Poster Titles and Abstracts

Elena  Agliari Cybernetical approaches in biochemical kinetics Cooperativity is one of the most important properties of molecular interactions in biological systems and it is often invoked to account for collective features in binding phenomena. In order to investigate and predict  the effects of cooperativity, chemical kinetics proved to be a fundamental tool and, also due to its broadness over several fields of biosciences, a number of cooperativity quantifiers (e.g. Hills number, Koshl and cooperativity test, global dissociation quotient, weak and strong fine tunings, etc.), apparently independent or distinct, have been introduced [1]. However, a clear, unified, theoretical scheme where all cooperative behaviors can be framed would be of great importance, especially in biotechnology research. To this task, statistical mechanics offers a valuable approach as, from its basic principles, it aims to figure out collective phenomena, possibly overlooking the details of the interactions to focus on the very key features. Indeed, a statistical mechanics description of reaction kinetics has already been paved through theoretical models based on linear Ising chains, spin lattices with nearest neighbors interactions, transfer matrix theory and structural probabilistic approaches (see [2] and reference therein). statistical mechanics, chemical kinetics, cybernetics UniRM1 - Fisica
Adriano Barra Finitely Connected Lymphocyte Networks in the Immune System In this talk I will review recent approaches in modeling emergent/collective features shown by real lymphocyte networks using tools stemmed from disordered statistical mechanics and graph theory. I will discuss in particular the phenomenon of "anergy" shown by self-directed B-cells both from Varela perspective and from the two-signal model outcomes and the capabilities of the immune system to perform as a parallel autonomous processor. spin-glasses, associative networks, lymphocytes UNIRM1 - Fisica
 Alberto Maria Bersani Enzyme kinetics and quasi-steady state approximations: a mathematical point of view Michaelis-Menten kinetics is often handled by means of the so-called quasi-steady state approximation.Recently a new type of quasi-steady state approximation, called total (tQSSA), has been proposed; it is valid in a very large range of parameters and initial conditions. We will present an overview of the tQSSA, showing the most recent applications and discussing its mathematical meaning, in terms of asymptotic expansions and singular perturbation techniques. enzyme kinetics, quasi-steady state approximations, singular perturbations UNIRM1-Dipartimento SBAI
Francesca Bonfigli Soft X-ray contact microscopy of dry biological samples and in vivo plant cells on high spatial resolution lithium fluoride fluorescent imaging detectors Versatile and multi-purpose solid state radiation imaging detectors based on optical reading of the visible photoluminescence (PL) of radiation-induced color centers (F2 and F3 +) in lithium fluoride (LiF) crystalsand thin films are currently under development [1]. They possess a large field of view ( > 1 cm2), wide dynamic range, are directly read by a fluorescence optical microscope without any development procedure and are insensitive at ambient light. The intrinsic high spatial resolution, in principle limited only by the electronic defects size at atomic scale, but in practice by the Abbe limit of the reading microscope at around 250 nm, eliminate the need of optical elements and make them suitable for lensless X-ray imaging, even with polychromatic sources. X-ray imaging, fluorescence microscopy, unicellular algae, lithium fluoride, radiation detectors ENEA
Lisa Beatrice  Caruso Topological Networks in the study of protein structure-function relationships This conformers obtained by NMR deals with the use of topological networks [1] in the characterization of the Myoglobin conformers obtained by NMR spectroscopy. The intrinsic flexibility of the protein structure in solution seems confirmed by the NMR information, which does not lead to a single structure but to a set of spectroscopically equivalent conformers. Using the topological representation of such conformers [5] and analyzing the network parameters obtained for each of them, one should highlight their specific molecular features (Fig. 3). In this frame we showed that the ND parameter (positively correlated with molecular ’compacteness’) and the average Shortest Path Length (ASPL = average length of the shortest paths between a generic node (i) and any other node (j), positively correlated with molecular ’flexibility’) are negatively correlated between each other. allostery, Hb, SW Mb, proteomics, topological networks UNIRM1- Dept. SAIMLAL
Fabio Cecconi Coarse-grained modeling of protein unspecifically bound to DNA There is now a certain consensus that Transcription Factors (Tfs) reach their target sites, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D-diffusion in solution (jumps), 1D-diffusion along DNA (sliding), and small jumps (hopping) achieving association rates higher than for 3D-diffusion only. We investigate the FD phenomenology through Molecular Dynamics simulations in the framework of coarse-grained modeling. Despite the crude approximations, we show that the model generates, upon varying the equilibrium distance of the DNA-TF interaction, a phenomenology matching a number of experimental and numerical results obtained by more refined models. In particular, by focusing on the kinematics of the process, we characterize the geometrical properties of TF trajectories during sliding. We find that sliding occurs via helical paths around the DNA helix leading to a coupling of translation along the DNA-axis with rotation around it. The 1D-diffusion constant measured in simulations is found to be interwoven with the geometrical properties of sliding and we develop a simple argument able to quantitatively reproduce the measured values. Transcription factors, DNA, Facilitated diffusion CNR-ISC
Mauro Chinappi All-atom MD Simulation of Protein Translocation through α-hemolysin Nanopore: Implications for Protein Sequence/Structural Analyses The cell insulation from the external environment and the cellular compartmentalization is due to the presence of membranes composed by phospholipidic bilayers. Different types of proteins that play numerous biological functions are present in the membrane. These proteins are mainly involved in the communication between the cell and the external environment and between the different cellular compartments. Some of them form pores into the lipid bilayer that allow the translocation of molecules of different size and with different chemical-physical properties. The transport of these molecules across the membrane is crucial for the cellular survival. This feature of membrane proteins has been extensively studied with the aim of using them as nanopores in biochemical and industrial fields. During the last decades nanopores have been exploited for the development of new techniques for nucleic acids sequencing. Much less effort has been dedicated to protein and polypeptide analysis using nanopores. Only in the last years pioneering studies appeared in the literature suggesting potentially revolutionary applications in the study of protein sequence and structure. Recent experimental data have demonstrated that, in order to be translocated across nanopores, proteins must be unfolded [1,2], with the unfolding process occurring through a multi-step mechanism [1-4]. It has been observed, for instance, that the transport of thioredoxin through the α-hemolysin nanopore occurs via a four step process [1]. The goal of our project is to perform an all atom molecular dynamics simulation of the thioredoxin translocation across the α-hemolysin nanopore. The data obtained will allow the description of the molecular mechanisms at the basis of the protein transport at the atomic level. The unfolding, to which the protein is subjected during the translocation, will be further analysed in comparison with data coming from mechanical unfolding simulations of thioredoxin in solution. Our results will allow us to gain a deeper knowledge regarding the translocation of protein through nanopores, potentially useful for the development of nanopore based applications for several crucial biochemical analyses. nanpore, protein translocation, molecular dynamics IIT - CLNS@Sapienza 
