Modelling excitonic-energy transfer in light-harvesting complexes

The theoretical and experimental study of energy transfer in photosynthesis has revealed an interesting transport regime, which lies at the borderline between classical transport dynamics and quantum-mechanical interference effects. Dissipation is caused by the coupling of electronic degrees of freedom to vibrational modes and leads to a directional energy transfer from the antenna complex to the target reaction-center. The dissipative driving is robust and does not rely on fine-tuning of specific vibrational modes. For the parameter regime encountered in the biological systems new theoretical tools are required to directly compare theoretical results with experimental spectroscopy data. The calculations require to utilize massively parallel graphics processor units (GPUs) for efficient and exact computations.Comment: 20 pages, submitted to the AIP conference proceedings of the Latin American School of Physics Marcos Moshinsky (ELAF 2013

Capacity for Half-Duplex Line Networks with Two Sources

The focus is on noise-free half-duplex line networks with two sources where the first node and either the second node or the second-last node in the cascade act as sources. In both cases, we establish the capacity region of rates at which both sources can transmit independent information to a common sink. The achievability scheme presented for the first case is constructive while the achievability scheme for the second case is based on a random coding argument.Comment: Proceedings of the IEEE International Symposium on Information Theory, Austin, TX, USA, June 12 - 18, 201

Exact Stochastic Unraveling of an Optical Coherence Dynamics by Cumulant Expansion

A numerically exact Monte Carlo scheme for calculation of open quantum system dynamics is proposed and implemented. The method consists of a Monte-Carlo summation of a perturbation expansion in terms of trajectories in Liouville phase-space with respect to the coupling between the excited states of the molecule. The trajectories are weighted by a complex decoherence factor based on the second-order cumulant expansion of the environmental evolution. The method can be used with an arbitrary environment characterized by a general correlation function and arbitrary coupling strength. It is formally exact for harmonic environments, and it can be used with arbitrary temperature. Time evolution of an optically excited Frenkel exciton dimer representing a molecular exciton interacting with a charge transfer state is calculated by the proposed method. We calculate the evolution of the optical coherence elements of the density matrix and linear absorption spectrum, and compare them with the predictions of standard simulation methods.Comment: 11 pages, 6 figure

Data Quality in Predictive Toxicology: Identification of Chemical Structures and Calculation of Chemical Descriptors

Every technique for toxicity prediction and for the detection of structure–activity relationships relies on the accurate estimation and representation of chemical and toxicologic properties. In this paper we discuss the potential sources of errors associated with the identification of compounds, the representation of their structures, and the calculation of chemical descriptors. It is based on a case study where machine learning techniques were applied to data from noncongeneric compounds and a complex toxicologic end point (carcinogenicity). We propose methods applicable to the routine quality control of large chemical datasets, but our main intention is to raise awareness about this topic and to open a discussion about quality assurance in predictive toxicology. The accuracy and reproducibility of toxicity data will be reported in another paper

High-performance solution of hierarchical equations of motions for studying energy-transfer in light-harvesting complexes

Excitonic models of light-harvesting complexes, where the vibrational degrees of freedom are treated as a bath, are commonly used to describe the motion of the electronic excitation through a molecule. Recent experiments point toward the possibility of memory effects in this process and require to consider time non-local propagation techniques. The hierarchical equations of motion (HEOM) were proposed by Ishizaki and Fleming to describe the site-dependent reorganization dynamics of protein environments (J. Chem. Phys., 130, p. 234111, 2009), which plays a significant role in photosynthetic electronic energy transfer. HEOM are often used as a reference for other approximate methods, but have been implemented only for small systems due to their adverse computational scaling with the system size. Here, we show that HEOM are also solvable for larger systems, since the underlying algorithm is ideally suited for the usage of graphics processing units (GPU). The tremendous reduction in computational time due to the GPU allows us to perform a systematic study of the energy-transfer efficiency in the Fenna-Matthews-Olson (FMO) light-harvesting complex at physiological temperature under full consideration of memory-effects. We find that approximative methods differ qualitatively and quantitatively from the HEOM results and discuss the importance of finite temperature to achieve high energy-transfer efficiencies.Comment: 14 pages; Journal of Chemical Theory and Computation (2011

Wave packet approach to transport in mesoscopic systems

Wave packets provide a well established and versatile tool for studying time-dependent effects in molecular physics. Here, we demonstrate the application of wave packets to mesoscopic nanodevices at low temperatures. The electronic transport in the devices is expressed in terms of scattering and transmission coefficients, which are efficiently obtained by solving an initial value problem (IVP) using the time-dependent Schroedinger equation. The formulation as an IVP makes non-trivial device topologies accessible and by tuning the wave packet parameters one can extract the scattering properties for a large range of energies.Comment: 12 pages, 4 figure

Formation of surface color centers at differently coordinated sites: MgO/Ag(1,1,19)

In order to find criteria for discrimination between surface color centers at terraces and steps, and bulk color centers, the characteristic losses of these centers have been investigated by electron energy loss spectroscopy on an epitaxial MgO film grown on a Ag (1,1,19) surface. This film contains a significantly higher step density compared with a film grown on Ag(100). The generation of four distinct losses at 2.0, 2.4, 2.8, and 3.4 eV and a broad loss centered at 5.5 eV have been observed that are induced by electron bombardment of the MgO surface. The latter loss is attributed to bulk color centers (Fb centers). By comparing the measured loss energies with experiments performed on MgO/Ag(100) and with theoretical literature data, the observed losses at 2.0 and 2.8 eV can be consistently assigned to transitions of color centers located on step sites, whereas those at 2.4 and 3.4 eV are attributed to terrace sites. The kinetics of color center formation during electron bombardment, as well as the annihilation of F centers by simple exposure to O2 gas at room temperature, was determined and compared for differently coordinated color centers. While all surface color centers follow the same kinetics, we show that the Fb centers can only decay as long as the existence of surface color centers provides active sites for dissociating oxygen molecules. This corroborates the assignment of Fb centers. © 2003 The American Physical Societ

Quarkonia Measurements with the Central Detectors of ALICE

A Large Ion Collider Experiment - ALICE will become operational with the startup of the Large Hadron Collider - LHC at the end of 2007. One focus of the physics program is the measurement of quarkonia in proton-proton and lead-lead collisions. Quarkonia states will be measured in two kinematic regions and channels: di-muonic decays will be measured in the forward region by the muon arm, the central part of the detector will measure di-electronic decays. The presented studies show the expected performance of the di-electron measurement in proton-proton and central lead-lead collisions.Comment: 6 pages, 7 figures, Proceedings of the QM 2006 poster sessio