Molecular dynamics and control following excitation with an ultra-short intense laser pulse

Vibronic excitations of the tri-atomic molecule OClO (A(2)A(2)(nu(1), nu(2), nu(3)) <-- (XB1)-B-2 (0, 0, 0)) with weak and strong ultra-short laser fields are studied within full quantum wavepacket dynamics in hyperspherical coordinates. Different dynamics is observed following excitation with laser pulses of different intensities. With a strong laser pulse, many vibrational states are excited and a spatially more localised wavepacket arises. The numerical results show that the population of different vibrational states of the wavepacket on the excited potential energy surface is altered by the intensity of the laser pulse. The numerical results also suggest a related effect on the phase of the wavepacket. These interesting phenomena can be understood by an analysis of the corresponding results for two model diatomic molecules. The possible physical mechanisms of control of chemical processes using strong laser fields are discussed. (C) 2004 Elsevier B.V. All rights reserved.

Iterative Linearized Density Matrix Propagation for Modeling Coherent Energy Transfer in Photosynthetic Light Harvesting

We present results of calculations [1] that employ a new mixed quantum classical iterative density matrix propagation approach (ILDM , or so called Is‐Landmap) [2] to explore the survival of coherence in different photo synthetic models. Our model studies confirm the long lived quantum coherence , while conventional theoretical tools (such as Redfield equation) fail to describe these phenomenon [3,4]. Our ILDM method is a numerical exactly propagation scheme and can be served as a bench mark calculation tools[2]. Result get from ILDM and from other recent methods have been compared and show agreement with each other[4,5]. Long lived coherence plateau has been attribute to the shift of harmonic potential due to the system bath interaction, and the harvesting efficiency is a balance between the coherence and dissipation[1]. We use this approach to investigate the excitation energy transfer dynamics in various light harvesting complex include Fenna‐Matthews‐Olsen light harvesting complex[1] and Cryptophyte Phycocyanin 645 [6]. [1] P.Huo and D.F.Coker ,J. Chem. Phys. 133, 184108 (2010) . [2] E.R. Dunkel, S. Bonella, and D.F. Coker, J. Chem. Phys. 129, 114106 (2008). [3] A. Ishizaki and G.R. Fleming, J. Chem. Phys. 130, 234111 (2009). [4] A. Ishizaki and G.R. Fleming, Proc. Natl. Acad. Sci. 106, 17255 (2009). [5] G. Tao and W.H. Miller, J. Phys. Chem. Lett. 1, 891 (2010). [6] P.Huo and D.F.Coker in preparation

Analog of Rabi oscillations in resonant electron-ion systems

Quantum coherence between electron and ion dynamics, observed in organic semiconductors by means of ultrafast spectroscopy, is the object of recent theoretical and computational studies. To simulate this kind of quantum coherent dynamics, we have introduced in a previous article [L. Stella, M. Meister, A. J. Fisher, and A. P. Horsfield, J. Chem. Phys. 127, 214104 (2007)] an improved computational scheme based on Correlated Electron-Ion Dynamics (CEID). In this article, we provide a generalization of that scheme to model several ionic degrees of freedom and many-body electronic states. To illustrate the capability of this extended CEID, we study a model system which displays the electron-ion analog of the Rabi oscillations. Finally, we discuss convergence and scaling properties of the extended CEID along with its applicability to more realistic problems. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3589165]

On transition rates in surface hopping

Trajectory surface hopping (TSH) is one of the most widely used quantum-classical algorithms for nonadiabatic molecular dynamics. Despite its empirical effectiveness and popularity, a rigorous derivation of TSH as the classical limit of a combined quantum electron-nuclear dynamics is still missing. In this work, we aim to elucidate the theoretical basis for the widely used hopping rules. Naturally, we concentrate thereby on the formal aspects of the TSH. Using a Gaussian wave packet limit, we derive the transition rates governing the hopping process at a simple avoided level crossing. In this derivation, which gives insight into the physics underlying the hopping process, some essential features of the standard TSH algorithm are retrieved, namely (i) non-zero electronic transition rate ("hopping probability") at avoided crossings; (ii) rescaling of the nuclear velocities to conserve total energy; (iii) electronic transition rates linear in the nonadiabatic coupling vectors. The well-known Landau-Zener model is then used for illustration. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4770280]

CO migration in native and mutant myoglobin: atomistic simulations for the understanding of protein function

Molecular dynamics simulations of the events after the photodissociation of CO in the myoglobin mutant L29F in which leucine is replaced by phenylalanine are reported. Using both classical and mixed quantum-classical molecular dynamics calculations, we observed the rapid motion of CO away from the distal heme pocket to other regions of the protein, in agreement with recent experimental results. The experimentally observed and calculated infrared spectra of CO after dissociation are also in good agreement. We compared the results with data from simulations of WT myoglobin. As the time resolution of experimental techniques is increased, theoretical methods and models can be validated at the atomic scale by direct comparison with experiment.

