Jans Alzate-Morales

Who I Am

About Me

Computational Chemist

AI/ML Practitioner

Bioinformatics Researcher

I am a researcher and educator with over 18 years of experience at the intersection of computational chemistry, bioinformatics, and molecular biology — and an active AI/ML student and practitioner bridging scientific rigor with modern data-driven methods.

Currently an Associate Professor at the Bioinformatics Department, University of Talca (Chile), and a second-year student of the AI/ML Diploma at Lambton College (Ottawa), I combine decades of academic expertise with cutting-edge machine learning applications.

My passion lies in using computational multiscale methods — from quantum mechanics to AI/ML models — to tackle critical challenges in drug discovery, antibiotic resistance, and cancer research. I have secured multiple competitive national research grants and authored 69 peer-reviewed articles with over 1,570 citations. I am a proud member of the Center for Bioinformatics and Molecular Simulations (CBSM) at UTalca.

My research trajectory began during my DAAD-funded Ph.D. at the University of Chile, where I studied protein-ligand interactions in the CDK2/Cyclin cancer system — including research stays at the University of Valencia (Spain) and the Fritz Haber Institute, Max Planck Society (Berlin, Germany). Since joining CBSM as a postdoctoral researcher in 2007 — supported by the Chilean Government's PBCT program — I have built a comprehensive research program spanning drug binding kinetics, enzymatic catalysis, and enzyme engineering.

                Dean's Honour List
                Winter 2025 — Lambton College, AI & ML
              

                Fellow of the Royal Society of Chemistry
                FRSC — RSC, United Kingdom (since November 2020)
              

                Member — American Chemical Society
                ACS, United States (Regular Member since May 2010)
              

Ottawa, Ontario, Canada

jalzatemorales@gmail.com

Spanish (Native) • English (Professional)

ORCID: 0000-0001-9624-7849

Scopus Author ID: 15829193100

ResearcherID: A-5407-2008

CBSM Lab, University of Talca

What I Do

Skills & Expertise

Artificial Intelligence & ML

Machine Learning (supervised/unsupervised)

Deep Learning & Neural Networks

Natural Language Processing (NLP)

Computer Vision & LVM (NVIDIA)

Digital Twins (NVIDIA IsaacSim)

Programming & Data Science

Python (Intermediate)

Data Visualization (Matplotlib, Seaborn, Plotly)

Feature Engineering & Data Preprocessing

Statistics & Probability / Linear Algebra

Big Data Analysis & Data Mining

Computational Chemistry & Biology

Molecular Mechanics (MM) & Dynamics

Quantum Mechanics (QM) & QM/MM

Drug Design & Molecular Docking

Bioinformatics & Protein Modeling

Multiscale Computational Methods

Systems & Research Tools

Linux (CentOS, Ubuntu — Admin level)

Scientific Writing & Grant Proposals

Project Management & Team Leadership

Academic Teaching & Mentoring

Dimensionality Reduction Techniques

Python PyTorch scikit-learn Pandas NumPy Matplotlib Seaborn Plotly NVIDIA LVM IsaacSim QM/MM Molecular Dynamics NLP Computer Vision Digital Twins Linux Office 365

My Journey

Experience & Education

December 2025 — Present

AI/ML Researcher

Global Sensor Systems Inc. • Ottawa, ON

5-month temporary & part-time contract

Technical liaison between GSS and Lambton College; supported AI architecture benchmarking and model comparison.
Performed simulation tests using synthetic and real-world data with computer vision models (NVIDIA LVM).
Supported research and prototyping of Digital Twin models using NVIDIA IsaacSim.
Provided technical documentation and contributed to project reporting.

Computer VisionDigital TwinsNVIDIA IsaacSimAI Benchmarking

September 2025 — Present

Member at Large — Parent Council (Volunteer)

Lady Evelyn Alternative School • Ottawa, ON

Collaborated with council members to support school community initiatives.
Led the successful campaign to save Lady Evelyn School: built the webpage and online petition.
Contributed to planning, logistics, and promotion of community events.

