Angela Acocella

What Is Adenine Doing in Photolyase

The short answer to the title question is that it acts as an electrostatic bouncer that shoves the charge flow from flavin toward the DNA lesion that photolyase repairs. This explanation is provided by an explicit time-dependent quantum mechanical approach, which is used to investigate the electron transfer process that triggers the repair mechanism. The transfer occurs from the flavin photolyase cofactor to the cyclobutane ring of DNA, previously formed by light-induced cycloaddition of adjacent pyrimidine bases. The electron wave function dynamics accurately accounts for the previously proposed mechanism of transfer via the terminal methyl group of the flavin moiety present in the catalytic electron-donor cofactor, FADH(-), which also contains adenine. This latter moiety, which has often been assumed to be present mainly for structural reasons, instantaneously modifies the interaction between acceptor and donor by a variation of the electrostatic interactions so that the presence of its local atomic charges is necessary to trigger the transfer. In principle, knowledge of the details of the electron transfer dynamics and of the important role of polarization effects can be exploited to improve the efficiency of the repair mechanism in artificial systems.

On-the-Fly, Electric-Field-Driven, Coupled Electron-Nuclear Dynamics

An on-the-fly, electric field driven, coupled electron-nuclear dynamics approach is developed and applied to model the photodissociation of water in the A((1)B1) excited state. In this method, a quantum propagator evolves the photon-induced electronic dynamics in the ultrafast time scale, and a quasi-classical surface hopping approach describes the nuclear dynamics in the slower time scale. In addition, strong system-field interactions are explicitly included in the electronic propagator. This theoretical development enables us to study rapid photon-induced bond dissociation dynamics and demonstrates the partial breakdown of electronic coherence as well as electronic population trapping in the excited state when the molecular vibrations detune the system with respect to the applied field. The method offers a practical way to use on-the-fly dynamics for modeling light-molecule interactions that lead to interesting photochemical events.

Excitation Energy Transfer and Low-Efficiency Photolytic Splitting of Water Ice by Vacuum UV Light

Experimental estimates of photolytic efficiency (yield per photon) for photodissociation and photodesorption from water ice range from about 10(-3) to 10(-1). However, in the case of photodissociation of water in the gas phase, it is close to unity. Exciton dynamics carried out by a quantum mechanical time-dependent propagator shows that in the eight most stable water hexamers, the excitation diffuses away from the initially excited molecule within a few femtoseconds. On the basis of these quantum dynamics simulations, it is hypothesized that the ultrafast exciton energy transfer process, which in general gives rise to a delocalized exciton within these clusters, may contribute to the low efficiency of photolytic processes in water ice. It is proposed that exciton diffusion inherently competes with the nuclear dynamics that drives the photodissociation process in the repulsive S1 state on the sub-10 fs time scale.

Quantum Study of Laser-Induced Initial Activation of Graphite-to-Diamond Conversion

Recently (Science 2009, 325, 181), femtosecond-resolved electron energy loss spectroscopy (FEELS) was used to map the structural changes of graphite upon laser irradiation, revealing the change from sp(2) to sp(3), i.e., diamond-like, hybridization. With a laser excitation energy of 2.39 eV and a fluence of 1.5 mJ/cm(2), the most pronounced changes were observed in approximately 180 fs, a time similar to the temporal resolution of the technique. The presence of the laser field turns the electronic wavefunction into a wavepacket whose quantum dynamics governs the onset of the structural rearrangement. Density functional theory calculations with a quantum propagator that include the laser field show that the charge density of graphite expands between the layers in an ultrafast process of the order of approximately 10 fs. Calculations as a function of the field/fluence further show different values of the maximum bond order reached at the stationary state. The experimentally used value is at the crossover between two regimes. It is tempting to associate the second regime with the electron organization necessary to achieve ablation or melting. The application of the model demonstrates its potential for examining the dynamical nature of the charge density and chemical bonding as it forms.

GPU-accelerated computation of electron transfer

Electron transfer is a fundamental process that can be studied with the help of computer simulation. The underlying quantum mechanical description renders the problem a computationally intensive application. In this study, we probe the graphics processing unit (GPU) for suitability to this type of problem. Time‐critical components are identified via profiling of an existing implementation and several different variants are tested involving the GPU at increasing levels of abstraction. A publicly available library supporting basic linear algebra operations on the GPU turns out to accelerate the computation approximately 50‐fold with minor dependence on actual problem size. The performance gain does not compromise numerical accuracy and is of significant value for practical purposes.

Real-Time Observation of Phonon-Mediated σ-π Interband Scattering in MgB2

In systems having an anisotropic electronic structure, such as the layered materials graphite, graphene, and cuprates, impulsive light excitation can coherently stimulate specific bosonic modes, with exotic consequences for the emergent electronic properties. Here we show that the population of E_{2g} phonons in the multiband superconductor MgB_{2} can be selectively enhanced by femtosecond laser pulses, leading to a transient control of the number of carriers in the σ-electronic subsystem. The nonequilibrium evolution of the material optical constants is followed in the spectral region sensitive to both the a- and c-axis plasma frequencies and modeled theoretically, revealing the details of the σ-π interband scattering mechanism in MgB_{2}.

Time-dependent quantum simulation of coronene photoemission spectra

Photoelectron spectroscopy is usually described by a simple equation that relates the binding energy of the photoemitted electron, Ebinding, its kinetic energy, Ekinetic, the energy of the ionizing photon, Ephoton, and the work function of the spectrometer, ϕ, Ebinding = Ephoton - Ekinetic - ϕ. Behind this equation there is an extremely rich physics, which we describe here using as an example a relatively simple conjugated molecule, namely coronene. The theoretical analysis of valence band and C1s core level photoemission spectra showed that multiple excitations play an important role in determining the intensities of the final spectrum. An explicit, time-evolving model is applied, which is able to count all possible photo-excitations occurring during the photoemission process, showing that they evolve on a short time-scale, of about 10 fs. The method reveals itself to be a valid approach to reproduce photoemission spectra of polycyclic aromatic hydrocarbons (PAHs).

Structural determinants in the bulk heterojunction

Photovoltaics is one of the key areas in renewable energy research with remarkable progress made every year. Here we consider the case of a photoactive material and study its structural composition and the resulting consequences for the fundamental processes driving solar energy conversion. A multiscale approach is used to characterize essential molecular properties of the light-absorbing layer. A selection of bulk-representative pairs of donor/acceptor molecules is extracted from the molecular dynamics simulation of the bulk heterojunction and analyzed at increasing levels of detail. Significantly increased ground state energies together with an array of additional structural characteristics are identified that all point towards an auxiliary role of the materials structural organization in mediating charge-transfer and -separation. Mechanistic studies of the type presented here can provide important insights into fundamental principles governing solar energy conversion in next-generation photovoltaic devices.