Scientific software
Proficient with commercial and open-source computational chemistry and biomolecular simulation ecosystems.
SchrodingerMOEDiscovery StudioMGLToolsAmberGROMACSNAMDGaussianCresset
RTD-A | PHYS-06/A | University of Cagliari
Dr. Mohd Athar
Computational Biophysicist | Molecular Modeling | Antimicrobial Resistance
I develop and apply molecular dynamics, enhanced sampling, quantum mechanics and multiscale simulations to understand molecular recognition, transport and inhibition in biological and supramolecular systems - with a current focus on RND-family multidrug efflux pumps such as AcrB, MdtF and MexB/D/F/Y.
Molecular Dynamics
Enhanced Sampling
RND Transporters
gEDES
Drug Discovery
DFT & QM/MM
01 | About
Computational chemistry across molecules, proteins and materials.
My work connects medicinal chemistry, computational physics, structural biology and chemical modeling.
My expertise is in the molecular modeling of systems ranging from small molecules and macromolecules to polymers, membranes and supramolecular assemblies. I have led computational medicinal-chemistry components of drug-discovery projects using docking, pharmacophore modeling, 3D-QSAR, quantum chemistry, molecular dynamics and binding free-energy workflows.
I enjoy building and testing new computational protocols, integrating software tools, automating analysis and applying emerging methods to difficult chemical and biological questions. My current research at the University of Cagliari focuses on the molecular basis of substrate recognition, transport and inhibition in RND efflux pumps, especially AcrB and the MexB/MexD/MexF/MexY transporters of Pseudomonas aeruginosa, using atomistic and coarse-grained simulations.
Beyond antimicrobial resistance, I work on flexible-protein recognition through the gEDES protocol, protein allostery, host-guest supramolecular chemistry, electronic structure modeling of nanomaterials and computational strategies for targeted drug discovery.
Current roleRTD-A researcher, SSD PHYS-06/A, Department of Physics, University of Cagliari.
Research identityPhysics-based modeling of molecular recognition, transport and free-energy landscapes.
MissionTurn simulations into mechanistic insight for antimicrobial resistance and molecular design.
TeachingMolecular modeling and computational biophysics for B.Sc. and M.Sc. Physics students.
02 | Expertise
Methods, software and computational workflows.
A compact view of the techniques I routinely use and develop in molecular modeling projects.
Molecular dynamics
Classical MD, membrane-protein simulations, enhanced sampling and trajectory analysis for complex biomolecular systems.
Umbrella samplingMetadynamicsMM/PBSAMM/GBSANetwork analysis
Structure-based design
Docking and virtual-screening workflows for protein-ligand and protein-peptide recognition problems.
Ensemble dockingInduced fit dockingQPLDVirtual screeningBinding sites
Ligand-based design
Computational lead optimization using feature mapping, descriptors, ADME/Tox prediction and statistical models.
Pharmacophores3D-QSARDescriptorsADME/ToxCore hopping
Quantum chemistry
DFT and quantum-mechanical modeling of host-guest systems, spectroscopic signatures, catalysis and self-assembly.
GaussianTurbomoleONIOMAIM/QTAIMNBOEDA
Parameterization
Small-molecule, inorganic and coarse-grained parameter development with validation against structural, energetic and thermochemical properties.
Small moleculesInorganic ligandsMartini CGValidation
HPC and GPU computing
Practical experience on high-performance computing systems, GPU workstations, long-timescale simulations and large-scale analysis.
CINECA LeonardoGPU workflowsBatch pipelinesBig data analysis
Automation and scripting
Custom scripts and workflow automation for docking, simulation setup, feature extraction, data processing and figure generation.
PythonBashPLUMEDWorkflow designReproducibility
Model building
Homology modeling, conformer generation, binding-site characterization and preparation of challenging protein-ligand systems.
Homology modelsConformersBinding volumesProtein-ligand prep
03 | Research lines
From efflux pumps to host-guest recognition.