Community LeadershipWeb DevelopmentAdvocacy

August 2014 — Present

Associate Professor — Bioinformatics Department

Faculty of Engineering, University of Talca • Talca, Chile

Led national and international research funding efforts; managed multi-disciplinary projects.
Authored high-impact research, establishing the Faculty as the top performer in scientific metrics within the University.
Taught semestral courses in Bioinformatics Engineering with student perception scores of 3.8/4.0.
Delivered hybrid Ph.D.-level courses in Modeling of Chemical & Biological Systems.
Mentored and supervised 16 undergraduate and 10 graduate students.
Directed a Ph.D. program through two accreditation processes (CNA-Chile).
Chaired and co-chaired several international conferences at UTalca.

Research LeadershipTeachingGrant ManagementMentoring

2010 — 2014

Lecturer & Assistant Professor — Bioinformatics Department

Faculty of Engineering, University of Talca • Talca, Chile

Hired as lecturer in 2010 and obtained a permanent position as Assistant Professor in 2012, attached to CBSM.
Taught undergraduate and graduate courses in computational chemistry and bioinformatics.
Led research projects in protein-ligand binding, securing the first FONDECYT Iniciación grant (2010) as Principal Researcher.

TeachingResearchFONDECYT Iniciación 2010

2007 — 2010

Postdoctoral Researcher

Center for Bioinformatics and Molecular Simulation (CBSM), University of Talca • Talca, Chile

Awarded a postdoctoral scholarship for Academy Insertion by the Chilean Government through the Bicentennial Program of Science and Technology (PBCT).
Continued research on computational methods for protein-ligand interactions and enzymatic catalysis.
Integrated into the CBSM research group, establishing the foundations of his long-term research agenda.

Postdoctoral ResearchPBCT FellowshipCBSM

Academic Impact

Research & Grants

0 Peer-Reviewed Articles

0+ Citations (Google Scholar)

0+ Students Supervised

0 Peer Reviews (ORCID)

0 Competitive Grants (Lead PI)

Research Funding History

Complete record of competitive research grants as Lead Researcher, Associate Researcher, and Sponsoring Researcher.

Lead & Principal Researcher

Research Focus Areas

Protein-Drug Interaction

Understanding the subtle phenomena at the molecular level in protein-drug binding, using molecular docking, molecular dynamics, and free energy methods.

Enzymatic Catalysis (QM/MM)

Mechanistic investigation of enzymatic reactions from X-ray structures to QM/MM simulations, covering phosphoryl transfer, oxidation, and biotransformation reactions.

Antibiotic Resistance & Cancer

Design of novel inhibitors targeting kinases and HMP-kinases linked to antibiotic resistance and cancer using multiscale computational approaches combined with experiments.

Drug Binding Kinetics

Computational protocols for estimating drug residence time in protein-ligand complexes via enhanced sampling molecular dynamics — a key predictor of in vivo efficacy.

Enzyme & Protein Design

Rational protein design using quantum mechanical calculations and site-directed mutagenesis; substrate recognition in protein kinases, ligninolytic enzymes, and proteases.

AI/ML for Molecular Sciences

Applying machine learning, deep learning, and data science to accelerate molecular discovery — bridging 18+ years of chemical intuition with modern data-driven approaches.

Peer Review Activity (ORCID Verified)

Journal of Chemical Information and Modeling

ACS Publications

The Journal of Physical Chemistry

ACS Publications

Journal of Medicinal Chemistry

ACS Publications

ACS Catalysis

ACS Publications

Environmental Science & Technology

ACS Publications

PLoS ONE

PLOS

Chemistry

MDPI

28 verified peer reviews for 7 journals • View on ORCID

Scholarly Output

Selected Publications

69 peer-reviewed articles in leading journals. Showing the most recent works.

2026 International Journal of Molecular Sciences

Discovery and Preliminary Characterization of Lactose-Transforming Enzymes in Ewingella americana L47: A Genomic, Biochemical, and In Silico Approach

Rivero K, Valenzuela R, Rivero I, General P, Neira N, Contreras F, Alzate-Morales J, Muñoz-Villagrán C, Vera C, Arenas-Salinas M, et al.

