Siam Ahmed

I am Md.

Siam Ahmed

Nishat, a recent M.Sc. graduate in Biomedical Engineering from Bangladesh University of Engineering and Technology with a background in Computer Science and Engineering from Rangamati Science and Technology University. My research interests include medical imaging, computational modeling, machine learning, bioinformatics, and computational biology. My master’s thesis focused on high-risk plaque identification using coronary CT imaging and computational fluid dynamics, where I worked on cardiovascular image analysis and hemodynamic modeling.

I also have experience in molecular docking, network biology, survival analysis, and biomedical research using genomic and imaging datasets. I am proficient in Python, R, MATLAB, and C, and I aim to pursue Ph.D. research in computational medicine, medical imaging, and AI-driven healthcare technologies.

Postgraduate Thesis Student at Department of Biomedical Engineering, Bangladesh University of Engineering and Technology (BUET) (2023-12 – 2026-04)

MSc. Thesis: Computational Identification of Key Geometrical Features of the Left Coronary Artery Influencing Atherosclerosis Using a Design of Experiment Framework. Registered at ClinicalTrials.gov (ID: NCT07002697). Thesis Advisor: Professor M Tarik Arafat

• Role: 3D modeling, simulations, result visualization, and interpretation.
• Outcome: Left main stem diameter and bifurcation angle are the most influential parameters and developing a complete LMS artery Fluid flow.
• Skill: Design of Experiment, image segmentation, Computational fluid dynamics

Research Assistant at Panacea Research Center (2025-05 – Present)

• Conduct structure-based drug discovery against infectious disease targets using AutoDock Vina, SwissDock, PyRx, and Discovery Studio.
• Perform molecular dynamics (MD) simulations with GROMACS to assess protein-ligand complex stability and analyze binding affinities, hydrogen bonding interactions, and structural stability metrics (RMSD, RMSF, binding free energy) to validate docking results.
• Interpret and visualize computational results to support rational drug design and therapeutic candidate prioritization.

Postgraduate Research Student at BioInnovation Research Group, Department of Biomedical Engineering, Bangladesh University of Engineering and Technology (BUET) (2023-04 – Present)

• Employing computational fluid dynamics and pulsatile blood pressure and velocity profile, the hemodynamic alterations in convoluted coronary arteries under hypertension conditions were examined.
• Working on a project titled 'Vascular geometry based Real-time risk prediction system' to predict vascular risk based on geometrical features, guided by computational fluid dynamics and a deep learning algorithm.
• Collaborated with the country's leading cardiologists to design intervention-assistive tools.
• Mentored Undergraduate & Graduate students on a complete computational modeling study pipeline.
• Consulted with healthcare industry leaders on integrating computation assistive tools in the clinical workflow of Bangladesh.
• Conducted a skill transfer session on manuscript quality, graph plotting, and schematic designing.

Undergraduate Researcher at Department of Computer Science and Engineering, Rangamati Science & Technology University (2020-03 – 2022-03)

Thesis Topic: 'Identification of Signature Hub Genes and Analysis of Protein Drug Compound among Subversive Cancer Diseases: A Bioinformatics Approach'. Thesis Advisor: Sayed Asaduzzaman

• Role: Common Gene Finding, Gene Analysis, Drug Design, and Data Mining.
• Outcome: Drug analysis for Cancer.
• Skill: Different Online Tools like STRING, NetworkAnalyst, GeneMANIA, Enrichr, Orange, etc.

Master of Science in Biomedical Engineering in Biomedical Engineering – Bangladesh University of Engineering and Technology (BUET) (2023-12 – 2026-04)

Bachelor of Science in Computer Science and Engineering in Computer Science and Engineering – Rangamati Science & Technology University (2022)