Research themes spanning molecular transport, flexible-protein recognition, therapeutic design and electronic structure.
Antimicrobial resistance and RND transporters
Biophysical characterization of transport cycles, substrate specificity and inhibition in AcrB, MdtF and MexB/D/F/Y efflux systems using atomistic and coarse-grained simulations.
A01A03A04A12A16
gEDES and predictive molecular recognition
Co-development of generalized Ensemble Docking with Enhanced Sampling to generate druggable conformations of flexible, multidomain and allosteric proteins.
MetadynamicsDUD-E 38PLUMEDA05
Medicinal chemistry and targeted strategies
Computational drug-discovery projects involving BRCT-domain PPIs, M. tuberculosis targets, sirtuin inhibitors, viral proteases, QSAR and pharmacophore-guided screening.
PPI designQSARDockingA26A41
Supramolecular host-guest chemistry
DFT and MD studies of calixarenes, oxacalixarenes and p-sulfocalixarenes as drug carriers, sensors and recognition hosts.
CalixarenesHost-guestA07A13A45
Protein dynamics and allosteric regulation
Long-range signal propagation in protein systems, including allosteric regulation of pyruvate kinase from Streptococcus pneumoniae in collaboration with Osaka University.
SpPYKNetwork analysisAllosteryU2
Electronic structure and sensing
DFT, EDA, QTAIM and NBO analysis of fullerene C60 non-covalent dyads, environmental sensors and self-assembly processes.
C60 dyadsQTAIMSensingA17
04 | Impact
Bibliometric and academic snapshot.
Scopus-based numbers from the updated CV. Values can be updated in the HTML as your profile grows.
69Scientific publications
57Research articles
8Review articles
4Book chapters
918Total citations
19H-index
05 | Publications
Selected publications and manuscripts.
Use the search/filter tools to browse selected papers. Full lists are available through Google Scholar, Scopus and the CV.
2026
Molecular mechanism of transition-state inhibitors of bacterial antibiotic efflux pumps
npj Antimicrobials and Resistance 4, 35. DOI: 10.1038/s44259-026-00207-6
2026
Integrated approach to design 5-indolyl-pyrazoles as anti-TB agents
Bioorganic & Medicinal Chemistry Letters. DOI: 10.1016/j.bmcl.2026.130534
Q1DOI
2025
Conformational plasticity across phylogenetic clusters of RND multidrug efflux pumps and its impact on substrate specificity
Nature Communications 16, 11649. DOI: 10.1038/s41467-025-66751-3
2025
Molecular basis for multidrug efflux by an anaerobic RND transporter
Nature Communications 16, 10601. DOI: 10.1038/s41467-025-65565-7
2025
Toward the prediction of binding events in very flexible, allosteric, multidomain proteins
Journal of Chemical Information and Modeling 65, 2052-2065. DOI: 10.1021/acs.jcim.4c01810
2025
Unlocking the Gates: A novel diagnostic molecule for quantifying efflux levels in Gram-positive bacteria
Advanced Healthcare Materials 14, 2404145. DOI: 10.1002/adhm.202404145
2025
Enhancing solubility, dissolution rate and anticancer activity of Genistein via host-guest inclusion complexation with p-sulfocalixarene
BioNanoScience 15, 157. DOI: 10.1007/s12668-024-01726-0
Q3DOI
2024
Targeting the cyclin-dependent kinase family in anticancer drug discovery: From computational to experimental studies
Chemical Physics Impact 9, 100768. DOI: 10.1016/j.chphi.2024.100768
Q2DOI
2024
Experimental and computational characterization of p-sulfocalixarene mediated delivery system for morin hydrate
Medicine in Drug Discovery 22, 100180. DOI: 10.1016/j.medidd.2024.100180
Q1DOI
2023
Tripartite efflux pumps of the RND superfamily: what did we learn from computational studies?
