Seminar by Dr. Ngo Xuan Kien and Dr. Le Duy Manh

At 2:00 PM on April 3, 2026, the IAST Institute will hold an seminar session on the 3rd floor of the IAST – Hanoi Office – 13 Hang Bot Alley, O Cho Dua Ward, Hanoi City, with the following details:

1/ Dr. Ngo Xuan Kien reported on the topic: Watching Proteins Move: From High-Speed ​​AFM to Atomic-Resolution Dynamics

Abstract: Our laboratory integrates experimental imaging, molecular dynamics simulations, and artificial intelligence to advance a new framework for dynamic atomic structural biology. We have recently developed the SimHS-AFMfit-MD approach, which transforms high-speed AFM movies into atomic-resolution conformational ensembles by combining flexible structural modeling, nonlinear normal mode analysis, and all-atom MD simulations.

Proteins are not static objects but dynamic mechanical systems that bend, twist, and reorganize to carry out biological functions. While X-ray crystallography and cryo-electron microscopy provide exquisite atomic detail, they capture only frozen snapshots. Molecular dynamics simulations describe continuous motion but often lack direct experimental validation.
In this seminar, I will introduce the principle of High-Speed ​​Atomic Force Microscopy (HS-AFM), which enables real-time visualization of single proteins in solution with nanometer spatial and millisecond temporal resolution. I will then present SimHS-AFMfit-MD, an integrative framework that reconstructs three-dimensional atomic conformations directly from experimental movies.
Finally, I will highlight selected achievements and ongoing projects from our newly established research group (LISAI-Bio) at IFIRSE, Quy Nhon, Vietnam.

2/ Dr. Le Duy Manh reported on the topic: An Introduction to Multiscale Computational Framework for Alzheimer's: From Molecular Toxicity to Systems-Level Aging

Abstract: Alzheimer's Disease (AD) is investigated through a multiscale computational lens, bridging molecular toxicity, systemic aging, and advanced signal processing.
At the nano-scale, Molecular Dynamics (MD) simulations characterize the "Pore Hypothesis," where Amyloid-beta oligomers form unregulated membrane pores. These pores induce lethal calcium (Ca2+) inflation, disrupting endogenous buffers such as Calbindin and misregulating sensors like Calmodulin (CaM).
At the macro-scale, Glymphatic system models simulate how age-related arterial stiffening (dynamic aging parameters) and extracellular space changes peptide clearance. This environmental failure facilitates the high-concentration states necessary for microscopic aggregation.
Finally, Empirical Mode Decomposition (EMD) and Transfer Entropy may be employed to analyze nonlinear, nonstationary bio-signals. Integrated with Machine Learning, these methods identify early-warning signatures of neural degradation by linking clearance systemic failure to the breakdown of information flow in the aging brain.