1,564 research outputs found
Quantum nuclear densities from semiclassical on-the-fly molecular dynamics
No full textSemiclassical molecular dynamics is a rigorous approximation to quantum dynamics obtained from the exact quantum propagator expressed as Feynman’s path integral.[1] Recently, our group has introduced the Multiple Coherent Semiclassical Initial Value Representation (MC SCIVR) technique to reduce the number of classical trajectories required to converge vibrational spectra calculations from thousands to just a handful.[2-4] MC SCIVR has been applied successfully to several medium and large-size molecular systems,[4-10] including fluxional and condensed phase ones.[11-13] In addition to the accurate anharmonic vibrational eigenvalue calculations, MC SCIVR yields vibrational eigenfunctions for both the ground and excited vibrational states.[14] In this talk, I will survey how we obtain the quantum anharmonic vibrational eigenfunctions from ab-initio on-the-fly trajectory simulations and how we extract the quantum nuclear densities and the geometry parameters probability distributions.[15,16] This information allows us to assign each peak in vibrational spectra, going beyond the usual harmonic normal-mode analysis. Our technique quantitatively determines how normal modes involving different functional groups cooperate to originate the spectroscopic
signal. Furthermore, it allows for the visualization of the nuclear vibrations in a purely quantum picture, letting us both directly observe and quantify the effects of the full potential energy surface anharmonicity on the molecular structure. In particular, I will illustrate applications to the protonated glycine to reveal quantum mechanical and anharmonic vibrational features. The method will allow for a better rationalization of experimental spectroscopy.
[1] W.H. Miller, J. Phys. Chem. A 2001, 105, 2942.
[2] M. Ceotto, S. Atahan, S. Shim, G.F. Tantardini, A. Aspuru-Guzik, Phys. Chem. Chem. Phys. 2009, 11, 3861.
[3] M. Ceotto, S. Atahan, G.F. Tantardini, A. Aspuru-Guzik J. Chem. Phys. 2009, 130, 234113.
[4] R. Conte, M. Ceotto, In Quantum Chemistry and Dynamics of Excited States: Methods and Applications (eds L. González and R. Lindh) 2020.
[5] M. Ceotto, G. Di Liberto, R. Conte, Phys. Rev. Lett. 2017, 119, 010401.
[6] F. Gabas, R. Conte, M. Ceotto, J. Chem. Theory Comput. 2017, 13, 2378.
[7] G. Di Liberto, R. Conte, M. Ceotto, J. Chem. Phys. 2018, 148, 014307.
[8] F. Gabas, G. Di Liberto, R. Conte, M. Ceotto, Chem. Sci. 2018, 9, 7894.
[9] F. Gabas, G. Di Liberto, M. Ceotto, J. Chem. Phys. 2019, 150, 224107.
[10] F. Gabas, R. Conte, M. Ceotto, J. Chem. Theory Comput. 2020, 16, 3476.
[11] G. Bertaina, G. Di Liberto, M. Ceotto, J. Chem. Phys. 2019, 151, 114307.
[12] A. Rognoni, R. Conte, M. Ceotto, Chem. Sci., 2021, 12, 2060.
[13] M. Cazzaniga, M. Micciarelli, F. Moriggi, A. Mahmoud, F. Gabas, and M. Ceotto, J. Chem. Phys. 2020, 152, 104104.
[14] M. Micciarelli, R. Conte, J. Suarez, M. Ceotto, J. Chem. Phys. 2018 149, 064115.
[15] C. Aieta, M. Micciarelli, G. Bertaina, M. Ceotto, Nat. Commun 2020, 11, 1.