Mario D'acunto Cell Motility, Contact Guidance and Mechanotaxis As the basic unit of life, cells are complex biological systems. Cells must express genetic information to perform their specialized functions: synthesize, modify, sort, store and transport biomolecule, covert different forms of energy, transduce signals, maintain internal structures and respond to external environments. All of these processes involve a combination of mechanical, chemical and physical processes. In a special way, mechanical forces play a fundamental role in cell migration, where contractile forces are generated within the cell and pull the cell body forward. On the other side, mechanical forces and deformations induce biological response in cells, and many normal and diseased conditions of cells are dependent upon or regulated by their mechanical environment. The effects of applied forces depend on the type of cells and how the forces are applied on, transmitted into, and distributed within cells. Traction forces exerted by cells on substrates can now be determined with a good degree of accuracy, but the intimate relation between cell shape and traction mechanics requires further qualitative investigation. Several imaging techniques and strategies have been developed with the purpose to study in situ and in real time the cell motility in different environments. In this talk, we overview Scanning Probe Microscopy (SPM) based imaging techniques developed to follow cell-cell and cell-substrate interactions during cell migration [1-2]. [1] M. D’Acunto et al., Nanotribological Perspectives In Tissue Engineering. In: Fundamentals of Friction and Wear on the Nanoscale / GNECCO; E.; MEYER; E. Springer-Verlag, BERLIN-HEIDELBERG, (2007),677-708. [2] M. D’Acunto, S. Danti, O. Salvetti, to published on a Springer Book review Cell motility, Contact Guidance, Mechanotaxis, Scanning Probe Microscopy CNR-ISM
Giuseppe  Dattoli Scaling laws, tumor evolution, capillary networks and metastasis diffusion   Angiogenesis, Kleiber law, Gompertz and Fisher equations, cancer metastasis ENEA
Adele De Ninno Microfluidics co-culture environments to explore complex cancer and immune cells related dynamics The limitations of conventional in vitro models have led to new alliances between cell biologists, bioengineers and physicists in order to recreate complex biological processes on chip in a more physiologically relevant context. This synergetic approach named ‘organs-on-Chips has recently enabled to develop sophisticated chemical and mechanical microenvironments, up to mimic tissue-tissue interfaces and key 3D human organs. Future research directions will tools that can be translated to biological laboratories on the pharmaceutical and cosmetical industry as alternatives suitable to animal replacements for drug discovery studies . microfluidics ,coculture , cancer microenvironment, immune system CNR-IMM
Antonella  De Ninno Effect of weak magnetic fields on acid-base equilibrium of L-Phe ttenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy has been used to investigate the effect of weak electromagnetic fields on the structure of L-glutamine (L-Gln) and L-phenylalnine (L-Phe) in aqueous solution. It has been found that the exposure to a DC field or a 50 Hz AC field, for a short time induces modifications in the spectra of exposed L-Phe samples. We suggest that the magnetic field modifies the water structure around the molecules and changes the hydrophobic interactions allowing the molecules of amino acids to aggregate. amino acids; acid-base equilibrium; weak elf ENEA
Pupa Gilbert Phase Transitions in CaCO3 biominerals mapped with 20-nm resolution One of the most fascinating aspects of calcite biominerals is their intricate and curved morphology, quite different from the rhombohedral crystal habit of geologic calcite. These morphologies, as well as space-filling and greater resistance to fracture, are achieved via amorphous precursor mineral phases (1). In this talk I will demonstrate that in sea urchin larval spicules two distinct phase transitions occur, Red®Green and Green®Blue in the figure (2). Both transitions are regulated by inhibiting proteins, which slow down the phase transitions, otherwise spontaneously, instantaneously occurring because they exothermic, and therefore thermodynamically downhill (3). Biominerals, Transitions, Sea Urchin UW-Madison
Leonardo Guidoni The molecular biophysics of photosynthesis explored by first principles     UNI L'aquila
Alessandro Magliano Molecular dynamics study on fibrillogenesis: all-atom self-aggregation of amyloidogenic peptides in explicit water A molecular dynamics study of self-aggregation of amyloid model peptides in explicit water have been performed. The amyloidogenic FLVHSS peptide (from hIAPP) and the non amyloidogenic NLGPVL peptide (from rIAPP ), were considered. Aggregates with different symmetric and structural features were obtained from simulations of multiple replicas of the two peptides. In particular, the characteristics of FLVHSS clusters resembled those describe in empirical studies on amyloidogenesis and amyloid fibrils. molecular dynamics, amyloidogenesis, amyloidogenic peptides, self-aggregation. UNIRM1 
Velia Minicozzi Computational and Experimental Studies on beta-Sheet Breakers Targeting Abeta(1–40) Fibrils NON Mandato Alzheimer's disease, Amyloid-beta peptide, beta-sheet breakers, Molecular Dynamics (MD), Fluorescence, Mass Spectrometry (MS) Physics Department and INFN, University of Rome Tor Vergata
A. Moleti Cochlear scale-invariance and time-frequency analysis of otoacoustic emissions The human cochlea is a tonotopic structure characterized by scaling symmetry. Cochlear mechanics and the otoacoustic emission (OAE) generation are invariant across frequency, provided that the phenomena are observed at the correspondingly shifted cochlear places. Time-frequency analysis provides an ideal framework to observe the cochlear scaling properties of and to separate OAE components associated with different generation mechanisms, based on their different phase gradient delay. cochlear mechanics, otoacoustic emissions, time-frequency analysis UNIRM2 - INFN
Antonio  Rinaldi Statistical methods for the design of bioscaffolds for tissue engineering Tissue engineering (TE) scaffolds produced by electrospinning are of enormous interest, but still lack a true understanding about the fundamental connection of outstanding functional properties with architecture, mechanical properties, and process parameters. One central issue addressed by TE researchers shall indeed be how to design such active biomaterials to get a specific biological response based on the material properties of the scaffold, which in turn depends on the raw materials and processing parameters. Fragmentary results from several parametric studies only render some partial insights that are hard to compare and generally miss the role of parameters interactions. To bridge this gap, statistical methods such as design of experiments (DOE) and standard regression models can be used to quantitatively identify the correlations existing between key scaffold properties and control parameters, in a systematic, consistent and comprehensive manner, disentangling main effects of each engineering parameter alone from interactions. As an illustrative example – meant to be a methodological proof of concept - we have conducted a case study on 32 (in triplicate for a total of 96 samples) different poly-l-lactide (PLLA) scaffolds fabricated by electrospinning to demonstrate how morphological and mechanical properties (i.e. the mean fiber diameter, the fiber diameter spread, the percent porosity ε%, and the effective Young’s modulus, which are referred to as Y1,Y2,Y3,Y4 hereafter.) can be “charted” as a function of molecular weight (MW) and other electrospinning process parameters (the Xs, Fig.1), and how they correlate with biological performance (i.e. Y5 hereafter), evaluated in terms of cell proliferation of seeded bone marrow-derived mesenchymal stromal cells (Fig.2) [1,2]. The study highlights perhaps two main findings above all. Overall the work demonstrates the power of the approach, but a thorough understanding of ideas and limitations underlying these statistical methods is crucial for their deployment, especially for defining screening and optimization strategies in a rational, cost-effective manner. parametric study, structure-property relations, process control, biomaterials, electrospinning ENEA
