Giorgio F. Signorini

ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

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. ORAC is an open‐source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac.

Characterisation of painting materials from Eritrea rock art sites with non-destructive spectroscopic techniques

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.

Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat

The Crooks equation [Eq. (10) in J. Stat. Phys. 90, 1481 (1998)], originally derived for microscopically reversible Markovian systems, relates the work done on a system during an irreversible transformation to the free energy difference between the final and the initial state of the transformation. In the present work we provide a theoretical proof of the Crooks equation in the context of constant volume, constant temperature steered molecular dynamics simulations of systems thermostated by means of the Nosé-Hoover method (and its variant using a chain of thermostats). As a numerical test we use the folding and unfolding processes of decaalanine in vacuo at finite temperature. We show that the distribution of the irreversible work for the folding process is markedly non-Gaussian thereby implying, according to Crooks equation, that also the work distribution of the unfolding process must be inherently non-Gaussian. The clearly asymmetric behavior of the forward and backward irreversible work distributions is a signature of a non-Markovian regime for the folding/unfolding of decaalanine.

Molecular dynamics and head-tail disorder in the Raman spectrum of crystalline N2O☆

Abstract The effect of head-tail disorder on the low frequency Raman spectrum of solid N2O is investigated by means of molecular dynamics simulations. The main features of the experimental spectrum are reproduced in the calculation under the assumption that about 10% of the molecules are orientationally disordered.

Energy decay mechanisms and anharmonic lattice dynamics: The case of solid nitrogen

Abstract The anharmonic frequencies and linewidths of the lattice phonons in α-N 2 are calculated on the basis of three different intermolecular potentials which include atom-atom and electrostatic interactions. The distinction between stationary anharmonicity and decay anharmonicity is stressed and the mechanism of energy transfer between the optical lattice phonons and the two-phonon manifold of the crystal is discussed in detail. The temperature dependence of the phonon self-energy is also considered. The results thus obtained for α-N 2 are compared with predictions from previous lattice dynamics. SCP and molecular dynamics calculations. The calculated anharmonic effects are substantially independent of the adopted potential: the agreement with experimental data is reasonably good as far as the linewidths are concerned, while the anharmonic deformation of the potential wells (and thus the frequency shifts) is overestimated. We suggest that, while higher orders in the diagram expansion are necessary for a proper account of the stationary anharmonicity, the decay anharmonicity limits its effectiveness to two-phonon processes, thus allowing proper predictions of the phonon lifetimes by using the lowest-order diagrams. Finally, α-N 2 is compared to α-CO, and the role played by the translation-rotation coupling is discussed.

Lattice dynamics of the orthorhombic phase of KClO4: Ewald's method in molecular coordinates

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 KClO 4 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.

Conformational Landscape of N-Glycosylated Peptides Detecting Autoantibodies in Multiple Sclerosis, Revealed by Hamiltonian Replica Exchange

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.

Serial Generalized Ensemble Simulations of Biomolecules with Self-Consistent Determination of Weights.

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.2010, 6, 1935-1950). 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.2010, 31, 1106-1116), with several variants of the BAR-SGE technique. An illustration of the specific BAR-SGE algorithms implemented in the ORAC program is also provided.

PHONON RELAXATION PROCESSES IN CRYSTALS (NANO3) AT HIGH PRESSURE AND LOW TEMPERATURE

NaNO3 is investigated in a diamond anvil cell in the pressure range of 0–9 GPa at 21 and 142 K by means of high‐resolution Raman spectroscopy (HRRS). The pressure dependent linewidth of ν1 (symmetric stretch) is determined and discussed in the framework of anharmonic lattice dynamics. The main relaxation pathways are depopulation processes which are influenced by anharmonic terms in the expansion of the crystal potential and by multiphonon densities of states. The interpretation is supported by numerical calculation of multiphonon densities of states.

Luminescence spectra of matrix isolated N2 at high pressure and low temperature

N2 molecules with a concentration of ca. 1% were isolated in Xe, Kr, and Ar. X-ray stimulated luminescence (A 3Σu+→X 1Σg+) was investigated as a function of pressure (<30 GPa), temperature (300 K and 77 K), and matrix material. Observed UV transitions were interpreted as rovibronic transitions of the impurity molecule along with phonon sidebands as lattice excitations. Spectra were analyzed due to band maxima of vibron progressions, bandwidth, and bandshape, Franck–Condon profiles, and molecule constants, each as a function of pressure. The main result was a shift of band maxima with pressure to lower energies at a rate of 100 cm−1/GPa in Xe, 50 cm−1/GPa in Kr, and 10 cm−1/GPa in Ar. We modeled and explained these pressure-induced shifts of electronic bands by two mechanisms: a dielectric effect and a volume effect.