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

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

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

Muscle adaptations in relation to different types of strength training: an application of diffusion tensor imaging technique

Several exercise methods are commonly used by fitness practitioners to increase muscle strength and body mass. Pre-exhaustion (PE) is a strength training method of combining two exercises, in which a single-joint exercise performed exhaustively is followed by a multi-joint exercise. The purpose of PE of the smaller muscle is to provide lower involvement of this muscle in the subsequent multi-joint exercise, thereby enabling greater participation of other muscles. Conversely, in the post-exhaustion (PO) method is reversed the sequence of the exercises: first a determined muscle is trained with a multi-joint exercise and after with a single-joint exercise (Augustsson et Al., 2003). The purpose of this study was to investigate the effects of pre-exhaustion and post-exhaustion methods on gastrocnemius muscles by Diffusion Tensor Imaging (DTI) and volumetric evaluation techniques. DTI allows for a non-invasive evaluation of water diffusion and its fractional anisotropy (FA) in tissues. Four adults men (aged 22 +/- 0.81) have been divided in two groups by two different strength trainings: pre-exhaustion method (PE) and post-exhaustion (PO) method. All subjects have been performed 3 days a week for 3 months of training. Before and after training they have been subjected to conventional T1-weighted magnetic resonance. Results, after both training protocols, have shown a growth of muscle volume differentiated in each subject, probably connected to individual variables. Moreover, we have observed that the volumetric changes are related to the FA mean and it can be assumed that this remodeling of the can’t exclude, in addition to hypertrophy, phenomena of hyperplasia

Effective Label-Free Sorting of Multipotent Mesenchymal Stem Cells from Clinical Bone Marrow Samples

Mesenchymal stem cells (MSC) make up less than 1% of the bone marrow (BM). Several methods are used for their isolation such as gradient separation or centrifugation, but these methodologies are not direct and, thus, plastic adherence outgrowth or magnetic/fluorescent-activated sorting is required. To overcome this limitation, we investigated the use of a new separative technology to isolate MSCs from BM; it label-free separates cells based solely on their physical characteristics, preserving their native physical properties, and allows real-time visualization of cells. BM obtained from patients operated for osteochondral defects was directly concentrated in the operatory room and then analyzed using the new technology. Based on cell live-imaging and the sample profile, it was possible to highlight three fractions (F1, F2, F3), and the collected cells were evaluated in terms of their morphology, phenotype, CFU-F, and differentiation potential. Multipotent MSCs were found in F1: higher CFU-F activity and differentiation potential towards mesenchymal lineages compared to the other fractions. In addition, the technology depletes dead cells, removing unwanted red blood cells and non-progenitor stromal cells from the biological sample. This new technology provides an effective method to separate MSCs from fresh BM, maintaining their native characteristics and avoiding cell manipulation. This allows selective cell identification with a potential impact on regenerative medicine approaches in the orthopedic field and clinical applications

Freestanding non-covalent thin films of the propeller-shaped polycyclic aromatic hydrocarbon decacyclene

Molecularly thin, nanoporous thin films are of paramount importance in material sciences. Their use in a wide range of applications requires control over their chemical functionalities, which is difficult to achieve using current production methods. Here, the small polycyclic aromatic hydrocarbon decacyclene is used to form molecular thin films, without requiring covalent crosslinking of any kind. The 2.5 nm thin films are mechanically stable, able to be free-standing over micrometer distances, held together solely by supramolecular interactions. Using a combination of computational chemistry and microscopic imaging techniques, thin films are studied on both a molecular and microscopic scale. Their mechanical strength is quantified using AFM nanoindentation, showing their capability of withstanding a point load of 26 ± 9 nN, when freely spanning over a 1 μm aperture, with a corresponding Young’s modulus of 6 ± 4 GPa. Our thin films constitute free-standing, non-covalent thin films based on a small PAH