Directed Evolution of a Genetically Encoded Indicator for Chloride.

Inarguably, the green fluorescent protein (GFP) family is an exemplary model for protein engineering, accessing a range of unparalleled functions and utility in biology. The first variant to recognize and provide an optical output of chloride in living cells was serendipitously uncovered more than 25 years ago. Since then, researchers have actively expanded the potential of GFP indicators for chloride through site-directed and combinatorial site-saturation mutagenesis, along with chimeragenesis.

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.

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.

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.

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 (, ) scaling algorithm for simulating mesoscale quantum dynamics.