DOI: 10.3390/ijms27021128 Journal Article

2025 The Journal of Physical Chemistry B

Molecular Insights into Phosphonium-Based Ionic Liquid Extraction of Phenolic Pollutants from Aqueous Solutions

Sadeghi Googheri MS, Hozhabr Araghi S, Alzate-Morales J, Amalraj J.

DOI: 10.1021/acs.jpcb.5c02909 Journal Article

2025 Journal of Chemical Information and Modeling

Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods

Bedoya M, Adasme-Carreño F, Peña-Martínez PA, Muñoz-Gutiérrez C, Peña-Tejo L, Márquez Montesinos JCE, Hernández-Rodríguez EW, González W, Martínez L, Alzate-Morales J.

DOI: 10.1021/acs.jcim.5c00871 Journal Article

2025 ACS Omega

Computational Estimation of Residence Time on Roniciclib and Its Derivatives against CDK2: Extending the Use of Classical and Enhanced Molecular Dynamics Simulations

Bravo-Moraga F, Bedoya M, Zinovjev K, Tuñon I, Alzate-Morales J.

DOI: 10.1021/acsomega.5c00555 Journal Article

2025 The Journal of Physical Chemistry A

Computational Study of the 1,3-Dipolar Cycloaddition between Criegee Intermediates and Linalool: Atmospheric Implications

Durán R, Barrales-Martínez C, Solorza J, Alzate-Morales J.

DOI: 10.1021/acs.jpca.4c06728 Journal Article

2024 Journal of Chemical Information and Modeling

Understanding the Differences of Danusertib's Residence Time in Aurora Kinases A/B: Dissociation Paths and Key Residues Identified Using Conventional and Enhanced Molecular Dynamics Simulations

Bravo-Moraga F, Bedoya M, Vergara-Jaque A, Alzate-Morales J.

DOI: 10.1021/acs.jcim.4c00387 Journal Article

2024 Journal of Chemical Information and Modeling

Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition

Velázquez-Libera JL, Caballero J, Alzate-Morales J, Ruiz-Pernía JJ, Tuñón I.

DOI: 10.1021/acs.jcim.3c01971 Journal Article

2023 ChemCatChem

Insights into the Structural and Energetic Descriptions of Ubiquitin Specific Protease 7 (USP7) Catalytic Mechanisms by Hybrid QM/MM Simulations

Velázquez-Libera JL, Caballero J, Alzate-Morales J, Ruiz-Pernía JJ, Tuñón I.

DOI: 10.1002/cctc.202300344 Journal Article

2023 Physical Chemistry Chemical Physics

Effect of Strand Register in the Stability and Reactivity of Crystals from Peptides Forming Amyloid Fibrils

Muñoz-Gutiérrez C, Adasme-Carreño F, Alzate-Morales J, Ireta J.

DOI: 10.1039/D3CP01762A Journal Article

2023 Physical Chemistry Chemical Physics

Can Graphene Improve the Thermal Conductivity of Copper Nanofluids?

Olguín-Orellana GJ, Soldano GJ, Alzate-Morales J, Camarada MB, Mariscal MM.

DOI: 10.1039/D3CP00064H Journal Article

2022 Journal of Chemical Information and Modeling

Structural Insights into the Inhibition Site in the Phosphorylcholine Phosphatase Enzyme of Pseudomonas aeruginosa

Bustos D, Hernández-Rodríguez EW, Poblete H, Alzate-Morales J, Challier C, Boetsch C, Vergara-Jaque A, Beassoni P.

DOI: 10.1021/acs.jcim.2c00059 Journal Article

2021 ACS Catalysis

How a Second Mg²⁺ Ion Affects the Phosphoryl-Transfer Mechanism in a Protein Kinase: A Computational Study

Recabarren R, Zinovjev K, Tuñón I, Alzate-Morales J.

DOI: 10.1021/acscatal.0c03304 Journal Article

2021 Protein Science

Crystal Structure and Molecular Dynamics Simulations of a Promiscuous Ancestor Reveal Residues and an Epistatic Interaction Involved in Substrate Binding and Catalysis in the ATP-Dependent Vitamin Kinase Family

Gonzalez-Ordenes F, Bravo-Moraga F, Gonzalez E, Hernandez-Cabello L, Alzate-Morales J, Guixé V, Castro-Fernandez V.

