616 research outputs found
Transforming growth factor beta-1 and interferon-alpha in the AIDS dementia complex (ADC): possible relationship with cerebral viral load?
No full textObservation of electromagnetically induced transparency (EIT) in Rb-filled hollow-core fibre
No full textAbstract not availableT.M. Stace, C. Perrella, P.S. Light, F. Benabid, A.N. Luite
Orthogonalizing the control of frequency combs for optical clockworks
No full textPublished 30 September 2021Abstract not availableNicolas Bourbeau Hebert, Sarah K. Scholten, Ashby P. Hilton, Rachel F. Offer, Christopher Perrella, and Andre N. Luite
Direct observation of the solvent organization and nuclear vibrations of [Ru(dcbpy)2(NCS)2]4-, [dcbpy = (4,4′-dicarboxy-2,2′-bipyridine)],: Via ab initio molecular dynamics
No full textEnvironmental effects can drastically influence the optical properties and photoreactivity of molecules, particularly in the presence of polar and/or protic solvents. In this work we investigate a negatively charged Ru(ii) complex, [Ru(dcbpy)2(NCS)2]4- [dcbpy = (4,4′-dicarboxy-2,2′-bipyridine)], in water solution, since this system belongs to a broader class of transition-metal compounds undergoing upon photo-excitation rapid and complex charge transfer (CT) dynamics, which can be dictated by structural rearrangement and solvent environment. Ab initio molecular dynamics (AIMD) relying on a hybrid quantum/molecular mechanics scheme is used to probe the equilibrium microsolvation around the metal complex in terms of radial distribution functions of the main solvation sites and solvent effects on the overall equilibrium structure. Then, using our AIMD-based generalized normal mode approach, we investigate how the ligand vibrational spectroscopic features are affected by water solvation, also contributing to the interpretation of experimental Infra-Red spectra. Two solvation sites are found for the ligands: the sulfur and the oxygen sites can interact on average with ∼4 and ∼3 water molecules, respectively, where a stronger interaction of the oxygen sites is highlighted. On average an overall dynamic distortion of the C2 symmetric gas-phase structure was found to be induced by water solvation. Vibrational analysis reproduced experimental values for ligand symmetric and asymmetric stretchings, linking the observed shifts with respect to the gas-phase to a complex solvent distribution around the system. This is the groundwork for future excited-state nuclear and electronic dynamics to monitor non-equilibrium processes of CT excitation in complex environments, such as exciton migration in photovoltaic technologies. This journal i
Second-Order Mass-Weighting Scheme for Atom-Centered Density Matrix Propagation Molecular Dynamics
No full textThe atom-centered density matrix propagation (ADMP) method is an extended Lagrangian approach to ab initio molecular dynamics, which includes the density matrix in an orthonormalized atom-centered Gaussian basis as additional, fictitious, electronic degrees of freedom, classically propagated along with the nuclear ones. A high adiabaticity between the nuclear and electronic subsystems is mandatory in order to keep the trajectory close to the Born-Oppenheimer (BO) surface. In this regard, the fictitious electronic mass μ, being a symmetric, nondiagonal matrix in its most general form, represents a free parameter, exploitable to optimize the propagation of the electronic density. Although mass-weighting schemes in ADMP exist, a systematic procedure to define an optimal value of the fictitious masses is not available yet. In this work, in order to rationally evaluate the electronic mass, fictitious electronic normal modes are defined through the diagonalization of the Hessian of the electronic density matrix. If the same frequency is imposed on all such modes (compatible with the chosen integration time step), then the corresponding μ matrix can be calculated and then employed for the following propagation. Analysis of several ADMP test simulations reveals that such Hessian-based mass-weighting approach is able to ensure, together with a 0.1/0.2 fs time steps, a high separation between the (real) nuclear and the (fictitious) electronic frequencies, which determines a high adiabaticity. This high, unprecedented, accuracy in the propagation leads, in turn, to low errors in the estimated nuclear vibrational frequencies, making the ADMP method totally comparable to a fully converged BO molecular dynamics simulation but more computationally efficient. This work, therefore, contributes to a further development of the ADMP ab initio molecular dynamics method, aimed at improving its accuracy through a more rational evaluation of the fictitious electronic mass parameter
Interferometric selection of frequency comb modes
No full textPublished online: 23 May 2013We demonstrate a scheme to split an optical frequency comb into four separate frequency combs, each with four times the repetition rate of the original, but which are offset in frequency from each other. These spectrally rarified “daughter” combs are generated using fibre interferometers that are actively stabilised. We describe how these “daughter” combs can be used to resolve ambiguities that occur when comparing an arbitrary frequency continuous-wave signal against an optical frequency comb.C. Perrella, P. S. Light, J. D. Anstie, F. N. Baynes, A. N. Luite
A Not Obvious Correlation Between the Structure of Green Fluorescent Protein Chromophore Pocket and Hydrogen Bond Dynamics: A Choreography From ab initio Molecular Dynamics
No full textThe Green Fluorescent Protein (GFP) is a widely studied chemical system both for its large amount of applications and the complexity of the excited state proton transfer responsible of the change in the protonation state of the chromophore. A detailed investigation on the structure of the chromophore environment and the influence of chromophore form (either neutral or anionic) on it is of crucial importance to understand how these factors could potentially influence the protein function. In this study, we perform a detailed computational investigation based on the analysis of ab-initio molecular dynamics simulations, to disentangle the main structural quantities determining the fine balance in the chromophore environment. We found that specific hydrogen bonds interactions directly involving the chromophore (or not), are correlated to quantities, such as the volume of the cavity in which the chromophore is embedded and that it is importantly affected by the chromophore protonation state. The cross-correlation analysis performed on some of these hydrogen bonds and the cavity volume, demonstrates a direct correlation among them and we also identified the ones specifically involved in this correlation. We also found that specific interactions among residues far in the space are correlated, demonstrating the complexity of the chromophore environment and that many structural quantities have to be taken into account to properly describe and understand the main factors tuning the active site of the protein. From an overall evaluation of the results obtained in this work, it is shown that the residues which a priori are perceived to be spectators play instead an important role in both influencing the chromophore environment (cavity volume) and its dynamics (cross-correlations among spatially distant residues)
Genome-Wide Identification of Histone Modification Gene Families in the Model Legume Medicago truncatula and Their Expression Analysis in Nodules
No full textHistone methylation and acetylation are key processes in the epigenetic regulation of plant growth, development, and responses to environmental stimuli. The genes encoding for the enzymes that are responsible for these chromatin post-translational modifications, referred to as histone modification genes (HMGs), have been poorly investigated in Leguminosae species, despite their importance for establishment and activity of nitrogen-fixing nodules. In silico analysis of Medicago truncatula HMGs identified 81 histone methyltransferases, 46 histone demethylases, 64 histone acetyltransferases, and 15 histone deacetylases. MtHMGs were analyzed for their structure and domain composition, and some combinations that were not yet reported in other plant species were identified. Genes have been retrieved from M. truncatula A17 and R108 genotypes as well as M. sativa CADL and Zhongmu No.1; the gene number and distribution were compared with Arabidopsis thaliana. Furthermore, by analyzing the expression data that were obtained at various developmental stages and in different zones of nitrogen-fixing nodules, we identified MtHMG loci that could be involved in nodule development and function. This work sets a reference for HMG genomic organization in legumes which will be useful for functional investigation that is aimed at elucidating HMGs involvement in nodule development and symbiotic nitrogen fixation
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