Ph.D in Mechanical Engineering with B.S. and M.S. degrees. Proficient in Molecular Dynamics simulations, scientific code development, and high-performance computing. Focused on simulations of materials for fusion environments and extreme conditions, with a strong passion for developing physics-based simulation and calculation tools.

Professional Highlights

PolyPal Project : Parallel Atomistic Structure Generation Code for Micro-Metre Scale Simulations

Project Manager / Core Developer

2022 - Present

Examples of (a) isotropic and (b) anisotropic polycrystalline structures. The isotropic one is generated with randomly sampled grain distribution and crystallographic orientations while the anisotropic one is generated using a layered grain distribution with preferred crystallographic orientations.

• Developed a parallelised code generating massive polycrystalline structures containing billions of atoms for atomistic simulations.

• Developed input-output routines, grain characterisation, load-balancing algorithm and atom generation.

• Designed a unique MPI-IO multi-file output format preserving domain decomposition information enabling fast input reading from parallelised molecular dynamics code by eliminating atom sorting.

• Developed versatile options for polycrystalline structure such as variation in average grain size in certain direction, preferred crystallographic orientation and solute atom mixing.

• Achieved a great performance with near-perfect scalability; The generation of polycrystalline structure containing 10 billions of atoms takes less than 3 minutes with 6,400 computing cores.

• Published a paper in Computer Physics Communications (2024) DOI: https://doi.org/10.1016/j.cpc.2024.109458

• Related article:

  PolyPal.specialArticle.pdf

• Source code available: https://gitlab.com/GeonbuShin/polypal.git

VITMAS Project : Parallel Molecular Dynamics Code for Micro-Metre Scale Simulation

Project Manager / Core Developer

2021 - Present

Snapshots of a mid cross-section of 600nm x 600nm x 400nm polycrystalline structure during the multi-PKA simulation. The atomistic structure is generated with PolyPal to mimic a real thin-film tungsten specimen fabricated by deposition. The darker (purple) regions indicates non-bcc atoms representing defects.

• Developed a parallelised molecular dynamics simulation code for handling massive atomistic systems in primary knock-on atom (PKA) simulations.
• Designed the overall code structure.
• Developed input-output routines, time integration, Nosé-Hoover thermostat, interatomic force calculations, and multi-PKA creation routines.
• Tested with a polycrystalline system with 8 billions of atoms.
• Conducted production runs on a supercomputing cluster, utilising approximately 100,000 cores at the national supercomputing centre (Nurion-5, Korea Institute of Science and Technology Information).
• Related promotional video available: click here.
  • Credit for the video: data preparation and scripting
• Available source code upon request.

Development of Electron Temperature Model for Molecular Dynamics Collision Cascade Simulations

First Author

2024

Thermal conductivity in the ⟨100⟩ direction predicted with X2TM up to the ionic temperature of 2000K.

Examplars at 50keV PKA energy that have connected type sub-cascades. Both (a) and (b) form a large interstitial defect cluster at the connected region.

• Modified LAMMPS code to enable the implementation of electron-temperature-dependent two-temperature model (2TM).
• Calculated electron specific heat and electron-phonon coupling constant over wide range of electron-temperature based on ab-initio calculations.
• Achieved great improvement in thermal conductivity prediction at high temperature.
• Confirmed electron-temperature dependent 2TM changes defect production.
• Published a paper in Nuclear Fusion DOI: https://doi.org/10.1088/1741-4326/ad64e7
• Available source code upon request.

Safety Assessment Code Development for Commercial Fission Reactor

Solo Developer

2020 - 2023

• Developed a safety assessment code for pressure tube in Canada Deuterium-Uranium (CANDU) reactor in collaboration with Korea Atomic Energy Research Institute.
• Developed Leak-Before-Break assessment code for pressure tube.
• Developed single flaw assessment code for pressure tube.
• Integrated assessment codes for Leak-Before-Break and single flaw in pressure tube in a comprehensive program.
• Verified physics-based calculation functions and probability-model-based prediction models with sensitivity analysis on key parameters.
• Authored extensive internal reports and manuals.
• Classified data.

Side Projects

Pi-Cluster Build

• Built and managed a small cluster composed of four RaspberryPi 3 computers configured with OpenMPI and Slurm job scheduler.
• Tested parallel codes on the RaspberryPi Cluster for benchmarking and debugging purposes.

Cardboard Cluster.

LAMMPS Benchmark on Cardboard Cluster

Real-Time Rendering in Digital Twin System of Smart Factory

Visiting Developer at German Institute of Artificial Intelligence (DFKI) in Kaiserslautern, Germany

On-site: 4 weeks in 2018 and 3 weeks in 2019

• Participated in the development of a digital twin system for monitoring real-time manufacturing processes in Smart Factory at DFKI, Germany.
• Contributed to code tracking and rendering real-time manufacturing process bridging the physical system and a mixed reality gear (Microsoft Hololens).
• Collaborated with colleagues from diverse cultural backgrounds.

Monitoring the status of a smart factory using a mixed reality gear.

Work Experience

Postdoctoral Researcher [September 2024 - Present]

Yonsei University, Republic of Korea

Publications

• Shin, Y., Moul, V, Kang, K., & Lee, B. (2026). Improved Defect Analysis for Polycrystalline Materials in Atomistic Simulation, Nano Technology, submitted.
• Shin, Y., Moul, V., Kang, K., & Lee, B. (2024). PolyPal: A parallel microscale virtual specimen generator. Computer Physics Communications, 109458.
• Shin, Y., Kang, K., & Lee, B. (2024). Temperature-dependent electron–phonon coupling changes the damage cascades in neutron-irradiation molecular dynamics simulation in W. Nuclear Fusion, 64(10), 106001.
• Moul, V., Shin, Y., & Lee, B. (2023). The Effects of Attractive Interaction on Viscosity in Undercooled Kob–Andersen Liquids. Multiscale Science and Engineering, 5(3), 160-165.
• Shin, Y., Kang, K., & Lee, B. (2021). Reduced interstitial mobility through multicomponent alloying in bcc W. Fusion Engineering and Design, 172, 112745.

International Conferences

• Shin, Y., Kang, K., & Lee, B. (2024). Implementation of Electron Temperature Model to W Damage Cascades Molecular Dynamics Simulation under Neutron Irradiation. In the 11th international conference on MMM.
• Yoo, S., Shin, Y., Oh, S., Park, H., Kim, Y., Yoo, A., Kwon, O., Kang, K., Lee, B.. (2023). Grain-boundary Effects on the Irradiated Damages in W-Re Alloys. In TMS annual Meeting.
• Yoo, S., Oh, S., Shin, Y., Kwon, O., Kang, K., & Lee, B. (2022). Parallel I/O optimization for micrometer-scale atomistic calculations under extreme conditions. In APS April Meeting Abstracts (Vol. 2022, pp. S07-009).
• Shin, Y., Lee, B., & Kang, K. (2022). Reduced Interstitial Mobility in W Based Transition Metal Ternary Systems. In TMS Annual Meeting.
• Shin, Y., Lee, B. (2018). Defect energetics in W-based transition-metal ternary systems. In the 9th international conference on MMM.

Awards

2024 대한기계학회 CAE 및 응용역학부분 우수논문상

2024 Korean Society of Mechanical Engineering CAE division, Distinguished paper award

2023 대한기계학회 CAE 및 응용역학부분 우수논문상

2023 Korean Society of Mechanical Engineering CAE divison, Distinguished paper award

2021 한국압력기기공학회 CANDU 분과 우수논문상

2021 Korean Society of Pressure Vessels & Piping CANDU division, Distinguished paper award

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