DOI: 10.1002/pro.4040 Journal Article

2020 Journal of Chemical Information and Modeling

Molecular Insights into the Trapping Effect of Ca²⁺ in Protein Kinase A: A Molecular Dynamics Study

Solorza J, Recabarren R, Alzate-Morales J.

DOI: 10.1021/acs.jcim.9b00857 Journal Article

2019 Chemical Science

Studying the Phosphoryl Transfer Mechanism of the E. coli Phosphofructokinase-2: From X-ray Structure to QM/MM Simulations

Murillo-López J, Zinovjev K, et al., Recabarren R, Alzate-Morales J, Caballero J, Tuñón I, et al.

DOI: 10.1039/c9sc00094a Journal Article

2019 PLOS ONE

Mechanistic Insights into the Phosphoryl Transfer Reaction in Cyclin-Dependent Kinase 2: A QM/MM Study

Recabarren R, Stein M, Osorio EH, Caballero J, Tuñón I, Alzate-Morales JH.

DOI: 10.1371/journal.pone.0215793 Journal Article

2018 Biochemistry

Multiscale Simulations of Clavulanate Inhibition Identify the Reactive Complex in Class A β-Lactamases and Predict the Efficiency of Inhibition

Fritz RA, Alzate-Morales JH, Spencer J, Mulholland AJ, Van Der Kamp MW.

DOI: 10.1021/acs.biochem.8b00480 Journal Article

Recent Work

Projects & Highlights

A growing portfolio bridging 18+ years of domain expertise in molecular sciences with applied AI/ML skills.

Featured Industry Project

Computer Vision • Digital Twins • AI Benchmarking

Digital Twin Simulation & AI Model Benchmarking

At Global Sensor Systems Inc. (Ottawa), served as technical liaison between GSS and Lambton College. Performed simulation testing with synthetic and real-world data using NVIDIA Large Vision Models (LVM) for real-time computer vision tasks. Prototyped Digital Twin models with NVIDIA IsaacSim and contributed to benchmarking and comparative evaluation of vision architectures. Produced technical documentation and project reports for industry stakeholders.

NVIDIA IsaacSimLVM / Large Vision ModelsDigital Twins Computer VisionPythonAI Benchmarking

AI/ML Coursework & Research Projects

Computer Vision • Deep Learning

Real-Time Object Detection: SSD vs. YOLO

Capstone project implementing and benchmarking SSD and YOLO object detection architectures on the COCO dataset (5k training images). Evaluated detection accuracy, inference speed, and trade-offs between the two models.

PyTorchSSDYOLOCOCOJupyter

View on GitHub

ML for Drug Discovery • Cheminformatics

Drug Activity Classifier from Binding Free Energies

Applied Gaussian Naïve Bayes classification to distinguish active vs. inactive drug compounds using 9 physicochemical descriptors (RDKit: MW, LogP, TPSA, HBD/HBA…) on 199 compounds across 8 protein targets. Achieved 78% accuracy and F1-score of 72%.

scikit-learnRDKitPandasNaive BayesPython

View on GitHub

ML + Computational Chemistry • Conference

ML Classifiers for Kinase Inhibitor Prediction

Developed and compared three ML classification algorithms on a curated kinase inhibitor dataset with physicochemical and molecular descriptors (RDKit). Presented at the MoML @ Mila conference, bridging domain expertise with modern ML practice.

scikit-learnRDKitPythonKinase DataJupyter

View on GitHub

Deep Learning • NLP • Language Models

MakeMore: Character-Level Language Model

Replication of Andrej Karpathy's MakeMore project as the final assignment for the Neural Networks & Deep Learning course. Built character-level generative models from scratch — from bigrams and MLPs to deeper networks — exploring backpropagation and training dynamics.

