Introduction to theory/modeling methods in photosynthesis

Theory and molecular modeling play an increasingly important role in complementing the experimental findings and supporting the interpretation of the data. Owing to the increase in computational power combined with the development of more efficient methods, computer simulations and modeling have emerged as primary ingredients of modern scientific inquiry. Here, we introduce the methods that in our view bring the largest promises in photosynthesis research, indicate how they have already contributed, and can in the near future assume a significant role in this field. Particular emphasis is given to density functional theory and its combination with molecular dynamics simulations. We point out the need for a multi-scale approach in facing the challenging task of describing processes which cover several orders of magnitude both in the time scale and in the size of the systems of interest

Excitations in photoactive molecules from quantum Monte Carlo

Despite significant advances in electronic structure methods for the treatment of excited states, attaining an accurate description of the photoinduced processes in photoactive biomolecules is proving very difficult. For the prototypical photosensitive molecules, formaldimine, formaldehyde and a minimal protonated Schiff base model of the retinal chromophore, we investigate the performance of various approaches generally considered promising for the computation of excited potential energy surfaces. We show that quantum Monte Carlo can accurately estimate the excitation energies of the studied systems if one constructs carefully the trial wave function, including in most cases the reoptimization of its determinantal part within quantum Monte Carlo. While time-dependent density functional theory and quantum Monte Carlo are generally in reasonable agreement, they yield a qualitatively different description of the isomerization of the Schiff base model. Finally, we find that the restricted open shell Kohn-Sham method is at variance with quantum Monte Carlo in estimating the lowest-singlet excited state potential energy surface for low-symmetry molecular structures.Comment: 10 pages, 6 figure

Design and synthesis of aromatic molecules for probing electric-fields at the nanoscale

We propose using halogenated organic dyes as nanoprobes for electric field and show their greatly enhanced Stark coefficients using density functional theory (DFT) calculations. We analyse halogenated variants of three molecules that have been of interest for cryogenic single molecule spectroscopy, perylene, terrylene, and dibenzoterrylene, with the zero-phonon optical transitions at blue, red, and near infrared. Out of all the combinations of halides and binding sites that are calculated, we have found that fluorination of the optimum binding site induces a dipole difference between ground and excited states larger than 0.5 D for all three molecules with the highest value of 0.69 D for fluoroperylene. We also report on synthesis of 3-fluoroterrylene and bulk spectroscopy of this compound in liquid and solid organic environments.Comment: Article presented in Faraday Discussions on September 201

A state-averaged orbital-optimized hybrid quantum-classical algorithm for a democratic description of ground and excited states

In the Noisy Intermediate-Scale Quantum (NISQ) era, solving the electronic structure problem from chemistry is considered as the "killer application" for near-term quantum devices. In spite of the success of variational hybrid quantum/classical algorithms in providing accurate energy profiles for small molecules, careful considerations are still required for the description of complicated features of potential energy surfaces. Because the current quantum resources are very limited, it is common to focus on a restricted part of the Hilbert space (determined by the set of active orbitals). While physically motivated, this approximation can severely impact the description of these complicated features. A perfect example is that of conical intersections (i.e. a singular point of degeneracy between electronic states), which are of primary importance to understand many prominent reactions. Designing active spaces so that the improved accuracy from a quantum computer is not rendered useless is key to finding useful applications of these promising devices within the field of chemistry. To answer this issue, we introduce a NISQ-friendly method called "State-Averaged Orbital-Optimized Variational Quantum Eigensolver" (SA-OO-VQE) which combines two algorithms: (1) a state-averaged orbital-optimizer, and (2) a state-averaged VQE. To demonstrate the success of the method, we classically simulate it on a minimal Schiff base model (namely the formaldimine molecule CH2NH) relevant also for the photoisomerization in rhodopsin -- a crucial step in the process of vision mediated by the presence of a conical intersection. We show that merging both algorithms fulfil the necessary condition to describe the molecule's conical intersection, i.e. the ability to treat degenerate (or quasi-degenerate) states on the same footing.Comment: 18 pages, 7 figure

Bortezomib with Thalidomide plus Dexamethasone Compared with Thalidomide plus Doxorubicin and Dexamethasone as Induction Therapy in Previously Untreated Multiple Myeloma Patients

We conducted a retrospective study to compare thalidomide, bortezomib and dexamethasone (VTD) with thalidomide plus doxorubicin and dexamethasone (TAD). Until now, first-line treatment with these combinations has not been reported in any comparative study. The principal objective of this study was to determine whether VTD would improve the complete response (CR) and CR plus very good partial response rates compared with TAD. Second, using additional methods, such as flow cytometric assays and polymerase chain reaction technology, we evaluated the molecular residual disease in the subgroup of patients that obtained CR. Our study shows that VTD is a superior induction regimen compared with TAD, with a higher response rate after induction, translating into greater CR plus very good partial response