Microbiology 169, 001307. DOI: 10.1099/mic.0.001307
ReviewDOI
2022
Through-bond driven through-space interactions in a fullerene C60 non-covalent dyad
Journal of Physical Chemistry A 126, 3629-3641. DOI: 10.1021/acs.jpca.1c10828
Q2DOI
2020
Pharmacophore modeling, molecular docking and molecular dynamics simulation for screening and identifying anti-dengue phytocompounds
Journal of Biomolecular Structure and Dynamics 38, 1726-1740. DOI: 10.1080/07391102.2019.1615002
65 cit.DOI
2019
Structure-based identification of novel sirtuin inhibitors against triple negative breast cancer
International Journal of Biological Macromolecules 140, 454-468. DOI: 10.1016/j.ijbiomac.2019.08.093
Q1DOI
2017
Investigation of structure and conformational equilibrium of Oxacalixarene: A DFT approach
Journal of Molecular Liquids 237, 473-483. DOI: 10.1016/j.molliq.2017.04.065
Q1DOI
2016
Pharmacophore model prediction, 3D-QSAR and molecular docking studies on vinyl sulfones targeting Nrf2 for anti-Parkinson drug design
Journal of Biomolecular Structure and Dynamics 34, 1282-1297. DOI: 10.1080/07391102.2015.1077343
47 cit.DOI
Full publication profiles: Google Scholar, Scopus, ORCID.
06 | Career
Academic and research timeline.
A career path connecting computational chemistry, structural biology, nanomaterials and computational biophysics.
Mar 2023 - Present
RTD-A Researcher, SSD PHYS-06/A
Department of Physics, University of Cagliari, Italy
Antimicrobial resistance and RND efflux mechanisms; Mex transporters; pyruvate kinase allostery; peptide hydrogels; gEDES refinement; coarse-grained force fields; INF-ACT and related computational projects.
Aug 2021 - Mar 2023
Postdoctoral Fellow / Assegnista di Ricerca
Department of Physics, University of Cagliari, Italy
Substrate and inhibitor transport through RND efflux pumps in Pseudomonas aeruginosa; enhanced sampling; EDES/gEDES protocol development; NIH and EFFORT-related activities.
Dec 2020 - Aug 2021
Institute Postdoctoral Fellow
Department of Chemistry, IIT Madras, India
First-principles electronic-structure modeling of fullerene C60 non-covalent dyads using DFT, EDA, QTAIM and NBO analyses.
Feb 2019 - Dec 2020
Postdoctoral Fellow, Computational Chemist
InStem / NCBS-TIFR, Bangalore, India
Protein-protein interactions, BRCT domain recognition, peptide design, mutational hotspots and SAR modeling for medicinal-chemistry lead optimization.
Sep 2013 - Oct 2019
Ph.D. in Chemical Sciences
Central University of Gujarat, India
Thesis: In-silico study of structural, energetic and biological properties of calixarene derivatives. Supervisor: Prof. Prakash C. Jha. Thesis link.
Jun 2011 - Jun 2013
M.Sc. Applied Chemistry - University Gold Medalist
Babasaheb Bhimrao Ambedkar University, Lucknow, India
Thesis on inclusion complexation of thiazolidinediones with cyclodextrins using docking and quantum-mechanical calculations.
Jul 2011
B.Sc. Biotechnology
H.N.B. Garhwal University, Uttarakhand, India
First class with distinction, establishing the biological foundation for later computational chemistry and biophysics work.
07 | Projects and funding
Funded research, consortia and HPC computing.
Selected projects where I contribute computational modeling, workflow development, simulation and analysis.
PNRR INF-ACT
One Health basic and translational actions addressing unmet needs on emerging infectious diseases. Role: RTD-A researcher working on RND efflux mechanisms and antimicrobial resistance.