PyTorchNLPDeep LearningPythonJupyter

View on GitHub

All coursework and research code is publicly available on GitHub. View all repositories →

About Me

Skills & Expertise

Artificial Intelligence & ML

Programming & Data Science

Computational Chemistry & Biology

Systems & Research Tools

Experience & Education

AI/ML Researcher

Member at Large — Parent Council (Volunteer)

Associate Professor — Bioinformatics Department

Lecturer & Assistant Professor — Bioinformatics Department

Postdoctoral Researcher

College Diploma — Artificial Intelligence & Machine Learning

Ph.D. in Chemistry

Bachelor's in Pharmaceutical Chemistry

Research & Grants

Research Funding History

Lead & Principal Researcher

Multiscale Inhibitors for Protein Kinases & HMP-Kinases

Residence Time in Protein-Ligand Complexes

Biotransformation by Ligninolytic Enzymes from P. chrysosporium

Protein-Ligand Binding via Hybrid Computational Approaches

Sponsoring & Associate Researcher

Cylindrin-Like Structures via Microsecond Molecular Dynamics

Multisteric Drugs for Polypharmacological Agents

Chemical Poly-Bullets for Nicotinic Receptors & Monoamine Transporters

Monoaminergic Proteins & Nicotinic Receptors Polypharmacology

PKA & Potassium Channel Structural Interactions

Molecular Simulations of Biological Catalysts

International Research Network Formation

Research Focus Areas

Protein-Drug Interaction

Enzymatic Catalysis (QM/MM)

Antibiotic Resistance & Cancer

Drug Binding Kinetics

Enzyme & Protein Design

AI/ML for Molecular Sciences

Peer Review Activity (ORCID Verified)

Selected Publications

Discovery and Preliminary Characterization of Lactose-Transforming Enzymes in Ewingella americana L47: A Genomic, Biochemical, and In Silico Approach

Molecular Insights into Phosphonium-Based Ionic Liquid Extraction of Phenolic Pollutants from Aqueous Solutions

Moltiverse: Molecular Conformer Generation Using Enhanced Sampling Methods

Computational Estimation of Residence Time on Roniciclib and Its Derivatives against CDK2: Extending the Use of Classical and Enhanced Molecular Dynamics Simulations

Computational Study of the 1,3-Dipolar Cycloaddition between Criegee Intermediates and Linalool: Atmospheric Implications

Understanding the Differences of Danusertib's Residence Time in Aurora Kinases A/B: Dissociation Paths and Key Residues Identified Using Conventional and Enhanced Molecular Dynamics Simulations

Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition

Insights into the Structural and Energetic Descriptions of Ubiquitin Specific Protease 7 (USP7) Catalytic Mechanisms by Hybrid QM/MM Simulations

Effect of Strand Register in the Stability and Reactivity of Crystals from Peptides Forming Amyloid Fibrils

Can Graphene Improve the Thermal Conductivity of Copper Nanofluids?

Structural Insights into the Inhibition Site in the Phosphorylcholine Phosphatase Enzyme of Pseudomonas aeruginosa

How a Second Mg²⁺ Ion Affects the Phosphoryl-Transfer Mechanism in a Protein Kinase: A Computational Study

Crystal Structure and Molecular Dynamics Simulations of a Promiscuous Ancestor Reveal Residues and an Epistatic Interaction Involved in Substrate Binding and Catalysis in the ATP-Dependent Vitamin Kinase Family

Molecular Insights into the Trapping Effect of Ca²⁺ in Protein Kinase A: A Molecular Dynamics Study

Studying the Phosphoryl Transfer Mechanism of the E. coli Phosphofructokinase-2: From X-ray Structure to QM/MM Simulations

Mechanistic Insights into the Phosphoryl Transfer Reaction in Cyclin-Dependent Kinase 2: A QM/MM Study

Multiscale Simulations of Clavulanate Inhibition Identify the Reactive Complex in Class A β-Lactamases and Predict the Efficiency of Inhibition

Projects & Highlights

Digital Twin Simulation & AI Model Benchmarking

AI/ML Coursework & Research Projects

Real-Time Object Detection: SSD vs. YOLO

Drug Activity Classifier from Binding Free Energies

ML Classifiers for Kinase Inhibitor Prediction

MakeMore: Character-Level Language Model

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