- Laboratory of Theoretical and Computational Biophysics
Understanding physical insights of biosystem behaviors at the atomic level are great interests. The TCB is established in order to apply the computational and theoretical methods to mimic the action of molecules that widely apply to investigate the problems involving computational physics/chemistry/biology, drug design, and material science, etc.
Apps & Tools:
1. Modifed AutoDock Vina. AutoDock Vina formed a very high successful-docking rate but a rather low correlation coefficient. This low correlation can be an obstacle for ranking of ligand-binding affinity, which is the main objective of docking simulations. The accuracy of Vina likely depends on the empirical parameters, which include the Gaussian steric interaction, repulsion, hydrophobic, hydrogen bond, and rotation metrics. A new set of empirical parameters was proposed to improve the docking accuracy. The modified AutoDock Vina was thus introduced and the accuracy of docking simulations was significantly increased. The version of Vina with a new set of parameters can be downloaded here.
List of members:
N0 Member Role Contact 1 Dr. Son Tung Ngo Head of Laboratory email@example.com 2 Dr. Trung Hai Nguyen Researcher firstname.lastname@example.org 3 Dr. Nguyen Minh Tam Researcher email@example.com 4 Thanh Hoa Le Assistant Researcher firstname.lastname@example.org 5 T. Ngoc Han Pham Collaborator 6 Quynh Mai Thai Collaborator 7 Nhat Truong Pham Collaborator
9 Phuong Nguyen, Ayyalusamy Ramamoorthy, Bikash Sahoo, Jie Zheng, Peter Faller, John Straub, Laura Domínguez, Joan-Emma Shea, Nikolay Dokholyan, Alfonso De Simone, Buyong Ma, Ruth Nussinov, Saeed Najafi, Son Tung Ngo, Antoine Loquet, Mara Chiricotto, Pritam Ganguly, James McCarty, Mai Suan Li, Carol Hall, Yiming Wang, Yifat Miller, Simone Melchionna, Birgit Habenstein, Stepan Timr, Jiaxing Chen, Brianna Hnath, Birgit Strodel, Rakez Kayed, Sylvain Lesne, Guanghong Wei, Fabio Sterpone, Andrew Doig, Philippe Derreumaux, Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes and Amyotrophic Lateral Sclerosis. Chem. Rev. 2021, 121, 2545–2647. 8 Nguyen Minh Tam, Minh Quan Pham, Huy Truong Nguyen, Nam Dao Hong, Nguyen Khoa Hien, Duong Tuan Quang, Huong Thi Thu Phung, and Son Tung Ngo, Potential inhibitors for SARS-CoV-2 Mpro from Marine compounds, RSC Adv. 2021,11, 22206-22213. [2021 RSC Advances HOT Article Collection] 7 Nguyen Minh Tam, Minh Quan Pham, Nguyen Xuan Ha, Pham Cam Nam and Huong Thi Thu Phung; Computational estimation of potential inhibitors from known drugs against the main protease of SARS-CoV-2; RSC Adv., 2021,11, 17478-17486. [selected for 2021 RSC Advances HOT Article Collection] 6 Nguyen Thi Mai, Son Tung Ngo, Peter Lievens, Ewald Janssens, Nguyen Thanh Tung, Photofragmentation Patterns of Cobalt Oxide Cations ConOm+ (n = 5-9, m = 4-13): from Oxygen-Deficient to Oxygen-Rich Species, J. Phys. Chem. A 2020, 124, 7333–7339. [selected for font cover] 5 Son Tung Ngo, Trung Hai Nguyen, Nguyen Thanh Tung, Pham Cam Nam, Khanh B. Vu, Van V. Vu. Oversampling Free Energy Perturbation Simulation in Determination of the Ligand-Binding Free Energy, J. Comput. Chem. 2020, 41, 611-618. [selected for font cover] 4 Nguyen Minh Tam, Long Van Duong, Hung Tan Pham, Minh Tho Nguyen and My Phuong Pham-Ho; Effects of single and double nickel doping on boron clusters: stabilization of tubular structures in BnNim, n = 2–22, m = 1, 2; Phys. Chem. Chem. Phys. 2019,21, 8365-8375. 3 Son Tung Ngo, Philippe Derreumaux, Van V. Vu; Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca2+ Ions, J. Phys. Chem. B 2019, 123, 2645-2653. 2 Nguyen Minh Tam, Nguyen Thi Mai, Hung Tan Pham, Ngo Tuan Cuong, and Nguyen Thanh Tung; Ultimate Manipulation of Magnetic Moments in the Golden Tetrahedron Au20 with a Substitutional 3d Impurity; J. Phys. Chem. C 2018, 122, 28, 16256-16264 1 Van V. Vu and Son Tung Ngo, Copper active site in polysaccharide monooxygenases. Coord. Chem. Rev. 2018, 368, 134-157. [Invited Review].
- Laboratory of Advanced Materials Chemistry (AMC)
- CVD Graphene and 2D Materials;
- Clean Transfer of Large area graphene onto the dielectric materials.
- Energy Materials: Electrocatalysis; Solar cells
- Triboelectric Nanogenerators
- Desalination of water.
- Fabrication of Graphene based Nanobiosensors.
- Wearable Devices (Biosensors)
- Biofunctionalization/bio-conjugation (with anticancer drugs) & toxicology studies of nanomaterials
List of members:
N0 Member Role Contact 1 Dr. Nguyen Le Minh Tri Researcher email@example.com 2 Assoc. Prof. Phan The Long Researcher firstname.lastname@example.org
- Atomic Molecular and Optical Physics Research Group (AMOG)
- Non-perturbation methods, algebraic methods for solving the Schrodinger equation of atom/molecule in electromagnetic fields;
- Quadratic and bilinear transformations (Kustannheimo-Stiefel, Levi-Civita, Hurwitz) and the connections between harmonic oscillators and the MICZ-Kepler problems;
- Magnetic monopole and its generalization for high-dimensional spaces;
- High-order harmonic generation and ab initio methods for its calculation; possibility of extracting dynamic molecular structures from high-order harmonic spectra; chemical imaging and tracking molecular dynamics by ultra-short laser pulses.
List of members:
N0 Member Role Contact 1 Dr. Le Thi Cam Tu Researcher email@example.com 2 Dr. Hoang Van Hung Researcher firstname.lastname@example.org 3 Dr. Bui Minh Loc Researcher email@example.com 4 Le Dai Nam Researcher firstname.lastname@example.org
- Computational Laboratory for Advanced Materials and Structures (COLAMS)
Nano, Micro and Macro Modelling of Materials: Computational analysis for Materials and Structures: Advanced Experiments on Materials and Composites.
List of members:
N0 Member Role Contact 1 2 MS.c. Le Tri Dat Researcher email@example.com 3