MesoHOPS: Size-invariant scaling calculations of multi-excitation open quantum systems.

The photoexcitation dynamics of molecular materials on the 10-100 nm length scale depend on complex interactions between electronic and vibrational degrees of freedom, rendering exact calculations difficult or intractable. The adaptive Hierarchy of Pure States (adHOPS) is a formally exact method that leverages the locality imposed by interactions between thermal environments and electronic excitations to achieve size-invariant scaling calculations for single-excitation processes in systems described by a Frenkel-Holstein Hamiltonian. Here, we extend adHOPS to account for arbitrary couplings between thermal environments and vertical excitation energies, enabling formally exact, size-invariant calculations that involve multiple excitations or states with shared thermal environments. In addition, we introduce a low-temperature correction and an effective integration of the noise to reduce the computational expense of including ultrafast vibrational relaxation in Hierarchy of Pure States (HOPS) simulations. We present these advances in the latest version of the open-source MesoHOPS library and use MesoHOPS to characterize charge separation at a one-dimensional organic heterojunction when both the electron and hole are mobile.

Formally Exact Simulations of Mesoscale Exciton Diffusion in a Light-Harvesting 2 Antenna Nanoarray.

The photosynthetic apparatus of plants and bacteria combine atomically precise pigment-protein complexes with dynamic membrane architectures to control energy transfer on the 10-100 nm length scales. Recently, synthetic materials have integrated photosynthetic antenna proteins to enhance exciton transport, though the influence of artificial packing on the excited-state dynamics in these biohybrid materials is not fully understood. Here, we use the adaptive hierarchy of pure states (adHOPS) to perform a formally exact simulation of excitation energy transfer within artificial aggregates of light-harvesting complex 2 (LH2) with a range of packing densities. We find that LH2 aggregates support a remarkable exciton diffusion length ranging from 100 nm at a biological packing density to 300 nm at the densest packing previously suggested in an artificial aggregate. The unprecedented scale of these formally exact calculations also underscores the efficiency with which adHOPS simulates excited-state processes in molecular materials.

Discovery of a monomeric green fluorescent protein sensor for chloride by structure-guided bioinformatics.

Chloride is an essential anion for all forms of life. Beyond electrolyte balance, an increasing body of evidence points to new roles for chloride in normal physiology and disease. Over the last two decades, this understanding has been advanced by chloride-sensitive fluorescent proteins for imaging applications in living cells. To our surprise, these sensors have primarily been engineered from the green fluorescent protein (GFP) found in the jellyfish Aequorea victoria. However, the GFP family has a rich sequence space that could already encode for new sensors with desired properties, thereby minimizing protein engineering efforts and accelerating biological applications. To efficiently sample this space, we present and validate a stepwise bioinformatics strategy focused first on the chloride binding pocket and second on a monomeric oligomerization state. Using this, we identified GFPxm163 from GFPxm found in the jellyfish Aequorea macrodactyla. In vitro characterization shows that the binding of chloride as well as bromide, iodide, and nitrate rapidly tunes the ground state chromophore equilibrium from the phenolate to the phenol state generating a pH-dependent, turn-off fluorescence response. Furthermore, live-cell fluorescence microscopy reveals that GFPxm163 provides a reversible, yet indirect readout of chloride transport via iodide exchange. With this demonstration, we anticipate that the pairing of bioinformatics with protein engineering methods will provide an efficient methodology to discover and design new chloride-sensitive fluorescent proteins for cellular applications.

Formally exact simulations of mesoscale exciton dynamics in molecular materials.

Excited state carriers, such as excitons, can diffuse on the 100 nm to micron length scale in molecular materials but only delocalize over short length scales due to coupling between electronic and vibrational degrees-of-freedom. Here, we leverage the locality of excitons to adaptively solve the hierarchy of pure states equations (HOPS). We demonstrate that our adaptive HOPS (adHOPS) methodology provides a formally exact and size-invariant (i.e., ) scaling algorithm for simulating mesoscale quantum dynamics. Finally, we provide proof-of-principle calculations for exciton diffusion on linear chains containing up to 1000 molecules.