Daiana Simone Modeling neuronal structure-function relationships: a computational approach The considerable number of high-level computational aids in designing biophysical models of neurons [1] complicates the adoption of a single programming environment for different, simulation problems. This consideration motivated the choice of different alternatives in the analyses of the neuronal biophysical properties at the single cell and at the network level. neural networks, neural models, simulations, computational biology UNIRM1- Dept. SAIMLAL
Lorenzo  Stella  Behaviour of antimicrobial peptides in phospholipid membranes: insights from combined spectroscopic and simulative studies Antimicrobial peptides (AMPs) kill bacteria by making their membranes permeable and are active against drug-resistant strains. By combining spectroscopic techniques and molecular dynamics simulations, we investigated their interaction with lipid bilayers, characterizing their location in the membrane, pore formation, effects on lipid dynamics and selectivity. The resulting atomic level picture provides a basis for the rational design of a new generation of AMPs-inspired molecules. fluorescence, molecular dynamics simulations, neutron reflectivity, peptides, liposomes UNIRM2 - fisica
Francesco Stellato Copper–Zinc cross-modulation in prion protein binding We use x-ray absorption spectroscopy to study the coordination modes of Cu(II) and Zn(II) ions with the tetraoctarepeat portion of the prion protein. We show that Zn(II) and Cu(II) ions compete for binding to the peptide by cross-regulating their relative binding modes. x-ray absorption spectroscopy, prion protein, protein folding, synchrotron radiation  
Euardo  Villareal Luminescence response of pure LiF crystals irradiated with 60Co gamma rays and MV x rays clinical beams The use of the luminescence response of pure LiF crystals exposed to 60Co gamma rays and 6 MV x rays in the 1-100 Gy dose range has been investigated. Preliminary results of Photo stimulated luminescence of the F2 and F3+ color centre using the 458 nm line of an Argon laser indicate the potential use of pure LiF crystals as a clinical dosemeter. Investigations are underway to increase the PL reading sensitivity as well as to investigate the potential role of dopants on the LiF PL sensitivity.  photoluminescence, dosimetry, optical microscopy, color centres University of Calgary
Caterina Arcangeli Simulation of the adsorption mechanism of titanium-binding peptide to TiO2 anatase surface Interfaces between biological matter and inorganic materials are now among one of the hottest research topics in various research fields and even industry. Recent progress in combinatorial biology (e.g. the phage display method) has permitted to select amino acid sequences possessing specific affinities to their target inorganic materials. Among peptide sequences that bind inorganic surfaces the sequence AMRKLPDAPGMHC has been demonstrated to display a large and selective affinity to titanium dioxide. Experimental characterization of the peptide-titania interface has revealed that electrostatic interactions play a role and that peptide flexibility may also be important. The understanding of these interfaces paves the way to the design of novel materials engineered at the nanometric scale. In order to shed some light on this interaction, we investigated at atomic level the binding mechanisms between the TiO2 anatase surface and the peptide. We adopted a computational approach consisting of three stages: 1. DFT calculations to characterize the hydrated inorganic surface and the adhesion of the amino acids (relevant to the binding) on the TiO2 anatase in the presence of water molecules. 2. Modeling of the folding of the full peptide through classical MD simulations in water, starting from a totally unfolded molecular conformation. 3. MD simulations of the folded peptide adsorbed onto the TiO2 surface in water solution and steered MD simulations to better investigate the force of the interaction between the peptide and the TiO2 surface . Our computational results supported that electrostatic interactions play a crucial role for the peptide-surface binding. The peptide-surface interface was characterized at atomic level, and the peptide structural conformation upon the surface was clarified. The dissociation pathway of the peptide from the surface was investigated by steered MD simulations. titanium-binding peptide, titania surface, first-principle simulations, classical molecular dynamics simulation ENEA
Daniele Bovi Magnetic interactions in the Mn4CaO5 core of Photosystem II by Quantum Mechanics / Molecular Mechanics simulations at room temperature The molecular mechanisms of water splitting in the oxygen-evolving complex of Photosystem II are still unclear and partially unknown. In the computational modelling of such complex system, the QM/MM approach based on DFT+U ab-initio molecular dynamics represents one of the best way to take into account all the effects due to the particular electron state of the catalytic core and to the biological environment of the PSII. The two different structural models (model-A and model-B) proposed for the S2 state were stable during the simulated time of 15ps. Along both simulations we analysed the dynamics fluctuations of the magnetic coupling constants and the geometry of the Mn4CaO5 cluster, extracting their spectral signals in the 300-700 cm-1 region. Photosysthem II, Quantum Mechanics / Molecular Mechanics, Oxygen-Evolving Complex, Magnetic Coupling constants, Vibrational Spectroscopy UNIRM1 - (Guidoni) Physics
Michela Chiarpotto Design, synthesis and characterization of a novel folate conjugated drug delivery system (DDS) based on apoferritin/platinum complexes. The aim of the project is the synthesis of a novel Folate-conjugated ApoFerritin-based drug delivery system (DDS) for targeted delivery of Platinum (Pt) anticancer drugs. This carrier is designed to combine the drug-loading capability of ApoFerritin (ApoFt) and the tumor specificity provided by conjugation with folic acid (FA). Folate conjugation, therefore, presents an alternative method of targeting the folate receptor that is a highly selective tumor marker overexpressed in greater than 90% of ovarian carcinomas. DDS, ApoFt-PEG-FA , Apoferritin, Folic acid UNICATT
Alessandro  Cicconi Characterization of the binding of the Drosophila telomeric protein Verrocchio to single-stranded DNA The Drosophila telomeric protein Ver has an OB-fold domain, a structural motif present also in other proteins that are capable of binding single-stranded DNA. We have analyzed Ver binding to a telomere model system using Atomic Force Microscopy. We found that Ver binds single-stranded DNA, without sequence specificity, in dimeric and tetrameric form. AFM, telomeres, Drosophila, single-stranded DNA UNIRM1 - Dip. di Biologia e Biotecnologie
Emanuele Coccia Ab initio geometry and bright excitation of carotenoids: Quantum Monte Carlo and Many Body Green’s Function Theory calculations on peridinin We report the singlet ground state structure of the full carotenoid peridinin by means of variational Monte Carlo (VMC) calculations. A gas phase model has been used to study the optical properties of the chromophore. optical properties, chromophore, excitation energies, quantum mechanics UNI L'aquila
