Our research lies at the intersection of single-molecule biophysics and nanomaterial-polymer science to develop new tools to probe and characterize complex biological systems. In particular, near-infrared emitters (fluorophores, zero-dimensional, and one-dimensional nanomaterials) provide emission wavelengths that are maximally permeable to biological materials. As such, we explore the potential of near-infrared and large stokes shift light emitters combined with conventional visible fluorophores to detect molecular processes in systems that are optically and physically dense. We develop these tools for single-molecule applications, with the goal of scaling them to the study of molecular processes in whole-organisms. We further explore nanoscale materials as scaffolds for the delivery of biological molecules into tissues, cells, and sub-cellular organelles. To these ends, we build and develop optical microscopy tools, functionalize and characterize nanomaterials, and combine these areas for in vitro and in vivo molecular detection.