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

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 : Massively 7Parallel Molecular Dynamics Code

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

• 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.

Picture of ‘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. (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.

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Contact

E-mail: [email protected]

Phone: +82-10-7493-3217

Social

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Education

Ph.D in Mechanical Engineering Kyung Hee University

Dissertation: Collision Cascade Molecular Dynamics Simulation with Realistic Test Samples

2017 – 2024

M.S. in Mechanical Engineering Kyung Hee University

Thesis: First Principles Calculations on Interstitial Defects in W-Re-Ta Ternary System

2015 – 2017

B.S. in Mechanical Engineering

Kyung Hee University

2009 – 2015

Professional Interests

• Fusion Materials
• Multiscale Modeling

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Personal Life