Alessandro Desideri Deciphering the effect of a supercoiled DNA substrate on the dynamical properties of topoisomerase 1B through molecular dynamics simulations Human topoisomerase 1B (hTop1B) represent a protein of medical being the target of anticancer compounds able to transform the enzyme in a poison for the cell. These drugs act by interacting not with the enzyme alone but only upon the formation of the protein-DNA covalent complex, by stacking between the DNA bases at the level of the cleavage site. As a matter of fact, understanding the dynamical features of the covalent complex can bring to a deeper characterization of the drugs action, leading to the development of even more effective compounds. To this aim, molecular dynamics (MD) simulations of the protein-DNA complex obtained so far have enriched our knowledge, even with the limitation that a linear 22 bps DNA has been used. Indeed, hTop1B preferentially binds to supercoiled substrates of larger length, for which however a three-dimensional structure doesn’t exist. Further, the use of such a larger system to be simulated was also limited by the great amount of calculations that it would have needed. The growing development of computing facilities allowed us to design the covalent complex of hTop1B bound to a negative supercoiled circle of 240 bps and to perform MD simulation. Our data revealed a higher affinity of the protein for the supercoiled substrate when compared to linear one. The stronger interaction with the DNA induces a deeper motion correlation between the protein domains, important for the catalytic mechanism. Finally, our data revealed the presence of a secondary binding site on subdomain III, explaining the higher affinity of the protein for the supercoiled substrate. Supercoiled DNA, Topoisomerase, Molecular Dynamics, protein-DNA interaction UNIRM2
Alessandro  Desideri Experimental Assembly And Simulative Analysis Of An Entirely Double-Stranded Octahedral Dna-Cage For Nanodelivery Purposes. We describe a novel rigid DNA cage cargo, able to release encapsulated molecules through enzymatic cleavage of the cage structure. In this structure the 24 single stranded linkers regions connecting the 12 structural double helices have been changed into double stranded regions including a restriction site cleavable by the BcnI endonuclease. Experimental results indicate that the entirely double stranded cage can be successfully assembled and the performance of the implemented opening mechanism, evaluated enzymatically, has been monitored and clarified using MD simulations. DNA nano-cage, controlled drug delivery, MD simulations UNIRM2 - Department of Biology
Luciana Di Gaspare Ion and plasma based treatments for enhanced chemic al speciation of metals in ferritin In the present work we investigated ferritin thin films treated with focused ion beam (FIB) and oxygen plasma, by using XPS and EDX techniques. We found that the detection capability of iron within the ferritin core was significantly enhanced due to the controlled disruption of the protein shell by means of FIB and oxygen plasma etching ferritin, focused ion beam, EDX, XPS, oxy gen plasma UNIRM3 - Dep of Science
Andrea Galluzzi  Parallel processing and multitasking capabilities of immune networks We have in recent years seen a renewed interest in statistical mechanical models of the immune system. These complement the standard approaches to immune system modelling, which are formulated in terms of dynamical systems. However, to make further progress, we need quantitative tools that are able to handle the complexity of immune system’s intricate signalling patterns. Fortunately, over the last decades a powerful arsenal of statistical mechanical techniques was developed in the disordered system community to deal with heterogeneous many-variable systems on complex topologies. Here we exploit these new techniques to model the multitasking capabilities of the (adaptive) immune network, where effector branches (B-cells) and coordinator branches (T-cells) interact via (eliciting and suppressive) signaling proteins called cytokines. statistical mechanics, immune network, parallel processing UNIRM1 - GNFM (Barra)
C. Giliberti A contribution to safe ultrasound-enhanced drug delivery: biophysical evidences in vitro n the attempt to operate molecular transient access through the cell membrane, an increasing biophysical interest has been directed to the study of the transfer of mechanical energy mediated by the propagation of ultrasonic waves through the skin cells and directed toward specific internal parts to body [1]. In this respect, it has been recently proposed a unified elastic model named BiLayer Sonophore (BLS) to demonstrate the real possibility that biological membranes exposed to ultrasound (US) well below the threshold of cavitation regime can undergo mechanical rupture of membrane lipid bilayers [2]. The phenomenon is known as membrane sonoporation (SP) and, under appropriate US exposure conditions, it could lead to the concrete development of new therapeutic techniques aimed at the efficient and safe release of drugs in situ [3,4]. On the other hand, cells exposed to the US field can exhibit concomitant effects, in function of exposure parameters such as frequency, intensity and exposure time. The failure probability of the cellular repair mechanisms is related to the irreversibility of these damages, and in turn to the risk of genotoxic and cytotoxic damage by US, thus constituting a serious risk to human health [4]. Some applications may benefit from killing cells, however drug delivery scenarios seek to maximise intracellular uptake while maintaining constant cell viability [3]. In this respect, the analysis of permeability effect of biological membranes induced by US can be considered an essential step towards a more informed medical use of US and it is also certainly valuable in the plan of new drug delivery strategies for multiple clinical relevance. With this purpose, our attention is focused firstly on in vitro effects of low intensity US on cell membrane permeability. The study was conducted mainly using 1 MHz US device on varying intensity and exposure time on fibroblasts and keratinocytes cell models (Figure 1), being the skin cells to direct contact with the US transducer of medical interest. The results have been used to better understand evidences of US-related mechanical stress on cell plasma membrane. The change in permeability was pointed out in terms of uptake efficiency of the fluoroprobes calcein and fitc-dextrans, thus resembling internalization of cell-impermeable model drugs, as measured by fluorescence microscopy and flow cytometry. Thus, the question of whether the presence of disruptions on the cell membrane (pore formation) is consistent with the uptake of cell-impermeable molecules has been successfully addressed in terms of time and intensity of exposure at which the sonoporation occurs, maximum size of molecules which can entry, and recovery of wild-type plasma membrane features. In this connection, also toxicological side effects was disclosed in terms of several cytotoxic and genotoxic endpoints assays and discussed in terms of possible mechanical stress affecting either cell viability or nuclear membrane barrier. According to the recently proposed BLS model our results demonstrate that US well below the intensity threshold of cavitation can promote efficient uptake of small drug model molecules. The cell permeability alteration we observed is consistent to reparable sonoporation, pointing out a direct correlation between efficiency of uptake with both time (Figure 2) and intensity of US exposure. The product of intensity and time is in fact the energy of irradiation. The latter parameter can be related to the size of the sonopores and in turn to the probability of finding cells with pores of sufficient size to pass the fluorophore in examination. Effects on membrane elastic modulus related to the occurrence of sonoporation as well as at viability (necrosis/apopthosis) and genetic level also evidenced below the threshold of US cavitation may be interpreted in terms of mechanical transduction mediated by increasing pressure by US. ultrasound, sonoporation, drug delivery, fluorescence microscopy, flow cytometry INAIL
