Doctoral research in the Kitao Laboratory (School of Life Science and Technology), focusing on enhanced sampling molecular dynamics and binding Read more free-energy modeling. Key contributions: - Extended the lab-developed dPaCS-MD/MSM framework from protein–ligand to protein–DNA systems, enabling mechanistic dissociation pathway analysis of the p53 DNA-binding domain - Published first-author paper in Journal of Chemical Information and Modeling (JCIM), 62(5), 1294–1307 (2022) - Co-authored binding free energy study in Biophysics and Physicobiology (2021) - Constructed Markov State Models from large MD trajectory ensembles to extract free-energy landscapes and kinetic transition networks - Developed automated simulation and analysis pipelines in Python and Bash Supervisor: Prof. Akio Kitao Awards: - Tokyo Tech Tsubame Scholarship (2019–2021) - Cross-the-Border Pioneering Doctoral Research Program (2021–2022) - Egypt-Japan Education Partnership (EJEP) PhD Scholarship (2019)

Independent research appointment at the World Premier International Research Center Initiative (WPI-PRIMe), University of Osaka, combining a Read more Specially Appointed Researcher role with a competitive JSPS KAKENHI Principal Investigator grant. Key responsibilities and achievements: - Led a JSPS KAKENHI-funded project (Grant Code: 25K17360, ¥4,810,000 budget, 3-year award) applying advanced gREST/REUS enhanced sampling frameworks to resolve protein–DNA binding and unbinding transitions inaccessible via standard MD - Executed large-scale GENESIS molecular dynamics workflows on Japan's national supercomputers: Fugaku, Tsubame-4, and IMS — systems up to 280,000 atoms using CHARMM36m force fields - Uncovered cooperative glycan stabilization mechanisms governing the IGF1/IGFBP3/ALS ternary complex (manuscript under review, Biophysical Journal, 2026) - Identified novel high-affinity peptide candidates targeting antibody-escaping SARS-CoV-2 variants - Developed quantitative binding analysis workflows using MM/GBSA, MM/PBSA, contact persistence mapping, and interaction network analysis (ProLIF, MDAnalysis, MDTraj) - Built and deployed a high-performance in-house MD workstation (RTX 4090 GPU, 128 GB RAM, 96 TB storage) for local simulation and trajectory analysis International presentations: - Molecular Modelling Conference 2025, Melbourne, Australia (Poster) - 63rd Annual Meeting of the Biophysical Society of Japan, Nara (Poster) - 2nd Serial Networking of Foreign Researchers, Sysmex–Osaka University (Oral)

Postdoctoral research position focused on developing rigorous computational frameworks for protein stability prediction using alchemical free-energy Read more methods. Project title: Predicting Salt-Bridge Contributions to Protein Stability Using Enhanced Sampling Key responsibilities and achievements: - Engineered a hybrid FEP/REST2 computational framework to precisely quantify mutation-induced protein stability changes in globular proteins - Performed alchemical free-energy calculations on ubiquitin to evaluate energetic contributions of double salt-bridge mutations to folding stability - Optimized REST2 temperature scaling and solute region definitions to improve configurational sampling efficiency and convergence rates - Established rigorous convergence validation protocols using energy overlap metrics and free-energy stability profiles - Benchmarked the predictive framework against experimental reference data, achieving higher accuracy than industry-standard Rosetta-based and standalone FEP methods - Presented results at the 67th Annual Meeting of the Biophysical Society, San Diego, USA (2023) - Presented at AMED Drug Discovery Project Annual Meeting, Kobe University, Japan (2022)