Casademunt i Viader, JaumeOrozco López, ModestoCanet Vidal, Martí2025-07-222025-07-222025-06https://hdl.handle.net/2445/222469Treballs Finals de Grau de Física, Facultat de Física, Universitat de Barcelona, Curs: 2025, Tutors: Jaume Casademunt i Viader, Modesto Orozco LópezThis project contributes to the development of a coarse-grained model at the MMB lab at IRB, designed to capture the sequence-dependent dynamics of DNA and its interactions with proteins using simplified Hamiltonians derived from atomistic potentials. A key objective was to assess its ability to reproduce the sequence-specific binding of transcription factors (TFs). To this end, a semi-stochastic algorithm was implemented to generate physically realistic initial configurations. Additionally, Free Energy Perturbation simulations were performed to quantify the impact of single-base mutations on TF binding affinity. Results highlight the differential energetic contribution of individual bases to protein-DNA interactions8 p.application/pdfengcc-by-nc-nd (c) Canet, 2025http://creativecommons.org/licenses/by-nc-nd/3.0/es/Seqüència de nucleòtidsDinàmica molecularTreballs de fi de grauNucleotide sequenceMolecular dynamicsBachelor's thesesinfo:eu-repo/semantics/bachelorThesisinfo:eu-repo/semantics/openAccess