Sveva  Grande 1H NMR metabolite profiling of glioblastoma stem-like cells identifies α-aminoadipic acid as putative biomarker of tumor aggressiveness. Glioblastoma multiforme (GBM) is very difficult to treat, patients facing a poor prognosis. High recurrence rate and failure of conventional treatments is attributed to the presence of cancer cells with stem-like properties. The expression of the members of ALDH gene superfamily are implicated in the lys catabolism, leading, in human brain, to the formation of α-aminoadipate (αAAD). We detected by 1H NMR, in a subset of GBM stem-like cells derived from primary GBM, a strong accumulation of αAAD; this latter may be putatively attributed as a biomarker of tumor aggressiveness. Glioblastoma stem cells, 1H NMR spectroscopy; alpha--aminoadipic acid ISS- Dipartimento di Tecnologie e Salute
Barbara Gregori Conformational Analyses of a Modified Peptide: Infrared Spectroscopy and Density Functional Theory Calculations S-nitrosation of glutathione play an important role in storage and trasport of NO, a key signaling molecule in vivo. An approach to detect this modification in the bare, charge amino acids is presented, based on IR multiple photon dissociation (IRMPD) spectroscopy.The interpretation of the IRMPD spectra is supported by quantum chemistry calculations of the optimized geometries, relative energies and IR spectra of [SNOgsn+H]+ Nitrosothiol, Glutathione, Gas Phase, IR spectroscopy, Density Functional Calculation UNIRM1 - (Guidoni) Physics
Leonardo Guidoni QM/MM simulations on Ca-replaced PSII In this work we perform QM and QM/MM DFT+U simulations on PSII, replacing Ca2+ with Sr2+ and Cd2+, trying to understand the role of the ion in the Ca site. Our results prove that such substitution doesn't affect in a relevant way neither the interconversion between the two S2 structures nor the PCET event going toward S3 state; furthermore, it support the suggestion that the inhibition/block of the O2 production after Ca2+ substitution is related to the pKa differences among the ions. PSII, OEC, Calcium UNI L'aquila
Leonardo Guidoni Structural properties of Polyacetylene chains: electronic correlation revisited through Quantum Monte Carlo The precise determination of the structural properties of long conjugated organic molecules, widespread in polymer chemistry and biological pigments and cofactors, represents a challenge for ab initio computational chemistry due to the necessity to correctly describe both the static and dynamic electron correlation[1,2,3]. The degrees of conjugation along the chain, which is reflected in the extent of the alternation between single and double bonds, significantly modulates their ground state and optical properties. Using Variational Monte Carlo calculations based on the antisymmetrized geminal power wave function, we have optimized the geometries of polyacetylene chains formed by a maximum number of 12 acetylene units, leading to an asymptotic value of 0.0910(7) Angstrom for the bond length alternation of infinite chains, in fair comparison with NMR and X-ray experiments. Our results demonstrate the capability of this fully ab initio approach to correctly describe the geometrical parameters of long conjugated organic molecules and provide a new reference for correlated method. The favorable scaling of VMC with the number of electrons N of the system (N3 − N4) opens the way to its application on large conjugated organic and biological molecules. In light of this new reference, we analyze the results of other quantum chemistry methods, revealing problematic inconsistencies of the non size-consistent post Hartree-Fock approaches, and revealing the good performance of long-range corrected density functionals. Quantum Chemistry, Structural properties, Quantum Monte Carlo UNIRM1 - (Guidoni) Physics
Antonella Lisi Low-Frequency Electromagnetic Fields, a tool to promote osteoblast commitment in human Mesenchymal Stem Cells.      
Luca Maiolo Wireless wearable sensor system to monitor movements in elderly or in hospitalized patients The purpose of this work is to develop a small wireless wearable device equipped with a set of inertial sensors with the aim of monitoring human body postures in subjects such as the older people in their homes, or patients during their hospital stay to avoid falls or recognize potentially dangerous behaviors. The monitoring system is composed of a series of small devices, the nodes, applied to the subject, and a gateway that acts as master of the network collecting all the information provided by the wearable nodes. Each node is equipped with a set of inertial sensors and a wireless network is properly set up allowing the devices to communicate with each other. There is a great variety of accelerometers, with respect to the range of acceleration of interest, in relation of the number of axis monitored and, furthermore,considering the sensing principle behind the MEMS technology. For some accelerometers at rest conditions, the static measure of acceleration is influenced by the presence of the gravity. Human body accelerations increase from the top to the bottom of the body and the major contribute during normal activities is along the vertical axis. For example, during the gait, frequency of the movements do not exceed 10Hz, acceleration values measured at the ankle are in the order of 2.9 - 3.7 g whereas along the torso are in the range of 0.3 – 0.8 g. The sensor network is designed and properly implemented to be embedded in smart garments with the intent of minimizing size and weight of the wearable sensors, thus improving the comfort of the tracking system. rehab monitoring system, wireless, wearable sensors system, posture analysis CNR-IMM
Alessandro Maiorana Effect of temperature on SdrF, a Staphylococcus epidermidis collagen binding protein. Staphylococcus epidermidis plays a critical role in catheter-related infections. The difference between the outer and inner temperature of the human body may functionally influence the initial colonization step of S. Epidermidis to medical devices. The aim of this study was to evaluate the effect of the temperature on biological activity and conformational structure of the staphylococcal SdrF protein. Structural and functional results indicate that the temperature acts as a switch turning off the ability of the fragment to bind collagen at physiological temperatures (37°C). Staphylococcus epidermidis, SdrF adhesin, collagen, Small Angle X-Ray Scattering (SAXS) UNICATT
Marco Marrani Compact MEA data acquisition system for neural signal analysis In this work, we focused on the design and realization of a compact system , composed by Ultra-Flexible MicroElectrode Arrays (UF-MEAs) and a Low-Noise Amp PCB (LNA-PCB). The UF-MEAs were fabricated by embedding a metal bi-layer of Cr/Au (250 nm thick) into 2 Polyimide (HD2611, HD MicroSystems) layers, reaching a final thickness of 8 μm. The array is composed by 28 electrodes of 50 µm ø, with 2 group of 4 electrodes in romboidal shape (d=10 µm) and 4 stimulation pads on the border limit of the MEA. Furthermore via-hole have been made through the PI in order to oxygenate the surface and achieve a better surface adhesion. At the same time we developed an active LNA-PCB, equipped with a digital electrophysiology interface commercial chip (RHD2132 - Intan Technologies), which is able to amplify (20x, up to 200x) and digitize the signal recorded using a low noise (Amplifier Input Reference Noise = 2,4 µV rms ) technology. The system UF-MEAs + LNA-PCB is controlled by a software that allows to read each channel and modify registers in order to adapt the settings to the type of measurement. Validation tests of the system have been performed sending a sinusoidal signal trough a platinum electrode submerged in a saline solution (NaCl 0,9%) , and reading it with an home-made developed software. In this work we proved that our compact standalone low noise amplification system is a reliable alternative to measure ECoG signals in vitro or in vivo. MicroElectrode Array, Ultrathin Polyimide, Local pre-amp, Neural signal analysis CNR-IMM