Fluctuations of doublet splittings using the annular billiard

We study the statistical distribution of quantum energy splittings due to a dynamical tunneling. The system. The annular billiard, has whispering quasimodes due to a discrete symmetry that exists even when chaos is present in the underlying classical dynamics. Symmetric and antisymmetric combinations of these quasimodes correspond to quantum doublet states whose degeneracies decrease as the circles become more eccentric. We construct numerical ensembles composed of splittings for two distinct regimes, one which we call semiclassical for high quantum numbers and high energies where the whispering regions are connected by chaos, and other which we call quantal for low quantum numbers, low energies, and near integrable where dynamical tunneling is not a dominant mechanism. In both cases we observe a variation on the fluctuation amplitudes, but their mean behaviors follow the formula of Leyvraz and Ullmo [J. Phys. A 29, 2529 (1996)]. A description of a three-level collision involving a doublet and a singlet is also provided through a numerical example.

Capacitive DNA detection driven by electronic charge fluctuations in a graphene nanopore

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The Role of Molecular Conformation and Polarizable Embedding for One- and Two-Photon Absorption of Disperse Orange 3 in Solution

Solvent effects on the one- and two-photon absorption (IPA and 2PA) of disperse orange 3 (DO3) in dimethyl sulfoxide (DMSO) are studied using a discrete polarizable embedding (PE) response theory. The scheme comprises a quantum region containing the chromophore and an atomically granulated classical region for the solvent accounting for full interactions within and between the two regions. Either classical molecular dynamics (MD) or hybrid Car-Parrinello (CP) quantum/classical (QM/MM) molecular dynamics simulations are employed to describe the solvation of DO3 in DMSO, allowing for an analysis of the effect of the intermolecular short-range repulsion, long-range attraction, and electrostatic interactions on the conformational changes of the chromophore and also the effect of the solute-solvent polarization. PE linear response calculations are performed to verify the character, solvatochromic shift, and overlap of the two lowest energy transitions responsible for the linear absorption spectrum of DO3 in DMSO in the visible spectral region. Results of the PE linear and quadratic response calculations, performed using uncorrelated solute-solvent configurations sampled from either the classical or hybrid CP QM/MM MD simulations, are used to estimate the width of the line shape function of the two electronic lowest energy excited states, which allow a prediction of the 2PA cross-sections without the use of empirical parameters. Appropriate exchange-correlation functionals have been employed in order to describe the charge-transfer process following the electronic transitions of the chromophore in solution.

Simulations of charge transport in organic compounds

To aid the design of organic semiconductors, we study the charge transport properties of organic liquid crystals, i.e. hexabenzocoronene and carbazole macrocycle, and single crystals, i.e. rubrene, indolocarbazole and benzothiophene derivatives (BTBT, BBBT). The aim is to find structure-property relationships linking the chemical structure as well as the morphology with the bulk charge carrier mobility of the compounds. To this end, molecular dynamics (MD) simulations are performed yielding realistic equilibrated morphologies. Partial charges and molecular orbitals are calculated based on single molecules in vacuum using quantum chemical methods. The molecular orbitals are then mapped onto the molecular positions and orientations, which allows calculation of the transfer integrals between nearest neighbors using the molecular orbital overlap method. Thus we obtain realistic transfer integral distributions and their autocorrelations. In case of organic crystals the differences between two descriptions of charge transport, namely semi-classical dynamics (SCD) in the small polaron limit and kinetic Monte Carlo (KMC) based on Marcus rates, are studied. The liquid crystals are investigated solely in the hopping limit. To simulate the charge dynamics using KMC, the centers of mass of the molecules are mapped onto lattice sites and the transfer integrals are used to compute the hopping rates. In the small polaron limit, where the electronic wave function is spread over a limited number of neighboring molecules, the Schroedinger equation is solved numerically using a semi-classical approach. The results are compared for the different compounds and methods and, where available, with experimental data. The carbazole macrocycles form columnar structures arranged on a hexagonal lattice with side chains facing inwards, so columns can closely approach each other allowing inter-columnar and thus three-dimensional transport. When taking only intra-columnar transport into account, the mobility is orders of magnitude lower than in the three-dimensional case. BTBT is a promising material for solution-processed organic field-effect transistors. We are able to show that, on the time-scales of charge transport, static disorder due to slow side chain motions is the main factor determining the mobility. The resulting broad transfer integral distributions modify the connectivity of the system but sufficiently many fast percolation paths remain for the charges. Rubrene, indolocarbazole and BBBT are examples of crystals without significant static disorder. The high mobility of rubrene is explained by two main features: first, the shifted cofacial alignment of its molecules, and second, the high center of mass vibrational frequency. In comparsion to SCD, only KMC based on Marcus rates is capable of describing neighbors with low coupling and of taking static disorder into account three-dimensionally. Thus it is the method of choice for crystalline systems dominated by static disorder. However, it is inappropriate for the case of strong coupling and underestimates the mobility of well-ordered crystals. SCD, despite its one-dimensionality, is valuable for crystals with strong coupling and little disorder. It also allows correct treatment of dynamical effects, such as intermolecular vibrations of the molecules. Rate equations are incapable of this, because simulations are performed on static snapshots. We have thus shown strengths and weaknesses of two state of the art models used to study charge transport in organic compounds, partially developed a program to compute and visualize transfer integral distributions and other charge transport properties, and found structure-mobility relations for several promising organic semiconductors.