[16] C. Aieta, M. Micciarelli, G. Bertaina, M. Ceotto, J. Chem. Phys., 2020, 153, 214117
Quantum nuclear densities from semiclassical on-the-fly molecular dynamics
No full textSemiclassical molecular dynamics is a rigorous approximation to quantum dynamics obtained from the exact quantum propagator expressed as Feynman’s path integral.[1] Recently, our group has introduced the Multiple Coherent Semiclassical Initial Value Representation (MC SCIVR) technique to reduce the number of classical trajectories required to converge vibrational spectra calculations from thousands to just a handful.[2-4] MC SCIVR has been applied successfully to several medium- and large-size molecular systems,[4-10] including fluxional and condensed phase ones.[11-13] In addition to the accurate anharmonic vibrational eigenvalue calculations, MC SCIVR yields vibrational eigenfunctions for both the ground and excited vibrational states.[14] In this talk, I will survey how we obtain the quantum anharmonic vibrational eigenfunctions from ab-initio on-the-fly trajectory simulations and how we extract the quantum nuclear densities and the geometry parameters probability distributions.[15,16] This information allows us to assign each peak in vibrational spectra, going beyond the usual harmonic normal-mode analysis. Our technique quantitatively determines how normal modes involving different functional groups cooperate to originate the spectroscopic signal. Furthermore, it allows for the visualization of the nuclear vibrations in a purely quantum picture, letting us both directly observe and quantify the effects of the full potential energy surface anharmonicity on the molecular structure. In particular, I will illustrate applications to the protonated glycine to reveal quantum mechanical and anharmonic vibrational features. The method will allow for a better rationalization of experimental spectroscopy.
[1] W.H. Miller, J. Phys. Chem. A 2001, 105, 2942.
[2] M. Ceotto, S. Atahan, S. Shim, G.F. Tantardini, A. Aspuru-Guzik, Phys. Chem. Chem. Phys. 2009, 11, 3861.
[3] M. Ceotto, S. Atahan, G.F. Tantardini, A. Aspuru-Guzik J. Chem. Phys. 2009, 130, 234113.
[4] R. Conte, M. Ceotto, In Quantum Chemistry and Dynamics of Excited States: Methods and Applications (eds L. González and R. Lindh) 2020.
[5] M. Ceotto, G. Di Liberto, R. Conte, Phys. Rev. Lett. 2017, 119, 010401.
[6] F. Gabas, R. Conte, M. Ceotto, J. Chem. Theory Comput. 2017, 13, 2378.
[7] G. Di Liberto, R. Conte, M. Ceotto, J. Chem. Phys. 2018, 148, 014307.
[8] F. Gabas, G. Di Liberto, R. Conte, M. Ceotto, Chem. Sci. 2018, 9, 7894.
[9] F. Gabas, G. Di Liberto, M. Ceotto, J. Chem. Phys. 2019, 150, 224107.
[10] F. Gabas, R. Conte, M. Ceotto, J. Chem. Theory Comput. 2020, 16, 3476.
[11] G. Bertaina, G. Di Liberto, M. Ceotto, J. Chem. Phys. 2019, 151, 114307.
[12] A. Rognoni, R. Conte, M. Ceotto, Chem. Sci., 2021, 12, 2060.
[13] M. Cazzaniga, M. Micciarelli, F. Moriggi, A. Mahmoud, F. Gabas, and M. Ceotto, J. Chem. Phys. 2020, 152, 104104.
[14] M. Micciarelli, R. Conte, J. Suarez, M. Ceotto, J. Chem. Phys. 2018 149, 064115.
[15] C. Aieta, M. Micciarelli, G. Bertaina, M. Ceotto, Nat. Commun 2020, 11, 1.
[16] C. Aieta, M. Micciarelli, G. Bertaina, M. Ceotto, J. Chem. Phys., 2020, 153, 214117
Quantum nuclear densities from semiclassical on-the-fly molecular dynamics
No full textSemiclassical molecular dynamics is a rigorous approximation to quantum dynamics obtained from the exact quantum propagator expressed as Feynman’s path integral.[1] Recently, our group has introduced the Multiple Coherent Semiclassical Initial Value Representation (MC SCIVR) technique to reduce the number of classical trajectories required to converge vibrational spectra calculations from thousands to just a handful.[2-4] MC SCIVR has been applied successfully to several medium-and large-size molecular systems,[4-10] including fluxional and condensed phase ones.[11-13] In addition to the accurate anharmonic vibrational eigenvalue calculations, MC SCIVR yields vibrational eigenfunctions for both the ground and excited vibrational states.[14] In this work, we obtain the quantum anharmonic vibrational eigenfunctions from ab-initio on-the-fly trajectory simulations, and we extract the quantum nuclear densities and the geometry parameters probability distributions.[15,16] This information allows us to assign each peak in vibrational spectra, going beyond the usual harmonic normal-mode analysis. Our technique quantitatively determines how normal modes involving different functional groups cooperate to originate the spectroscopic signal. Furthermore, it allows for the visualization of the nuclear vibrations in a purely quantum picture, letting us directly observe and quantify the effects of the full potential energy surface anharmonicity on the molecular structure. In particular, for the protonated glycine molecule, our calculations reveal quantum mechanical and anharmonic vibrational features. The method will allow for a better rationalization of experimental spectroscopy.
