Papers by Giorgio Signorini
Il Manuale per Formatori della Scienza Aperta
Il <strong>Manuale per Formatori della Scienza Aperta</strong>, tradotto in italiano ... more Il <strong>Manuale per Formatori della Scienza Aperta</strong>, tradotto in italiano dal testo originale in inglese "<strong>The Open Science Training Handbook</strong>", fornisce un'ampia e dettagliata panoramica sulle risorse, metodi e strumenti disponibili ai formatori impegnati a formare -e soprattutto- ad ispirare ricercatori, dottorandi e simpatizzanti su tutti i diversi aspetti della Scienza Aperta. Il manuale non solo illustra concetti e principi che sono alla base della Scienza Aperta, esso offre altresì informazioni sulle pratiche della Scienza Aperta includendo una serie di esempi e di esercitazioni pratiche nonchè consigli e suggerimenti su come meglio affrontare una platea eterogenea ed adulta ottenendo i migliori risultati di apprendimento, su come organizzare attività di advocacy a sostegno della Scienza Aperta ed infine su come e quali eventi di formazione organizzare. Il manuale online è stato scritto da 14 esperti internazionali durante un "book sprint" nel 2018.La traduzione in italiano è anch'essa il risultato di un lavoro di traduzione e di revisione collettiva al quale hanno partecipato diversi traduttori-volontari in servizio presso diversi atenei italiani. Il manuale è un'opera in continua costruzione; la versione più aggiornata è depositata in GitHub. Per chi volesse scaricare e/o stampare l'intero volume ne abbiamo predisposto una copia in formato pdf disponibile su questa piattaforma. Il manuale è disponibile anche in spagnolo e in portoghese.
ArXiv, 2019
One important goal in sustainability is making technologies available to the maximum possible num... more One important goal in sustainability is making technologies available to the maximum possible number of individuals, and especially to those living in less developed areas (Goal 9 of SDG). However, the diffusion of technical knowledge is hindered by a number of factors, among which the Intellectual Property Rights (IPR) system plays a primary role. While opinions about the real effect of IPRs in stimulating and disseminating innovation differ, there is a growing number of authors arguing that a different approach may be more effective in promoting global development. The success of the Open Source (OS) model in the field of software has led analysts to speculate whether this paradigm can be extended to other fields. Key to this model are both free access to knowledge and the right to use other people’s results. After reviewing the main features of the OS model, we explore different areas where it can be profitably applied, such as hardware design and production; we then discuss how ...
In a recent article (J. Comput. Chem. 2013, 34, 132-140), convective Replica-Exchange (convective... more In a recent article (J. Comput. Chem. 2013, 34, 132-140), convective Replica-Exchange (convective-RE) has been presented as an alternative to the standard even-odd transition scheme. Computations on systems of various complexity have shown that convective-RE may increase the number of replica round-trips in temperature space with respect to the standard exchange scheme, leading to a more effective sampling of energy basins. Moreover, it has been shown that the method may prevent the formation of bottlenecks in the diffusive walk of replicas through the space of temperature states. By using an ideal temperature-RE model and a classical harmonic-oscillator RE scheme, we study the performances of convective-RE when ergodicity is not broken and convergence of acceptance probabilities is attained. In this dynamic regime, the round-trip ratio between convective and standard-RE is at maximum ∼ 1.5, a value much smaller than that observed in non-ergodic simulations. For large acceptance probabilities, the standard-RE outperforms convective-RE. Our observations suggest that convective-RE can safely be used in either ergodic or non ergodic regimes; however, convective-RE is advantageous only when bottlenecks occur in the state-space diffusion of replicas, or when acceptance probabilities are globally low. We also show that decoupling of the state-space dynamics of the stick replica from the dynamics of the remaining replicas improves the efficiency of convective-RE at low acceptance probability regimes.
ORAC is a FORTRAN suite to simulate complex biosystems at the atomistic level. The program’s engi... more ORAC is a FORTRAN suite to simulate complex biosystems at the atomistic level. The program’s engine is supplemented by multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature algorithms. Quite recently, several advanced techniques for enhanced sampling in atomistic systems have been implemented, including replica exchange with solute tempering, metadynamics, steered molecular dynamics, serial generalized ensemble simulations and nonequilibrium alchemical transformations. All these computational technologies have been devised for parallel architectures using the standard MPI communication protocol. [...]