Quantum biology. Simulazioni di trasferimento di energia in una struttura dimerica

La quantum biology (QB) è un campo di ricerca emergente che cerca di affronta- re fenomeni quantistici non triviali all’interno dei contesti biologici dotandosi di dati sperimentali di esplorazioni teoriche e tecniche numeriche. I sistemi biologici sono per definizione sistemi aperti, caldi,umidi e rumorosi, e queste condizioni sono per loro imprenscindibili; si pensa sia un sistema soggetto ad una veloce decoerenza che sopprime ogni dinamica quantistica controllata. La QB, tramite i principi di noise assisted transport e di antenna fononica sostiene che la presenza di un adeguato livello di rumore ambientale aumenti l’efficienza di un network di trasporto,inoltre se all’interno dello spettro ambientale vi sono specifici modi vibrazionali persistenti si hanno effetti di risonanza che rigenerano la coerenza quantistica. L’interazione ambiente-sistema è di tipo non Markoviano,non perturbativo e di forte non equi- librio, ed il rumore non è trattato come tradizionale rumore bianco. La tecnica numerica che per prima ha predetto la rigenerazione della coerenza all’interno di questi network proteici è stato il TEBD, Time Evolving Block Decimation, uno schema numerico che permette di simulare sistemi 1-D a molti corpi, caratterizzati da interazioni di primi vicini e leggermente entangled. Tramite gli algoritmi numerici di Orthopol l’hamiltoniana spin-bosone viene proiettata su una catena discreta 1-D, tenendo conto degli effetti di interazione ambiente-sistema contenuti nello spettro(il quale determina la dinamica del sistema).Infine si esegue l’evoluzione dello stato.

Quantifying the complexity of chaos in multibasin multidimensional dynamics of molecular systems

The simulated classical dynamics of a small molecule exhibiting self-organizing behavior via a fast transition between two states is analyzed by calculation of the statistical complexity of the system. It is shown that the complexity of molecular descriptors such as atom coordinates and dihedral angles have different values before and after the transition. This provides a new tool to identify metastable states during molecular self-organization. The highly concerted collective motion of the molecule is revealed. Low-dimensional subspaces dynamics is found sensitive to the processes in the whole, high-dimensional phase space of the system. © 2004 Wiley Periodicals, Inc.

Macroscopic Quantum Resonators (MAQRO): 2015 update

Do the laws of quantum physics still hold for macroscopic objects - this is at the heart of Schrödinger’s cat paradox - or do gravitation or yet unknown effects set a limit for massive particles? What is the fundamental relation between quantum physics and gravity? Ground-based experiments addressing these questions may soon face limitations due to limited free-fall times and the quality of vacuum and microgravity. The proposed mission Macroscopic Quantum Resonators (MAQRO) may overcome these limitations and allow addressing such fundamental questions. MAQRO harnesses recent developments in quantum optomechanics, high-mass matter-wave interferometry as well as state-of-the-art space technology to push macroscopic quantum experiments towards their ultimate performance limits and to open new horizons for applying quantum technology in space. The main scientific goal is to probe the vastly unexplored ‘quantum-classical’ transition for increasingly massive objects, testing the predictions of quantum theory for objects in a size and mass regime unachievable in ground-based experiments. The hardware will largely be based on available space technology. Here, we present the MAQRO proposal submitted in response to the 4th Cosmic Vision call for a medium-sized mission (M4) in 2014 of the European Space Agency (ESA) with a possible launch in 2025, and we review the progress with respect to the original MAQRO proposal for the 3rd Cosmic Vision call for a medium-sized mission (M3) in 2010. In particular, the updated proposal overcomes several critical issues of the original proposal by relying on established experimental techniques from high-mass matter-wave interferometry and by introducing novel ideas for particle loading and manipulation. Moreover, the mission design was improved to better fulfill the stringent environmental requirements for macroscopic quantum experiments.

Pion Production in Heavy-ion Collisions in the 1 A GeV region

Within the framework of the improved isospin dependent quantum molecular dynamics (ImIQMD) model, the pion emission in heavy-ion collisions in the region 1AGeV is investigated systematically, in which the pion is considered to be mainly produced by the decay of resonances ∆(1232) and N∗(1440). The in-medium dependence and Coulomb effects of the pion production are included in the calculation. Total pion multiplicity and π−/π+ yields are calculated for the reaction 197Au+197Au in central collisions for selected Skyrme parameters SkP, SLy6,Ska, SIII and compared them with the measured data by the FOPI collaboration.