Giuseppe Maulucci Functional imaging of cells and tissues Introduction: Fluorescence microscopy offers the possibility to map biomolecules in time and space with high resolution and specificity in living cells and tissues. Besides traditional morphological and co-localization studies, quantitative techniques for the detection of conformational changes of fluorescence probes allow the detection of functional observables, as redox state of different redox couples, pH, calcium, cAMP , fluidity, protein-protein interactions, post-translational modifications, cell dynamics and morphodynamics. Materials and methods: The stationary spatial patterns of signaling events are determined through intracellular fluorescent probes, and are related with the frequency and entity of dynamic events, i.e. the zones of formation of membrane protrusions and retractions, which are in turn quantified through a stochastic approach which allows to extract dynamic and morphodinamic features, in live cells or in tissues. Results: The simultaneous and multiple construction of these maps, allows to visualize stationary spatial patterns of signaling events and to relate them with hot spots of morphodynamic events. The method is tested on cells and tissues, in which the distribution of the hot spots in different pathophysiological conditions is related to the distribution of redox state and membrane fluidity. Conclusions: These tools offer the opportunity to probe biological systems to map biochemical events, in order to dissect the molecular events that underlie physiological and pathological states of cells and tissues. They are a useful diagnostic tool since they easily permit multiple detection of unbiased observables not only in live cells, but also in tissues. Functional imaging, ROS, confocal microscopy, ratiometric probes, cell signaling UNICATT
Piero Morales Directed selfassemblage of DNA nano”motherboards” onto e-beam patterned inorganic  We report on the selfassemblage of flat origami type DNA boards onto electron beam lithography fabricated gold nanopillars. The concept is based on demonstrations that properly designed DNA sequences will self-assemble [1] into ordered nanoscale architectures; these, in turn, spontaneously assemble “plug-in” protein-based components on designated sites. A further self-assembling process based on properly positioned thiol groups in the DNA is explored here to direct the DNA motherboards onto designated locations of the chip where suitable anchoring nanopillars are fabricated. DNA nanothechnology, DNA origami, nanopillars, ebeam lithography ENEA
Sandra Moreno Intranuclear vacuoles in neurons of a mouse model lacking type 2 transglutaminase Transglutaminases (TGs) are ubiquitous calcium-dependent acyl-transferases, catalysing post-translational protein modifications. Among the family members, TG2 (or "tissue" transglutaminase) acts as a multifunctional protein regulating cell processes, including autophagy [1,2]. TG2 is highly expressed in the nervous tissue and reportedly involved in neurodegenerative disorders [3]. Indeed, the pathophysiology of these diseases includes insoluble aggregate formation, and covalent cross-linking of pathogenic proteins by TG2 has been suggested. Another hallmark of neurodegeneration is dysregulated autophagy, thus making the role played by TG2 in this cellular process especially relevant. The present study aims to clarify the role of TG2 in neuronal ultrastructure as well as redox balance and autophagy. Electron microscopic analyses were carried out in various brain regions, namely neocortex, hippocampus, brainstem, and cerebellum of 12-month-old TG2-/- and wild-type (WT) mice. TG2-/- neurons show abnormal features including intranuclear vacuoles surrounded by a single membrane and aberrant autophagic bodies. Moreover, the expression levels of antioxidant enzymes and pro-autophagic proteins were investigated in the same brain regions. Superoxide dismutase 1 and 2 (SOD1, SOD2), catalase (CAT), glutathione peroxidase 1/2 (GPx 1/2), Beclin1, LC3 and Ambra1 were evaluated by western blotting (WB) and immunohistochemistry. Overall higher levels of autophagic proteins in the brain areas considered, compared to their WT counterparts, were detected. This strongly argues for an induction of autophagy in the absence of a modulatory role played by TG2, related to its interaction with Beclin1. Concerning antioxidants, upregulation or downregulation of specific enzymes, strictly dependent on the brain area considered, were observed. A specific involvement of mitochondrial and peroxisomal dysfunction is suggested in TG2-/- mice. transmission electron microscopy, type 2 transglutaminase, autophagy, oxidative stress, proteinaceus aggregates, intranuclear vacuoles UNIRM3
Sandra Moreno Mitochondrial and peroxisomal alterations in a mouse model of genomic instability Aging is a biological process characterized by the progressive loss of homeostatic reserves in all tissues. It can be explained by a complex network of interdependent processes [1]. Many studies demonstrated that both unrepaired DNA damage and oxidative stress contribute to the onset of aging [2]. Genomic instability associated with DNA repair mechanisms defects is consistent with the manifestation of aging signs and age-related diseases. Excision repair cross-complementation group 1 protein-xeroderma pigmentosum group F-complementing protein (ERCC1/XPF) is a complex involved in the Nucleotide Excision Repair mechanism (NER) and it functions as the nuclease that incises the damaged strand 5’ to the adduct [3]. Deficiency in this complex results in a variety of progeroid syndromes and accelerated aging [4]. The present study aims to shed light on age-related processes using ERCC1-/d mouse model, focusing on peroxisomes and mitochondria. Indeed, these organelles play an important role in aging because of their involvement in ROS and lipid metabolism, and share common biogenesis pathways [5]. We performed ultrastructural analyses by transmission electron microscopy (TEM), and focussed ion-beam/scanning electron microscopy (FIB/SEM) of ERCC1-/D mouse liver, as compared to its wild-type (WT) counterpart. Results show a severe hepatocellular suffering in ERCC1-/D genotype. To better identify peroxisomal population, catalase cytochemistry procedure was performed and only few organelles in ERCC1-/D liver were observed. Mitochondria appear polymorphic and characterized by membranes disorganization, suggesting possible ROS and lipid dys-metabolism. Molecular analyses of the same hepatic tissue revealed gene expression and protein levels variations, involving antioxidant enzymes (CAT, SOD1 and SOD2) and their transcriptional regulators (PGC1a, Nrf2), suggesting that ERCC1-/d genotype is hallmarked by altered redox balance in hepatocytes. In particular, PGC1a reduction suggests alterations of mitochondrial and peroxisomal biogenesis. Moreover, the marker of peroxisomal proliferation Pex11 is decreased, supporting results concerning the reduced number of peroxisomes. Low transcription levels of ABCD2 suggests very long chain fatty acid accumulation. In contrast, significantly higher expression levels of ABCD3 were found, probably to balance fatty acid accumulation. PPARs also were investigated, as regulators of peroxisome/mitochondrial biogenesis and lipid metabolism. PPARa expression fails to show any variation, while the expression of PPARg and its target gene CD36 is increased. These data suggest that modulation of inflammatory response occurs in ERCC1-/D mice. Abnormalities involving both organelles are not surprising because peroxisomes and mitochondria are closely related, sharing common/integrated functions and biogenetic pathways. Transmission electron microscopy, aging, genomic instability, oxidative stress, peroxisomes, mitochondria UNIRM3 - Dep of Science
