All papers in this volume were peer-reviewed. The BIFI2006 Conference represents an interactive forum for physicists, chemists, biologists, and mathematicians for sharing ideas as well as adressing recent advances in the frontier between physics and biology. Current challenges in molecular and cell biology, biomedicine, and biotechnology require the interdisciplinary collaborative effort of theoretical and experimental researchers benefiting from the interplay between the latest computational and experimental developments. There were three main topics at the conference: nucleic acids, proteins and peptides, and collective behavior of biomolecules. This volume includes papers on: protein folding, nucleic acid structure, ligand binding, proteomics, network dynamics and topology, cell signaling, collective behavior, biomolecular modeling, systems biology, and biophysical computational methods.