Duc Nguyen | Homepage

Duc D. Nguyen

Associate Professor

Email: ducnguyen[at]utk.edu

Phone: TBA

Location: Ayres Hall 203

My Resume Update: Dec-23

Research Group

Trung Nguyen PhD Student (2024 - Present)

Masud Rana Postdoc (2021 - 2024) Now: Assistant Professor at KSU

Farjana Tasnim Mukta PhD Student (2021 - 2024) Now: Lecturer at KSU

Benjamin Philpot Undergrad (2022 - 2023)

Avery Meyer Undergrad (2022 - 2023)

Research Assistant (RA) Positions Available

Several Research Assistant (RA) positions are available for Ph.D. students who 1) have passed the prelims and 2) possess a strong interest in the exciting blend of Tologogy, Differential Geometry, Graph Theory, and AI

Introduction

I am an Associate Professor in the Department of Mathematics at the University of Tennessee. My research has been partially supported by the NSF, NIH, and pharmaceutical companies.

News

Among top 2% of world’s most-cited researchers

Math and AI-based Repositioning of Existing Drugs for COVID-19

Research Interests

Topological Data Analysis (TDA) Biomolecular data representations, Drug repurpose, SARS-CoV-2 inhibitors

Differential Geometry Solvation modeling, Differential geometric learning of molecules, Interactive manifolds for drug design

Graph Theory Flexibility of protein, Algebraic graph learning for drug discovery, Manifold learning

Machine Learning Multiscale manifold regularization, Convolution neural network (CNN), Graph convolution neural network (GNN), Multitask learning, Transfer learning, Autoencoder, Generative network complex (GNC), Generative adversarial network (GAN), Reinforcement learning.

Data analysis Low-dimensional mathematical representations, Knowledge based driven data analysis.

Mathematical models for bioscience Differential geometry representations, Multiscale weighted colored algebraic graphs, Topological learning, Flexibility-rigidity index (FRI) for biomolecules, Geometry based solvation modeling.

Drug Discovery D3R Grand Challenges (pose prediction, drug screening, affinity prediction), Small Molecular Property Predictions, Protein-Protein Binding Free Energy and Protein Thermodynamic Stability Changes Upon Mutation, Drug Repurposing, Drug Generation.

Quantitative systems pharmacology Develop mechanistic system biology model, Investigate potential therapeutic drug targets.

Numerical methods for PDEs High order interface methods, Geophysical flow, Electrostatic binding analysis.

NSF-2053284

NSF-2151802

NSF-2245903

Bristol-Myers Squibb

Pfizer

D3R Grand Challenges 4

Our team was the top performer

D3R Grand Challenges 3

Predictions of our team were ranked 1st in 10 of 26 predictive tasks

D3R Grand Challenges 2

Our prediction was ranked 1st for Set 1 (Stage2)

Online Server: FRI

Online server for the flexibility analysis of biomolecules based on flexibility and rigidity index.

FRI

Online Server: RI-Score

Online server for geometric graph theory or rigidity index (RI) based scoring function for protein ligand binding affinity prediction.

RI-Score

Online Server: DG-GL

Online server for differential geometry based geometric data analysis of molecular datasets.

DG-GL

Online Server: AGL-Score

Online server for algebraic graph theory based protein-ligand binding scoring, ranking, docking and screening.

AGL-Score