Molecular self-assembly involves spontaneous structuring or self-organization of molecules and represents a ubiquitous phenomenon observed at multiple length scales representing a key strategy in building biological architectures and molecular machines that execute life’s functions. Dynamic and environmentally directed assembly of molecules in biological systems is essential for the fabrication of micron-scale, hierarchical, functional structures. In this complementary experimental and computational study, the directed assembly of genetically selected graphite binding peptides on 2D solid surfaces is demonstrated. Structural and kinetic analyses as well as molecular dynamics simulations yield the self-assembly process as thermally controllable upon tuning the solvated peptide conformational states. The ability to tailor the structure of two-dimensional soft bio/nano interfaces via external stimuli shows the potential for the bottom-up fabrication of complex materials with nanotechnological importance, such as biosensors, bioelectronics, and biomolecular fuel cells.