Real-Space Density Functional Theory on Graphical Processing Units: Computational Approach and Comparison to Gaussian Basis Set Methods

We discuss the application of graphical processing units (GPUs) to accelerate real-space density functional theory (DFT) calculations. To make our implementation efficient, we have developed a scheme to expose the data parallelism available in the DFT approach; this is applied to the different procedures required for a real-space DFT calculation. We present results for current-generation GPUs from AMD and Nvidia, which show that our scheme, implemented in the free code Octopus, can reach a sustained performance of up to 90 GFlops for a single GPU, representing a significant speed-up when compared to the CPU version of the code. Moreover, for some systems, our implementation can outperform a GPU Gaussian basis set code, showing that the real-space approach is a competitive alternative for DFT simulations on GPUs

Scalable High-Performance Algorithm for the Simulation of Exciton Dynamics. Application to the Light-Harvesting Complex II in the Presence of Resonant Vibrational Modes

The accurate simulation of excitonic energy transfer in molecular complexes with coupled electronic and vibrational degrees of freedom is essential for comparing excitonic system parameters obtained from ab initio methods with measured time-resolved spectra. Several exact methods for computing the exciton dynamics within a density-matrix formalism are known but are restricted to small systems with less than 10 sites due to their computational complexity. To study the excitonic energy transfer in larger systems, we adapt and extend the exact hierarchical equation of motion (HEOM) method to various high-performance many-core platforms using the Open Compute Language (OpenCL). For the light-harvesting complex II (LHC II) found in spinach, the HEOM results deviate from predictions of approximate theories and clarify the time scale of the transfer process. We investigate the impact of resonantly coupled vibrations on the relaxation and show that the transfer does not rely on a fine-tuning of specific modes

Modeling Coherent Anti-Stokes Raman Scattering with Time-Dependent Density Functional Theory: Vacuum and Surface Enhancement.

We present the first density functional simulations of coherent anti-Stokes Raman scattering (CARS) and an analysis of the chemical effects upon binding to a metal surface. Spectra are obtained from first-principles electronic structure calculations and are compared with available experiments and previously available theoretical results following from Hartree–Fock polarizability derivatives. A first approximation to the nonresonant portion of the CARS signal is also explored. We examine the silver pyridine cluster models of the surface chemical signal enhancement, previously introduced for surface-enhanced Raman scattering. Chemical resonant intensity enhancements of roughly 10² are found for several model clusters. The prospects of realizing further enhancement of CARS signal with metal surfaces is discussed in light of the predicted chemical enhancements

Coherent Dynamics of Mixed Frenkel and Charge-Transfer Excitons in Dinaphtho[2,3‑<i>b</i>:2′3′‑<i>f</i>]thieno[3,2‑<i>b</i>]‑thiophene Thin Films: The Importance of Hole Delocalization

Charge-transfer states in organic semiconductors play crucial roles in processes such as singlet fission and exciton dissociation at donor/acceptor interfaces. Recently, a time-resolved spectroscopy study of dinaphtho­[2,3-<i>b</i>:2′3′-<i>f</i>]­thieno­[3,2-<i>b</i>]-thiophene (DNTT) thin films provided evidence for the formation of mixed Frenkel and charge-transfer excitons after the photoexcitation. Here, we investigate optical properties and excitation dynamics of the DNTT thin films by combining ab initio calculations and a stochastic Schrödinger equation. Our theory predicts that the low-energy Frenkel exciton band consists of 8–47% CT character. The quantum dynamics simulations show coherent dynamics of Frenkel and CT states in 50 fs after the optical excitation. We demonstrate the role of charge delocalization and localization in the mixing of CT states with Frenkel excitons as well as the role of their decoherence

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry

While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles

Construction of the Fock Matrix on a Grid-Based Molecular Orbital Basis Using GPGPUs