In a recent article (J. Comput. Chem. 2013, 34, 132-140), convective Replica-Exchange (convective... more In a recent article (J. Comput. Chem. 2013, 34, 132-140), convective Replica-Exchange (convective-RE) has been presented as an alternative to the standard even-odd transition scheme. Computations on systems of various complexity have shown that convective-RE may increase the number of replica round-trips in temperature space with respect to the standard exchange scheme, leading to a more effective sampling of energy basins. Moreover, it has been shown that the method may prevent the formation of bottlenecks in the diffusive walk of replicas through the space of temperature states. By using an ideal temperature-RE model and a classical harmonic-oscillator RE scheme, we study the performances of convective-RE when ergodicity is not broken and convergence of acceptance probabilities is attained. In this dynamic regime, the round-trip ratio between convective and standard-RE is at maximum ∼ 1.5, a value much smaller than that observed in non-ergodic simulations. For large acceptance probabilities, the standard-RE outperforms convective-RE. Our observations suggest that convective-RE can safely be used in either ergodic or non ergodic regimes; however, convective-RE is advantageous only when bottlenecks occur in the state-space diffusion of replicas, or when acceptance probabilities are globally low. We also show that decoupling of the state-space dynamics of the stick replica from the dynamics of the remaining replicas improves the efficiency of convective-RE at low acceptance probability regimes.
Chem Phys, 2006
Additional information on J. Chem. Phys.
ORAC is a FORTRAN suite to simulate complex biosystems at the atomistic level[1, 2]. The program&... more ORAC is a FORTRAN suite to simulate complex biosystems at the atomistic level[1, 2]. The program's engine is supplemented by multiple time steps integration , smooth particle mesh Ewald method, constant pressure and constant temperature algorithms. Quite recently , several advanced techniques for enhanced sampling in atomistic systems have been implemented, including replica exchange with solute tempering[2], metadynamics[2], steered molecular dynamics[2], serial generalized ensemble simulations[3, 4] and nonequilib-rium alchemical transformations[5]. All these computational technologies have been devised for parallel archi-tectures using the standard MPI communication protocol. Further instances are being implemented in the ORAC code, concerning algorithms aimed at improving speedup of nonequilibrium molecular dynamics simulations. In particular, two quite recent computational schemes, called path-breaking[6, 7] and dynamical freezing[8], are currently under study. The former a...
In a recent article (J. Comput. Chem. 2013, 34, 132-140), an alternative approach to the standard... more In a recent article (J. Comput. Chem. 2013, 34, 132-140), an alternative approach to the standard even-odd transition scheme of replica-exchange (RE) method, called convective-RE, has been introduced. Tests on systems of varying complexity have shown that convective-RE may increase the number of replica round-trips in temperature space with respect to the standard exchange scheme, leading to a more effective sampling of energy basins. Moreover, it has been shown that the method may prevent the formation of bottlenecks in the diffusive walk of replicas through the space of temperature states. By using an ideal temperature-RE model and a classical harmonic-oscillator RE scheme, we show that, when ergodicity is not broken and convergence of the acceptance probabilities is attained, the round-trip ratio between convective and standard-RE is at maximum $\sim 1.5$ (a much smaller value than that observed in non-ergodic simulations), while the standard-RE actually outperforms convective-RE...
The Journal of Physical Chemistry B, 2012
The synthetic N-glycosylated CSF114(Glc) and related peptides were proved to be able to recognize... more The synthetic N-glycosylated CSF114(Glc) and related peptides were proved to be able to recognize specific and high affinity autoantibodies circulating in blood of relapsing-remitting Multiple Sclerosis (MS) patients and correlating with disease activity. The effect of these peptides has been linked to the β -turn structure around the minimal epitope Asn(Glc). In this work we performed Hamiltonian Replica Exchange Molecular Dynamics simulations on the central heptapeptide fragment of a CSF114(Glc)-derived peptide in water and in a water/hexafluoroacetone mixture, confirming a significant incidence of β -turn structures in both solvents. The structural similarity of the glycosylated and unglycosylated forms in all environments proves that the conformation of the heptapeptide is only marginally affected by the presence of the sugar. Moreover, the presence of a significant amount of bioactive hairpin-like conformations in the water environment suggests a possible use not only in the diagnosis but also in the treatment of MS.
Journal of Cultural Heritage, 2002
Rock painting samples from Eritrean archaeological sites were studied by means of micro-Raman spe... more Rock painting samples from Eritrean archaeological sites were studied by means of micro-Raman spectroscopy and proton-induced X-ray emission technique (PIXE). Hematite and manganese oxides/hydroxides were determined in red and black paints, respectively. Since colours do not contain carbon, the paintings cannot be dated with 14 C. Moderate amounts of calcium carbonate or sulphate were also observed in most red drawings, while traces of phosphorus were found by PIXE only in a few red and black samples.