New applications of Diffusion Tensor Imaging techniques in the morphological evaluation of healthy and injured muscles

Purpose of this study was to evaluate a new approach with a DTI technique for the study of architecture of healthy and injured striated muscle tissue in cases of strain injury. DTI technique allows to highlight the magnitude and direction of the diffusion of water molecules in tissues and it becomes an indicator of the functional organization, allowing the identification of connections between the different structures showing any pathological changes. Currently this technique is routinely used in the study of CNS but recently it has also been proposed in the morphological evaluation of skeletal muscle. The application of this technique allows us to detect the presence of anomalies such as the alteration and displacement of the muscle bundles [1,2] and could play a crucial role not only in diagnosis but also in managing the rehabilitation of muscle injuries. The entire study was performed using a 3T Achieva Philips scanner; a SENSE 8 channels head coil, acquiring DTI sequence and T1 weighted 3D TFE. DTI was performed in 10 men with a strain injuries (grade I or II) in the lower limb muscles previously diagnosed by ultrasound examination. For each patient, we analyzed both healthy and injured limbs. The examination performed in the acute phase (within ten days from the injury) showed the presence of an area of oedema or haemorrhage of variable size. The perilesional area, if compared to healthy tissue, showed a marked alteration of the alignment of fibers. The examination carried out at a distance of 15-20 days showed a progressive reduction in the extent of haemorrhage that highlighted the structural alterations of the injured area, and noted a reduction in muscle fiber size of the affected muscle. The DTI provides detailed information on anatomical alterations in muscles strain and therefore may play a crucial role in diagnostic classification of the lesions. The evaluation of the scar may also be used to evaluate the healing has occurred not only from the clinical but also from anatomical perspective

Limiting Molecular Twisting:Upgrading a Donor–Acceptor Dye to Drive H₂ Evolution

The donor–acceptor (D–A) dye 4-(bis-4-(5-(2,2-dicyano-vinyl)-thiophene-2-yl)-phenyl-amino)-benzoic acid (P1) has been frequently used to functionalize NiO photocathodes and induce photoelectrochemical reduction of protons when coupled to a suitable catalyst. Photoinduced twisting of the P1 dye is steered on NiO by co-adsorption of tetradecanoic acid (C14, myristic acid (MA)). Density Functional Theory and time-resolved photoluminescence studies confirm that twisting lowers the energy levels of the photoexcited D–A dye. The apolar environment provided by the MA suppresses photoinduced D–A twisting, retards charge recombination following photoinduced charge separation between P1 and NiO, and provides a larger electrochemical potential increasing the photocurrent. Very interestingly, co-adsorption of MA induces H2 evolution upon photoexcitation without the presence of an H2 evolution catalyst. Based on prior art, the formation of H2 is assigned to the dissolution of Ni2+, followed by reduction and re-deposition of Ni nanoparticles acting as the catalytically active site. It propose that only excited P1 with suppressed twisting provides the sufficient electrochemical potential to induce deposition of Ni nanoparticles. The work illustrates the importance of understanding the effects of photoinduced intramolecular twisting and highlights the promise of designing twisting-limited D–A dyes to create efficient solar fuel devices.</p

Subchondral Bone Regenerative Effect of Two Different Biomaterials in the Same Patient

This case report aims at highlighting the different effects on subchondral bone regeneration of two different biomaterials in the same patient, in addition to bone marrow derived cell transplantation (BMDCT) in ankle. A 15-year-old boy underwent a first BMDCT on a hyaluronate membrane to treat a deep osteochondral lesion (8 mm). The procedure failed: subchondral bone was still present at MRI. Two years after the first operation, the same procedure was performed on a collagen membrane with DBM filling the defect. After one year, AOFAS score was 100 points, and MRI showed a complete filling of the defect. The T2 mapping MRI after one year showed chondral tissue with values in the range of hyaline cartilage. In this case, DBM and the collagen membrane were demonstrated to be good biomaterials to restore subchondral bone: this is a critical step towards the regeneration of a healthy hyaline cartilage

Giant endobronchial hamartoma resected by fiberoptic bronchoscopy electrosurgical snaring

Less than 1% of lung neoplasms are represented by benign tumors. Among these, hamartomas are the most common with an incidence between 0.025% and 0.32%. In relation to the localization, hamartomas are divided into intraparenchymal and endobronchial