2023-presentRND pumpsAMR
ISCRA-C on Leonardo
Coordinator of the CINECA HPC project "Stochastic vs. Coordinated: Redefining RND Efflux Mechanisms" with 80,000 GPU hours on Leonardo.
2026Coordinator80k GPU h
EFFORT consortium
Efflux pump inhibitors to overcome antibiotic resistance, including atomistic and coarse-grained modeling of inhibitor binding and transport accessibility.
ANRProject link
NIH efflux project
Optimization of efflux avoidance and inhibition for antibiotic development, with modeling of antibiotic specificities in Pseudomonas aeruginosa efflux pumps.
R01-AI136799Uni Oklahoma
DP4DD webserver
Webserver to generate druggable conformations of difficult proteins for accurate drug design; workflow development and gEDES simulations on DUD-E 38.
Sardegna Ricerche71K EUR
Take the (bi)cycle
Computational pipeline for transformative screening and design of bicyclic peptides, including gEDES-style methodology and protein/peptide interaction modeling.
2025-present38K EUR
08 | Teaching and supervision
Courses, tutorials and mentorship.
University teaching, hands-on schools and supervision of research trainees.
| Year | Course / activity | Level and institution | Hours / credits |
|---|---|---|---|
| 2025-26 | Laboratory of Molecular Modeling of Biological Systems | M.Sc. Physics, University of Cagliari | 48 h / 6 CFU |
| 2025-26 | Methods and Models in Computational Biophysics | B.Sc. Physics, University of Cagliari | 24 h / 3 CFU |
| 2024-25 | Molecular Modeling of Biological Systems | M.Sc. Physics, University of Cagliari | 24 h / 6 CFU |
| 2023-24 | Molecular Modeling of Biological Systems | M.Sc. Physics, University of Cagliari | 24 h / 6 CFU |
| 2023-25 | BioExcel School: Molecular modeling through enhanced sampling and docking | Practical tutorial, Pula (CA) | Three editions |
| 2017-18 | Introduction to Drug Discovery / Computational Chemistry Experiments | Central University of Gujarat, India | Undergraduate and master's teaching |
1PhD co-supervised
1Postdoctoral researcher coordinated
2Research fellows supervised
3M.Sc. theses co-supervised
09 | Service, talks and awards
Academic service and recognition.
Selected service roles, external recognition, invited lectures and conference contributions.
Awards and honours
- 2026 Programma Mobilità Giovani Ricercatori (MGR) Grant, University of Cagliari.
- 2026 ISCRA Class C HPC project coordinator, 80,000 GPU hours on Leonardo.
- 2018 DST-SERB International Travel Grant for ABCchem 2018, Mexico.
- 2018 Cover article in Molecular Diversity.
- 2015-19 DST-INSPIRE Junior/Senior Research Fellowship.
- 2013 University Gold Medal, M.Sc. Applied Chemistry.
Invited talks and presentations
- 2025 Gordon Research Conference on Multi-Drug Efflux Systems, Lucca, Italy - oral contribution.
- 2024 Computational Approaches for Investigating Metabolites Fate, MICROS 2024.
- 2024 A Computational Protocol to Improve Drug Discovery, Aligarh Muslim University.
- 2023 Computational Chemistry and Molecular Modelling, Parul University.
- 2022 International Desktop Seminar on Chemical Sciences, Ganpat University.
- 2018 10th International Congress on Structural Biology, Helsinki.
Peer review and evaluation
Reviewer for Nature, Journal of Chemical Information and Modeling, Journal of Biomolecular Structure and Dynamics, Scientific Reports, ACS Infectious Diseases, Journal of Medicinal Chemistry and Frontiers in Microbiology.
Grant evaluator for the National Science Center (NCN), Poland in 2025. Editorial Board Member: Medicon Microbiology.
Training and professional development
Certified training includes Python development, laboratory practices and ethics, structure-based drug design, LaTeX, advanced material characterization, open resources, IPR and patent topics, CADD/PK-PD modeling and hands-on biotechnology training.