We present a GPGPU implementation of the construction of the Fock matrix in the molecular orbital basis using the fully numerical, grid-based <i>bubbles</i> representation. For a test set of molecules containing up to 90 electrons, the total Hartree–Fock energies obtained from reference GTO-based calculations are reproduced within 10^–4 <i>E</i>_h to 10^–8 <i>E</i>_h for most of the molecules studied. Despite the very large number of arithmetic operations involved, the high performance obtained made the calculations possible on a single Nvidia Tesla K40 GPGPU card

Excitonics: A Set of Gates for Molecular Exciton Processing and Signaling

Regulating energy transfer pathways through materials is a central goal of nanotechnology, as a greater degree of control is crucial for developing sensing, spectroscopy, microscopy, and computing applications. Such control necessitates a toolbox of actuation methods that can direct energy transfer based on user input. Here we introduce a proposal for a molecular exciton gate, analogous to a traditional transistor, for regulating exciton flow in chromophoric systems. The gate may be activated with an input of light or an input flow of excitons. Our proposal relies on excitation migration <i>via</i> the second excited singlet (S₂) state of the gate molecule. It exhibits the following features, only a subset of which are present in previous exciton switching schemes: picosecond time scale actuation, amplification/gain behavior, and a lack of molecular rearrangement. We demonstrate that the device can be used to produce universal binary logic or amplification of an exciton current, providing an excitonic platform with several potential uses, including signal processing for microscopy and spectroscopy methods that implement tunable exciton flux

Separation of Electromagnetic and Chemical Contributions to Surface-Enhanced Raman Spectra on Nanoengineered Plasmonic Substrates

Raman signals from molecules adsorbed on a noble metal surface are enhanced by many orders of magnitude due to the plasmon resonances of the substrate. Additionally, the enhanced spectra are modified compared to the spectra of neat molecules; many vibrational frequencies are shifted, and relative intensities undergo significant changes upon attachment to the metal. With the goal of devising an effective scheme for separating the electromagnetic and chemical effects, we explore the origin of the Raman spectra modification of benzenethiol adsorbed on nanostructured gold surfaces. The spectral modifications are attributed to the frequency dependence of the electromagnetic enhancement and to the effect of chemical binding. The latter contribution can be reproduced computationally using molecule−metal cluster models. We present evidence that the effect of chemical binding is mostly due to changes in the electronic structure of the molecule rather than to the fixed orientation of molecules relative to the substrate

Fast Delocalization Leads To Robust Long-Range Excitonic Transfer in a Large Quantum Chlorosome Model

Chlorosomes are efficient light-harvesting antennas containing up to hundreds of thousands of bacteriochlorophyll molecules. With massively parallel computer hardware, we use a nonperturbative stochastic Schrödinger equation, while including an atomistically derived spectral density, to study excitonic energy transfer in a realistically sized chlorosome model. We find that fast short-range delocalization leads to robust long-range transfer due to the antennae’s concentric-roll structure. Additionally, we discover anomalous behavior arising from different initial conditions, and outline general considerations for simulating excitonic systems on the nanometer to micrometer scale

Conformation and Electronic Population Transfer in Membrane-Supported Self-Assembled Porphyrin Dimers by 2D Fluorescence Spectroscopy

Two-dimensional fluorescence spectroscopy (2D FS) is applied to determine the conformation and femtosecond electronic population transfer in a dimer of magnesium meso tetraphenylporphyrin. The dimers are prepared by self-assembly of the monomer within the amphiphilic regions of 1,2-distearoyl-<i>sn</i>-glycero-3-phosphocholine liposomes. A theoretical framework to describe 2D FS experiments is presented, and a direct comparison is made between the observables of this measurement and those of 2D electronic spectroscopy (2D ES). The sensitivity of the method to varying dimer conformation is explored. A global multivariable fitting analysis of linear and 2D FS data indicates that the dimer adopts a “bent T-shaped” conformation. Moreover, the manifold of singly excited excitons undergoes rapid electronic dephasing and downhill population transfer on the time scale of ∼95 fs. The open conformation of the dimer suggests that its self-assembly is favored by an increase in entropy of the local membrane environment