References
[1]W. Miller, J. Phys. Chem. A, 105, 2942-2955 (2001)
[2]M. Ceotto, S. Atahan, S. Shim, G. Tantardini, A. Aspuru-Guzik, Phys. Chem. Chem. Phys., 11, 3861 (2009)
[3]M. Ceotto, S. Atahan, G. Tantardini, A. Aspuru-Guzik, The Journal of Chemical Physics, 130, 234113 (2009)
[4]R. Conte, M. Ceotto, Semiclassical Molecular Dynamics for Spectroscopic Calculations, 2020
[5]M. Ceotto, G. Di Liberto, R. Conte, Phys. Rev. Lett., 119, 010401 (2017)
[6]F. Gabas, R. Conte, M. Ceotto, J. Chem. Theory Comput., 13, 2378-2388 (2017)
[7]G. Di Liberto, R. Conte, M. Ceotto, The Journal of Chemical Physics, 148, 014307 (2018)
[8]F. Gabas, G. Di Liberto, R. Conte, M. Ceotto, Chem. Sci., 9, 7894-7901 (2018)
[9]F. Gabas, G. Di Liberto, M. Ceotto, J. Chem. Phys., 150, 224107 (2019)
[10]F. Gabas, R. Conte, M. Ceotto, J. Chem. Theory Comput., 16, 3476-3485 (2020)
[11]G. Bertaina, G. Di Liberto, M. Ceotto, J. Chem. Phys., 151, 114307 (2019)
[12]A. Rognoni, R. Conte, M. Ceotto, Chem. Sci., 12, 2060-2064 (2021)
[13]M. Cazzaniga, M. Micciarelli, F. Moriggi, A. Mahmoud, F. Gabas, M. Ceotto, J. Chem. Phys., 152, 104104 (2020)
[14]M. Micciarelli, R. Conte, J. Suarez, M. Ceotto, The Journal of Chemical Physics, 149, 064115 (2018)
[15]C. Aieta, M. Micciarelli, G. Bertaina, M. Ceotto, Nat. Commun., 11, 4348 (2020)
[16]C. Aieta, G. Bertaina, M. Micciarelli, M. Ceotto, J. Chem. Phys., 153, 214117 (2020
Linear Response of One-Dimensional Liquid 4He to External Perturbations
No full textWe study the response of one-dimensional liquid (Formula presented.) to weak perturbations relying on the dynamical structure factor, (Formula presented.), recently obtained via ab-initio techniques (Bertaina et al. in Phys Rev Lett 116:135302, 2016). We evaluate the drag force, (Formula presented.), experienced by an impurity moving along the system with velocity v and the static response function, (Formula presented.), describing the density modulations induced by a periodic perturbation with wave vector q
Impact of HCMV infection on NK cell development and function after HSCT
No full textNatural Killer (NK) cell function is regulated by an array of inhibitory and activating surface receptors that during NK cell differentiation, at variance with T and B cells, do not require genetic rearrangement. Importantly, NK cells are the first lymphocyte population recovering after hematopoietic stem cell transplantation (HSCT). Thus, their role in early immunity after HSCT is considered crucial, as they can importantly contribute to protect the host from tumor recurrence and viral infections before T-cell immunity is fully recovered. In order to acquire effector functions and regulatory receptors, NK cell precursors undergo a maturation process that can be analyzed during immune reconstitution after HSCT. In this context, the occurrence of human cytomegalovirus (HCMV) infection/reactivation was shown to accelerate NK cell maturation by promoting the differentiation of high frequencies of NK cells characterized by a KIR+NKG2A- and NKG2C+ mature phenotype. Thus, it appears that the development of NK cells and the distribution of NK cell receptors can be deeply influenced by HCMV infection. Moreover, in HCMV-infected subjects the emergence of so called "memory-like" or "long-lived" NK cells has been documented. These cells could play an important role in protecting from infections and maybe from relapse in patients transplanted for leukemia. All the aspects regarding the influence of HCMV infection on NK cell development will be discussed. © 2013 Della Chiesa, Falco, Muccio, Bertaina, Locatelli and Moretta
Dynamical correlations in one-dimensional 4He beyond Luttinger theory
No full textWe study a collection of He atoms confined to strictly one dimension at zero temperature. We use the exact Path Integral Ground State method to evaluate the equation of state and the radial distribution function, and we find that the system behaves as a Luttinger liquid with parameter that takes all the possible values , depending on the density , being the He mass and the sound velocity\cite{uno}. Actually the system goes from in the high density quasi--solid regime to close to the low density spinodal decomposition. By inverting the imaginary--time intermediate scattering function with the Genetic Inversion via Falsification of Theories method\cite{due}, we also evaluate the dynamical structure factor in the whole range