Algorithm Development

The Coker group is interested in development of trajectory based theoretical approach to propagate the density matrix for a general class of systems described in terms of a quantum subsystem with discrete states that are coupled to a complex environment represented by continuous phase space degrees of freedom (DOF). Our most recently developed method, The Partial Linearized Density Matrix (PLDM) propagation method, accurately capture short time coherent behavior and also gives a reliable description of the relaxation to thermal equilibrium at long times. This has made the approach particularly useful for exploring realistic models of natural multi-chromophore photosynthetic light harvesting systems that show long lived coherence at early times and decoherence as equilibrium is approached in the long time limit. Another major advantage of our PLDM approach is the ability to treat arbitrary forms of system-bath coupling. Not only can the approach handle general non-linear coupling, but we also make no assumptions about the form of the spectral density that determines the frequency dependence of the system-bath coupling strength.

Selected Publications

Photosynthetic Energy Transfer

We use our linearized quantum dynamics methods to explore the mechanisms underlying the fundamental processes by which natural photosynthetic light-harvesting systems transfer excitation energy through networks for chromophore molecules and feed this excitation into producing charge separation in reaction centers. The key general findings of this work explore how various characteristics of the different parts of the model hamiltonian influence the relaxation dynamics of these quantum dissipative networks as probed, for example, in non-linear spectroscopy experiments. Our most recent work presents some of the first detailed ab initio calculations of the spectral densities describing the different environments arising from chromophores in different regions of the protein support scaffolding and demonstrates that the heterogeneity of the spectral density can have a significant influence on the relaxation dynamics of these light harvesting systems.

Selected Publications

  1. E. Rivera, D. Montemayor, M. Masia, and D.F. Coker J. Phys. Chem. B. 117, 55105521 (2013)
  2. Coherent Excitation Energy Transfer in the LH II Light Harvesting System: A Partial Linearized Density Matrix Dynamics Study of Energy Transfer Rates Between Different Sub-units, in preparation for submission to J. Chem. Phys. (2013)

Organic Photochemical Reactions

There have been signifcant recent advances in the development of organic synthetic methodology that make use of phto-activation of substrates for directed synthesis. Several important developments in this area have been pioneered by synthetic organic chemistry groups at Boston University (particularly the Porco group). Our group works to develop theoretical models and to study the mechanism underlying this important new excited state synthetic methodology. In particular, we developed a new genetic programming approach capable of fitting highly accurate and flexible reactive empirical valence bond (EVB) potential models using very limited ab initio single point energy data on these very large complex organic systems. This approach has been shown to be accurate and reliable, especially for treating solvent interaction effects on spectral line shapes. A cartesian reaction plane model for use in quantum dynamics calculations employing our PLDM propagation schemes has also been developed for analyzing high resolution matrix isolation spectra. Finally, our work extends new theoretical techniques like the string method for obtaining minimum energy paths on complex, high dimensional ab initio potential energy surfaces and the temperature accelerated molecular dynamics (TAMD) approach to map out the free energy surface and explore most probably reaction channels in condensed phase excited state reactive systems.

Selected Publications

Artificial Light Harvesting Systems

Organic photovoltaic (OPV) cells have been shown to be a possible low-cost alternative at the silicon-based cells.These organic solar cells usually consist of conjugated polymers and either fullerene or semiconducting carbon nanotubes (see image). Since several processes are involved in determining the power conversion energy efficiency (e.g. charge separation, exciton-exciton annihilation), a microscopic and yet realistic modeling of all processes involved is needed to provide design principles for more energy efficient OPV cells.

To this end, we combine high accuracy electronic structure methods (DFT, TDDFT, GW, Bethe-Salpeter equation) and semiclassical quantum evolution schemes to theoretically describe the non-adiabatic quantum dissipative dynamics of such complex systems.

Optically Regulated Biological Probes

Forster resonance energy transfer (FRET) is used to identify signaling dynamics of biochemical pathways, to be used as an important tool in optical microscopy. The standard experimental setup uses high concentration of intra-molecular fluorophores to achieve target signal strength which, problematically, often scales non-linearly to target biological observables. Our work aims to design and identify linkers which addresses this issue at a molecular level. Our approach combines rare event methods and ab-initio computations to better understand the molecular and electronic processes relevant to predicting and designing nano-linkers.


Magnetic Materials

Magnetization reversal and precession in the presence of thermal agitation and spin-transfer torques. Spin-torque transfer involves creating a spin-polarized current and passing it through a ferromagnetic material in order to transfer angular momentum and alter the magnetization of the ferromagnet. Spin-torque can be used to induce high-frequency magnetic precession or increase the probability of switching due to thermal agitation.

Dye-Sensitised Solar Cells (DSSC)

Dye-sensitised solar cells (DSSC) nowadays represent one of the most promising routes for photovoltaic power generation, which could eventually provide an abundant supply of clean and renewable energy. Typical DSSC devices consist of an electrode made of a semiconducting oxide such as TiO2, ZnO, or SnO2, whose surface is covered by photoactive molecules (chromophores) absorbing light in the visible range. Photons impinging on the chromophores excite electrons, injecting them into the conduction band of the semiconducting electrode. To reach a steady state, the electron charge on the chromophores has to be replenished by a current flowing through an electrolyte solution, which is therefore a third essential component of these devices. Many years of constant development have raised the overall efficiency of DSSC to a level slightly in excess of 10%, close to the limit of economic viability. A major weakness of the standard set-up is the heterogeneous character of the device, encompassing solid and liquid phases. Innovative electrolytes such as room temperature ionic liquids (RTIL's) could overcome this problem, providing a decisive step towards the deployment of DSSC in the field.At the conditions of DSSC operation, RTIL's display liquid-like electric conductivity, but solid-like mechanical properties.

Rotational Properties in Super Critical Fluids

Super critical fluids (SCFs) are versatile solvents that can be an environmentally friendly alternative to organic solvents. This project incorporates anisotropic time domain Raman spectroscopy to probe changes in the rotational transition energies of hydrogen rotors that result from solvent/solute interactions. These diatomics are effective probes for monitoring solvent properties because of their J-specific rotational Raman transition bands that remain discrete even when solvated in liquid solutions. Computationally, these diatomic solutes function as rigid rotors and their angular momentum components can be computed quantum mechanically to calculate the Raman correlation functions. This unique probe/solvent system allows for a combined computational/experimental approach to study the solvation properties of super critical CO2, H2O, and CHF3 as functions of density and temperature via comparison of the experimentally and computationally determined Raman correlation functions and corresponding Raman frequencies.

Selected Publications