Shane Morley The Role of Acetlyated Microtubules in Mechanosensation. Here we describe a novel function for acetylated microtubules as essential elements of the mechanosensory apparatus in Mus musculus. In KO mice with a sensory neuron specific deletion of the microtubule acetylating enzyme ATAT1, an almost complete loss of mechanical (touch) sensitivity is observed compared to WT specimens. By examining a number of cellular attributes of knockout sensory neurons such as membrane elasticity, microtubule ultrastructure, innervation of sensory end organs, axonal transport, and direct regulation of mechanosensory ion channels. We aim to shed light on the role of ATAT1 in mechanosensation and uncover the function of microtubules in this process. Microtubules, mouse, mechanosensation, electrophysiology, atomic force microscopy, microfluidics  
Eleonora Nicolai Evaluation of BiesseBioscreen as a new methodology for bacteriuria screening Urinary tract infection is a common disease diagnosed in the clinical microbiology laboratory through bacterial count per volume of urine. In this study we have evaluated the BiesseBioscreen analyzer as a new way to analyze urine samples enabling fast screening of urine, prior to reference standard methods currently utilized in microbiology analysis laboratory. We analyzed 962 urine samples from outpatients and inpatients of the Polyclinic Tor Vergata (PTV), University Hospital of the University of Rome “Tor Vergata”. All samples were processed both with the BiesseBioscreen and with the standard methodology adopted by the clinical microbiology laboratory of Policlinic Tor Vergata and the results were compared. Of samples analyzed 54.9% resulted concordant negative with reference method and 21.6% concordant positive, 23.3% resulted false-positive and 0.2% false-negative. The results obtained from BiesseBioscreen showed a sensitivity of 99.0%, indicating it as a reliable system for the diagnosing of urinary tract infection; BiesseBioscreen could represent a valid method for screening negative samples to exclude from culture test with a potential reduction in time, workload and costs of the diagnosis. bacteriuria screening, fluorescent assays, urinary tract infection, nucleic probe, bacterial culture. Department of Experimental Medicine and Surgery, University of Rome “Tor Vergata”
Alessandro Nucara The interaction of (-)-epicatechin with b-lactoglobulin B studied by infrared spectroscopy Among flavanols, (-)-epicatechin (EC) has recently gained renewed consideration since it has been reported to have multiple health benefits in humans, preventing cardiovascular disease, diabetes and some cancers [1]. This compound is a common polyphenol in the human diet, being contained in high concentrations in many fruits, wine, tea and cocoa products. Bioavailability of polyphenols, as well as of their in vivo metabolites, is rather low and highly affected by non-covalent interaction with food macronutrients, especially proteins [2]. b-Lactoglobulin (BLG), the major whey protein from cow milk, is a protein with still unknown function and of high interest to the food and pharmaceutical industries, because of its capacity to bind several bioactive compounds, polyphenols included. Contrasting results are available in the literature concerning binding mechanism between flavonoids and milk proteins. In particular, binding of catechins to BLG in low affinity sites is controversial. In this study, the interaction between BLG B and EC was investigated at a molecular level by Fourier transform infrared spectroscopy in physiological conditions. Amide I spectra of EC-BLG complexes, in D2O buffer solutions, pD = 6.8, at molar ratios from 0.5:1 to 15:1, were measured by using a cell device specifically created by a photolithographic technique b-lactoglobulin, epicatechin, secondary structure, infrared UNIRM1 - Physics
Mohammad Nurul Islam Study of solvent effects on the optical and vibrational properties of peridinin Photosynthetic organisms use light-harvesting (LH) complexes to extend the overall spectral range of the antenna and to protect it from radiation damage. As an example, the Peridinin-Chlorophyll-Protein (PCP) light harvesting complex of algae dinoflagellates has this types of properties and have been studied extensively. The protein contains both chlorophylls and peridinins molecules, the latter being a carotenoid responsible to extend the spectral range of captured light to regions where chlorophylls do not absorb [1]. The crystal structure of the main PCP form reveals that each chlorophyll is surrounded by 4 or 3 molecules of peridinin, located in non-equivalent positions. The different protein environment of the sites might be responsible of a spectral shift [2] of the pigments with the functional role to extend the absorption spectra of the complex and enhance its light harvesting capabilities. In peridinin the lowest-lying excited singlet state is an intramolecular charge transfer (ICT) state, which is the main responsible of energy transfer to chlorophyll. Its formation might be strongly affected by the dipole moment in the ground state [3]. In the present work we have performed quantum mechanical/classical molecular dynamic (QM/MM) simulations of the peridinin in different types of solvents (eg., hexane, acetonitrile, methanol). The main goal of this work were the analysis of the optical and vibrational properties of the complete peridinin model in different environments and compare it with the experimental values. The shifts of vibrational spectra of different normal modes as well as the analysis of the excited electronic states showed interesting results and were comparable to the experimental values in most cases. The vibrational properties of the reduced model of peridinin in different environments have been analysed from the QM/MM perspectives in earlier studies [4]. Further investigations are under progress to better understand the effect of the protein environment on the optical and vibrational properties of the PCP pigments. photosynthesis, peridinin-chlorophyll a- protein (PCP), QM/MM, vibrational spectroscopy, optical properties UNIRM1 - (Guidoni) Physics
Alessandra Palma Two subtypes of stem-like cells from glioblastoma multiforme with different metabolic profiles identified by NMR spectroscopy. Glioblastoma multiforme (GBM) is a malignant brain tumour with very aggressive characteristics. Recurrence of the tumour is attributed to the presence of stem-like cancer (CSC) cells that are resistant to treatments. The unsupervised analysis performed on spectral data of 27 CSCs from different GBM patients suggested the presence of 2 subtypes with different metabolic phenotypes. In cluster 1, a mixed neural–astrocyte metabolic phenotype, with a neuronal fingerprint, prevailed, while in cluster 2 an astrocytic/glioma-like metabolism was observed according to a previous work. Glioblastoma stem cells, 1H NMR spectroscopy, cluster analysis  
Fabrizio  Parente Associating brain topological networks to cognitive. NON Mandato fMRI, resting state, graph theory, network theory, WCST UNIRM1 - Fisiologia
Lorenzo  Stella (Farrotti)) Computational methods to determine peptide orientation in membranes. We tested different computational approaches to overcome the sampling problems involved in the determination of the location of membrane-active peptide inside lipid bilayers. Our test-case was the artificial antimicrobial peptide LAH4, which is known to reorient from surface-bound to transmembrane when the pH changes from acidic to basic. All the techniques employed yielded similar results: neutral His LAH4 inserted into the bilayer core, while His protonation promoted peptide interaction with the superficial phospholipid headgroups. antimicrobial peptides, membrane, molecular dynamics simulations UNIRM2- Dep of Chemical Sciences and Technologies
Lorenzo  Stella (Roversi) How many antimicrobial peptide molecules kill a bacterium? Spectroscopic determination of PMAP-23 binding to E. coli We determined the number of antimicrobial peptide molecules necessary to kill an E. coli cell by developing a method to measure peptide/bacteria association and microbial killing under the same conditions. Bacteria died only when peptides completely saturated their membranes, supporting the view that in vivo a microbicidal mechanism is possible only at micromolar concentrations. Surprisingly, we found that peptide partition in model bilayers is representative of peptide binding to bacterial membranes. antimicrobial peptides, bacteria, liposomes, fluorescence spectroscopy UNIRM2- Dep of Chemical Sciences and Technologies