in , exploring the behavior of the dynamical correlations beyond the limits of applicability of Luttinger liquid theory. We find that the famous phonon--maxon--roton excitation spectrum of He is not present in 1D. On the contrary, manifests a particle--hole continuum typical of a fermionic system, as expected from the Bose-Fermi mapping valid for 1D hard-core interactions. In qualitative agreement with recent non--linear Luttinger liquid theories, we find that the main weight of density fluctuations continuously shifts from the lower threshold branch in the quasi--solid regime, to the upper Bogoliubov branch in the compressible low--density regime. At an intermediate density near \AA, the system corresponds to and maps to a non interacting Fermi gas at very low energies , while at higher energies display non--universal effects depending on the He interaction potential
Microscopic Study of Static and Dynamical Properties of Dilute One-Dimensional Soft Bosons
No full textWe study static properties and the dynamical structure factor of zero-temperature dilute bosons interacting via a soft-shoulder potential in one dimension. Our approach is fully microscopic and employs state-of-the-art quantum Monte Carlo and analytic continuation techniques. By increasing the interaction strength, our model reproduces the Lieb–Liniger gas, the Tonks–Girardeau and the hard-rods models
Itinerant ferromagnetism of a repulsive atomic fermi gas : a quantum monte Carlo Study
No full textWe investigate the phase diagram of a two-component repulsive Fermi gas at T=0 by means of quantum Monte Carlo simulations. Both purely repulsive and resonant attractive model potentials are considered in order to analyze the limits of the universal regime where the details of interatomic forces can be neglected. The equation of state of both balanced and unbalanced systems is calculated as a function of the interaction strength and the critical density for the onset of ferromagnetism is determined. The energy of the strongly polarized gas is calculated and parametrized in terms of the physical properties of repulsive polarons, which are relevant for the stability of the fully ferromagnetic state. Finally, we analyze the phase diagram in the interaction-polarization plane under the assumption that only phases with homogeneous magnetization can be produced
Detection of ultra-high energy cosmic ray showers with a single-pixel fluorescence telescope
No full textAbstract not available.T. Fujii, M. Malacari, M. Bertaina, M. Casolino, B. Dawson, P. Horvath, M. Hrabovsky, J. Jiang, D. Mandat, A. Matalon, J.N. Matthews, P. Motloch, M. Palatka, M. Pech, P. Privitera, P. Schovanek, Y. Takizawa, S.B.Thomas, P. Travnicek, K. Yamaza
Representing molecular ground and excited vibrational eigenstates with nuclear densities obtained from semiclassical initial value representation molecular dynamics
No full textWe present in detail and validate an effective Monte Carlo approach for the calculation of the nuclear vibrational densities via integration of molecular eigenfunctions that we have preliminary employed to calculate the densities of the ground and the excited OH stretch vibrational states in the protonated glycine molecule [Aieta et al., Nat Commun 11, 4348 (2020)]. Here, we first validate and discuss in detail the features of the method on a benchmark water molecule. Then, we apply it to calculate on-The-fly the ab initio anharmonic nuclear densities in the correspondence of the fundamental transitions of NH and CH stretches in protonated glycine. We show how we can gain both qualitative and quantitative physical insight by inspection of different one-nucleus densities and assign a character to spectroscopic absorption peaks using the expansion of vibrational states in terms of harmonic basis functions. The visualization of the nuclear vibrations in a purely quantum picture allows us to observe and quantify the effects of anharmonicity on the molecular structure, also to exploit the effect of IR excitations on specific bonds or functional groups, beyond the harmonic approximation. We also calculate the quantum probability distribution of bond lengths, angles, and dihedrals of the molecule. Notably, we observe how in the case of one type of fundamental NH stretching, the typical harmonic nodal pattern is absent in the anharmonic distribution
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