We present examples from our group where biophysical chemistry impacts unsolved problems in infectious diseases and auto-immune diseases. We start with bacterial biofilms, which are structured multi-cellular communities that are fundamental to the biology and ecology of bacteria. By using population tracking algorithms, we dissect bacterial social behavior at the single cell level.  We will also discuss how we can learn from innate immunity peptides to renovate antibiotic design, and make precision antibiotics and antibiotics against persister bacterial populations. Finally, we examine the pathological role of antimicrobial peptides in a range of autoimmune disorders.