10 | Collaborations
Research Groups, Collaborations & Scientific Network.
Research groups, mentors and collaborators who shaped my scientific development from computational chemistry to computational biophysics, antimicrobial resistance and molecular modeling.
University of Cagliari, Italy
Current research environment at the Department of Physics, focused on RND efflux pumps, antimicrobial resistance, gEDES methodology, allostery and coarse-grained simulations.
Current group
RTD-A
PHYS-06/A
Computational Chemistry Group, CUG India
Doctoral research under Prof. Prakash C. Jha at Central University of Gujarat. Work focused on calixarenes, host–guest chemistry, DFT, molecular docking, molecular dynamics and computational drug discovery.
InStem / NCBS-TIFR Bangalore
Postdoctoral research with Prof. Ashok Venkitaraman and Dr. Kavitha Bharatham on BRCT domains, protein–peptide interactions, mutational hotspots and computational medicinal chemistry.
IIT Madras, India
Institute Postdoctoral Fellow with Prof. Archita Patnaik working on fullerene C60 non-covalent dyads, electronic structure, QTAIM, NBO and non-covalent interactions.
Italy Collaborations
Collaborations with University of Pavia and University of Trieste on antibiotic adjuvants, membrane interactions, heterochiral antimicrobial peptides and peptide self-assembly.
University of Pavia
University of Trieste
EFFORT & AMR Network
International collaborations with Institut Pasteur Lille, Goethe University Frankfurt, Aix-Marseille Université and University of Oklahoma on RND transporters, efflux-pump inhibitors and antibiotic resistance mechanisms.
Pasteur Lille
Goethe Frankfurt
University of Oklahoma
Osaka University, Japan
Collaboration with Prof. Kunihiko Nishino and Dr. Atsushi Taguchi on allosteric regulation of Streptococcus pneumoniae pyruvate kinase using molecular simulations and network analysis.
Allostery
SpPYK
Network analysis
Indian Academic Network
Collaborations with Gujarat University, Central University of Gujarat, Pandit Deendayal Energy University and Aligarh Muslim University on drug discovery, QSAR, pharmacophores, supramolecular systems and computational chemistry.
Gujarat University
CUG
PDEU
AMU
Software & User Communities
Participation in Molecular Operating Environment and Cresset user-group meetings, with interests in workflow development, ligand design, reproducible modeling and scientific software.
MOE
Cresset
Workflow development
11 | Useful links
Profiles, documents and selected evidence links.
Links extracted from the CV and from your existing webpage.
Research profiles
Academic documents
- Download full CV PDF (upload this PDF with the website files)
- Ph.D. thesis: Calixarene derivatives
- Ph.D. thesis reviewer evidence
- Previous personal website archive
12 | Media
Media & Public Recognition
News coverage, outreach and public engagement activities highlighting research contributions in computational biophysics and antimicrobial resistance.
University of Cagliari Magazine (2026)
Research on multidrug efflux pumps and antimicrobial resistance featured by the University of Cagliari. The article discusses computational approaches to understanding bacterial resistance mechanisms and future antibiotic strategies.
Featured in Amar Ujala (India) (2026)
National newspaper coverage highlighting research contributions to combating antibiotic resistance and international research activities at the University of Cagliari.
University Gold Medal Featured in Newspaper (2013)
Following the award of the University Gold Medal for securing first rank in the M.Sc. Applied Chemistry programme at BBAU, Lucknow, local media highlight.
2013
University Gold Medal
Media Coverage
13 | Gallery
Photo Gallery
Selected moments from academic, research, conference and outreach activities.
14 | Contact
Get in touch.
For collaborations, teaching, supervision and computational chemistry or biophysics inquiries.
Contact information
AddressVia Carlo Baudi di Vesme 14, 09121 Cagliari (CA), Italy
Phone+39 334 305 7554
Online profiles
Academic and professional profiles are linked below.