Lorenzo  Stella (Vaezi) Testing the “sand in a gearbox” model: effects of antimicrobial peptides on membrane dynamics Antimicrobial peptides exhibit their bactericidal activity by forming pores in bacterial membranes.  However, according to the “sand in a gearbox” model, they could act also by perturbing lipid dynamics and thus the function of membrane proteins.  We characterized by fluorescence spectroscopy the effects of melittin and magainin on membrane dynamics. Both peptides reduced lipid motions, lateral diffusion and water penetration, likely due to a peptide-induced tightening of the bilayer. antimicrobial peptides, fluorescence spectroscopy, membrane dynamics UNIRM2- Dep of Chemical Sciences and Technologies
Daniele Tantari Anergy in self-directed B-cells through a statistical mechanics perspective Self-directed lymphocytes may evade clonal deletion at ontogenesis but still remain harmless due to a mechanism called clonal anergy. For B-lymphocytes, two major explanations for anergy developed over the last decades: according to Varela theory, anergy stems from a proper orchestration of the whole B-repertoire, such that self-reactive clones, due to intensive feed-back from other clones, display strong inertia when mounting a response. Conversely, according to the model of cognate response, self-reacting cells are not stimulated by helper lymphocytes and the absence of such signaling yields anergy. Through statistical mechanics we show that helpers do not prompt activation of a sub-group of B-cells which prove to be just those broadly interacting. Hence Varela theory can finally be reabsorbed into the prevailing framework of the cognate response model. Further, we show how the B-repertoire architecture may emerge, where highly connected clones are self-directed as a natural consequence of ontogenetic learning. Immune system, statistical mechanics, self-non-self discrimination UNIRM1 - Matematica (Barra)
Sonja Visentin A KINETIC STUDY BY STOPPED FLOW OF THE INTERACTION BETWEEN POTENTIAL PHOTOSENSITIZERS AND ALBUMIN Photodynamic therapy (PDT) efficency is affected by the nature of the binding between Photosensitizers (PS) and serum albumin. In the present work we studied the kinetic interaction between Bovine Serum Albumin (BSA) and different photosensitizers (porphyrin and squaraines ) by a stopped flow technique in order to obtain KD, Kon and Koff values. The stopped-flow fluorescence intensity method offers a powerful tool for detailed kinetic analysis of protein-protein or ligand-protein interactions and has gained considerable importance during the last few years. stopped floe, squaraines, kintecs, PDT UNITO- Dep. of Molecular Biotechnology and Health Science
Andrea Zen Static and dynamical correlation in diradical molecules by Quantum Monte Carlo using the Jastrow Antisymmetrized Geminal Power ansatz Diradical molecules are essential species involved in many organic and inorganic chemical reactions. The computational study of their electronic structure is often challenging, because a reliable description of the correlation, and in particular of the static one, requires multireference techniques. The Jastrow correlated antisymmetrized geminal power (JAGP) is a compact and efficient wave function ansatz, based on the valence-bond representation, which can be used within quantum Monte Carlo (QMC) approaches. The AGP part can be rewritten in terms of molecular orbitals, obtaining a multideterminant expansion with zero-seniority number. In the present work we demonstrate the capability of the JAGP ansatz to correctly describe the electronic structure of two diradical prototypes: the orthogonally twisted ethylene, C2H4, and the methylene, CH2, representing respectively a homosymmetric and heterosymmetric system. In the orthogonally twisted ethylene, we find a degeneracy of π and π* molecular orbitals, as correctly predicted by multireference procedures, and our best estimates of the twisting barrier, using respectively the variational Monte Carlo (VMC) and the lattice regularized diffusion Monte Carlo (LRDMC) methods, are 71.9(1) and 70.2(2) kcal/mol, in very good agreement with the high-level MR-CISD+Q value, 69.2 kcal/mol. In the methylene we estimate an adiabatic triplet–singlet (X̃3B1–ã1A1) energy gap of 8.32(7) and 8.64(6) kcal/mol, using respectively VMC and LRDMC, consistently with the experimental-derived finding for Te, 9.363 kcal/mol. On the other hand, we show that the simple ansatz of a Jastrow correlated single determinant (JSD) wave function is unable to provide an accurate description of the electronic structure in these diradical molecules, both at variational level (VMC torsional barrier of C2H4 of 99.3(2) kcal/mol, triplet–singlet energy gap of CH2 of 13.45(10) kcal/mol) and, more remarkably, in the fixed-nodes projection schemes (LRDMC torsional barrier of 97.5(2) kcal/mol, triplet–singlet energy gap of 13.36(8) kcal/mol) showing that a poor description of the static correlation yields an inaccurate nodal surface. The suitability of JAGP to correctly describe diradicals with a computational cost comparable with that of a JSD calculation, in combination with a favorable scalability of QMC algorithms with the system size, opens new perspectives in the ab initio study of large diradical systems, like the transition states in cycloaddition reactions and the thermal isomerization of biological chromophores. quantum Monte Carlo, diradical molecules, static correlation, ethylene, methylene UNIRM1 - (Guidoni) Physics
Mauro Chinappi Protein translocation through nanopores: multistep translocation pathways from Molecular Dynamics simulations Nanopore-based protocols for macromolecule detection constitute a promising technology for the development of innovative sensors able to operate at single-molecule level. Here we present our recent results on multistep protein translocations through nanopores obtained via molecular dynamics simulations. The emerging picture is that the dynamics is characterized by the presence of translocation intermediates, which are generated by the protein sticking in the pore at specific conformations. nanopore, translocation, stall, coarse-grain, free-energy, molecular dynamics IIT - CLNS@Sapienza 
Leonardo Guidoni Pathway for Mn cluster oxidation by Tyrosine-Z in the S2 state of Photosystem II Water oxidation in photosynthetic organisms occurs through the five intermediate steps S0 - S4 of the Kok's cycle in the Oxygen Evolving Complex of Photosystem II. Along the catalytic cycle, four electrons are subsequently removed from the Mn4CaO5 core by the nearby tyrosine Tyr-Z, which is in turn oxidized by the chlorophyll special pair P680, the photo-induced primary donor in PSII. Recently, two Mn4CaO5 conformations, consistent with the S2 state (namely S2A and S2B models, see also Figure 1) were suggested to exist, maybe playing a different role within the S2 to S3 transition. Here, we report multi-scale ab initio DFT+U simulations revealing that upon such oxidation the relative thermodynamic stability of the two previously proposed geometries is reversed, the S2B state becoming the leading conformation (see Figure 2). In this latter state a proton coupled electron transfer is spontaneously observed on about 100 fs at room temperature dynamics. The Mn-cluster, which is tightly electronically coupled along dynamics to the Tyr-Z tyrosyl group, upon oxidation releases a proton from the nearby W1 water molecule to the close Asp-61 on the fs timescale, thus undergoing a conformational transition increasing the available space for the subsequent coordination of an additional water molecule. The results can help to rationalize previous spectroscopic experiments and confirm for the first time that the water splitting reaction has to proceed through the S2B conformation, providing the basis for a structural model of the S3 state. Oxygen-Evolving Complex, Proton-Coupled Electron Tranfer, Kok’s Cycle, QM/MM Molecular Dynamics UNI L'aquila
Monia Vadrucci Characterization of GafChromic EBT3 films with 60CO and low energy protons for radiobiology dosimetry   Medical Physics ENEA