular instabilities, some changes to LIGO SNRs, Appendix added on the asymptotic expansion of energy sensitivity, corrected supernova rates. Results available at http://www.physics.umd.edu/rgroups/gen_rel_exp/snr.html Submitted to Phys. Rev.

Analysis of 3 years of data from the gravitational wave detectors EXPLORER and NAUTILUS

We performed a search for short gravitational wave bursts using about 3 years of data of the resonant bar detectors Nautilus and Explorer. Two types of analysis were performed: a search for coincidences with a low background of accidentals (0.1 over the entire period), and the calculation of upper limits on the rate of gravitational wave bursts. Here we give a detailed account of the methodology and we report the results: a null search for coincident events and an upper limit that improves over all previous limits from resonant antennas, and is competitive, in the range h_rss ~1E-19, with limits from interferometric detectors. Some new methodological features are introduced that have proven successful in the upper limits evaluation.Comment: 12 pages, 12 figure

Gravitational wave astronomy

The first decade of the new millenium should see the first direct detections of gravitational waves. This will be a milestone for fundamental physics and it will open the new observational science of gravitational wave astronomy. But gravitational waves already play an important role in the modeling of astrophysical systems. I review here the present state of gravitational radiation theory in relativity and astrophysics, and I then look at the development of detector sensitivity over the next decade, both on the ground (such as LIGO) and in space (LISA). I review the sources of gravitational waves that are likely to play an important role in observations by first- and second-generation interferometers, including the astrophysical information that will come from these observations. The review covers some 10 decades of gravitational wave frequency, from the high-frequency normal modes of neutron stars down to the lowest frequencies observable from space. The discussion of sources includes recent developments regarding binary black holes, spinning neutron stars, and the stochastic background.Comment: 29 pages, 2 figures, as submitted for special millenium issue of Classical and Quantum Gravit

Host defense responses to infection by Mycobacterium tuberculosis. Induction of IRF-1 and a serine protease inhibitor.

Alveolar macrophages and newly recruited monocytes are targets of infection by Mycobacterium tuberculosis. Therefore, we examined the expression of interferon regulatory factor 1 (IRF-1), which plays an important role in host defense against M. tuberculosis, in undifferentiated and differentiated cells. Infection induced IRF-1 in both. IRF-1 from undifferentiated, uninfected monocytic cell lines was modified during extraction to produce specific species that were apparently smaller than intact IRF-1. After infection by M. tuberculosis or differentiation, intact IRF-1 was recovered. Subcellular fractions were assayed for the ability to modify IRF-1 or inhibit its modification. A serine protease on the cytoplasmic surface of an organelle or vesicle in the "lysosomal/mitochondrial" fraction from undifferentiated cells was responsible for the modification of IRF-1. Thus, the simplest explanation of the modification is cleavage of IRF-1 by the serine protease. Recovery of intact IRF-1 correlated with induction of a serine protease inhibitor that was able to significantly reduce the modification of IRF-1. The inhibitor was present in the cytoplasm of M. tuberculosis-infected or -differentiated cells. It is likely that induction of both IRF-1 and the serine protease inhibitor in response to infection by M. tuberculosis represent host defense mechanisms