Convective Replica-Exchange in Ergodic Regimes
Journal of Chemical Theory and Computation, 2014
In a recent article (J. Comput. Chem. 2013, 34, 132-140), convective replica-exchange (convective... more In a recent article (J. Comput. Chem. 2013, 34, 132-140), convective replica-exchange (convective-RE) has been presented as an alternative to the standard even-odd transition scheme. Computations on systems of various complexity have shown that convective-RE may increase the number of replica round-trips in temperature space with respect to the standard exchange scheme, leading to a more effective sampling of energy basins. Moreover, it has been shown that the method may prevent the formation of bottlenecks in the diffusive walk of replicas through the space of temperature states. By using an ideal temperature-RE model and a classical harmonic-oscillator RE scheme, we study the performances of convective-RE when ergodicity is not broken and convergence of acceptance probabilities is attained. In this dynamic regime, the round-trip ratio between convective and standard-RE is at maximum ∼ 1.5, a value much smaller than that observed in nonergodic simulations. For large acceptance probabilities, the standard-RE outperforms convective-RE. Our observations suggest that convective-RE can safely be used in either ergodic or non-ergodic regimes; however, convective-RE is advantageous only when bottlenecks occur in the state-space diffusion of replicas, or when acceptance probabilities are globally low. We also show that decoupling of the state-space dynamics of the stick replica from the dynamics of the remaining replicas improves the efficiency of convective-RE at low acceptance probability regimes.
Journal of Chemical Theory and Computation, 2012
Serial generalized ensemble simulations, such as simulated tempering, enhance phase space samplin... more Serial generalized ensemble simulations, such as simulated tempering, enhance phase space sampling through non-Boltzmann weighting protocols. The most critical aspect of these methods with respect to the popular replica exchange schemes is the difficulty in determining the weight factors which enter the criterion for accepting replica transitions between different ensembles. Recently, a method, called BAR-SGE, was proposed for estimating optimal weight factors by resorting to a self-consistent procedure applied during the simulation (J. Chem. Theory Comput. 2010Comput. , 6, 1935Comput. −1950. Calculations on model systems have shown that BAR-SGE outperforms other approaches proposed for determining optimal weights in serial generalized ensemble simulations. However, extensive tests on real systems and on convergence features with respect to the replica exchange method are lacking. Here, we report on a thorough analysis of BAR-SGE by performing molecular dynamics simulations of a solvated alanine dipeptide, a system often used as a benchmark to test new computational methodologies, and comparing results to the replica exchange method. To this aim, we have supplemented the ORAC program, a FORTRAN suite for molecular dynamics simulations (J. Comput. Chem. 2010Chem. , 31, 1106Chem. −1116, with several variants of the BAR-SGE technique. An illustration of the specific BAR-SGE algorithms implemented in the ORAC program is also provided.
Lattice dynamics of the orthorhombic phase of KClO4: Ewald's method in molecular coordinates
Chemical Physics, 1991
ABSTRACT The algorithm of the Ewald lattice sums is formulated in a form suited for application t... more ABSTRACT The algorithm of the Ewald lattice sums is formulated in a form suited for application to lattice dynamics calculations for ionic molecular crystals, employing molecular coordinates and a discrete-charges representation of the Coulomb interactions. The method is used for a lattice dynamics calculation of KClO4 crystal, including external and internal degrees of freedom. An atom/atom plus charge/charge potential is used, providing a remarkably good agreement with the experimental data. The calculation is extended also to the anharmonic properties: the calculated linewidths of the external phonons compare satisfactorily to the observed values.
Chemical Physics Letters, 1993
... 154(1991) 245. 125] LA Carreira, TC Maguire and TB. Malloy Jr., J. Chem. Phys.66 (1977) 2621.... more ... 154(1991) 245. 125] LA Carreira, TC Maguire and TB. Malloy Jr., J. Chem. Phys.66 (1977) 2621. [26] R. Bini, P. Foggi, G. Marconi and E. Castellucci, J. Luminesceneei3 (1992) 541. ... Phys. 151(1991)127. (31] R. Bini, P. Foggi, PR Salvi, R. Simone and V. Schettino, J.Mol. Stnict. ...
Journal of Computational Chemistry, 2009
We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834, a FOR... more We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834, a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol.
Molecular dynamics and head-tail disorder in the Raman spectrum of crystalline N2O
Chemical Physics Letters, 1987
Page 1. Volume 142, number 6 CHEMICAL PHYSICS LEITERS Decombei lvh&quot; MOLECULAR DYNAMICS A... more Page 1. Volume 142, number 6 CHEMICAL PHYSICS LEITERS Decombei lvh&quot; MOLECULAR DYNAMICS AND HEAD-TAIL DISORDER IN THE RAMAN SPECTRUM OF CRYSTALLINE N,0 * Gianni CARDINI. ... Phys. 116 (1987) 171. [8]JO Clayton and WF Giauque, J. Am. Chem. ...
Chemical Physics, 1994
The widths of lattice and internal Raman lines in ferroelectric NaN& were measured in the tempera... more The widths of lattice and internal Raman lines in ferroelectric NaN& were measured in the temperature interval 4-200 K. Calculations of the double-vertex self-energy series based on an atom/atom and charge/charge potential agree well with observations. A better fit of data is obtained if auharmouic constants are treated as adjustable parameters. 0301-0104/94/$07.00 Q 1994 Elsevier Science B.V. All rights resmed SSD10301-0104(94)00193-E
Uploads
Papers by Giorgio Signorini