Publications
Journal articles, workshop papers and manuscripts from my doctoral and current research, linked by the questions they build on.
Doctoral thesis · Indian Institute of Technology Delhi · 2026
Rational Design of Functionalized Nanomaterials for Biological Applications Using Molecular Dynamics and Machine Learning
Advised by Prof. Divya Nayar
Research lineage
2026
Prediction of Polymer Adhesion and Inverse Design of Heterogeneous Surfaces using Data-Driven Approaches
S. Panigrahy, A. James, D. Nayar
Molecular Systems Design & Engineering · 2026 · under review
Forward prediction at R² = 0.995, and a tandem network that designs surface patterns for a target free-energy profile.
Cite
@article{panigrahy2026adhesion, title = {Prediction of Polymer Adhesion and Inverse Design of Heterogeneous Surfaces using Data-Driven Approaches}, author = {S. Panigrahy and A. James and D. Nayar}, journal = {Molecular Systems Design & Engineering}, year = {2026}, }
2025
Data-driven prediction of polymer surface adhesion using high-throughput MD and hybrid network models
S. Panigrahy, A. James, D. Nayar
AI for Accelerated Materials Design (AI4Mat) Workshop, NeurIPS · 2025 · workshop paper
A CNN–GRU–attention network trained on about 470k umbrella-sampling runs predicts full adhesion free-energy profiles.
Paper ↗Cite
@inproceedings{panigrahy2025neurips, title = {Data-driven prediction of polymer surface adhesion using high-throughput MD and hybrid network models}, author = {S. Panigrahy and A. James and D. Nayar}, booktitle = {AI for Accelerated Materials Design (AI4Mat) Workshop, NeurIPS}, year = {2025}, }
2024
Differential local ordering of mixed crowders determines effective size and stability of ss-DNA capped gold nanoparticle
S. Panigrahy, D. Nayar
The Journal of Chemical Physics 160, 014901 · 2024
Small crowders act through soft, direct adsorption rather than depletion; a glycine + serine mixture gives the largest particle radius.
Paper ↗Cite
@article{panigrahy2024jcp, title = {Differential local ordering of mixed crowders determines effective size and stability of ss-DNA capped gold nanoparticle}, author = {S. Panigrahy and D. Nayar}, journal = {The Journal of Chemical Physics}, volume = {160}, pages = {014901}, year = {2024}, doi = {10.1063/5.0179238}, }
In Silico View of Crowding: Biomolecular Processes to Nanomaterial Design
S. Rajput, S. Panigrahy, D. Nayar
ACS Omega 9, 29953–29965 · 2024
A review of how simulation has reshaped our picture of crowding, from protein folding to nanomaterial design.
Paper ↗Cite
@article{rajput2024crowding, title = {In Silico View of Crowding: Biomolecular Processes to Nanomaterial Design}, author = {S. Rajput and S. Panigrahy and D. Nayar}, journal = {ACS Omega}, volume = {9}, pages = {29953–29965}, year = {2024}, doi = {10.1021/acsomega.4c03344}, }
2023
Structure, energetics and dynamics in crowded amino acid solutions: a molecular dynamics study
S. Panigrahy, R. Sahu, S. K. Reddy, D. Nayar
Physical Chemistry Chemical Physics 25, 5430–5442 · 2023
A one-parameter NBFIX correction removes artificial aggregation and recovers experimental osmotic coefficients, viscosities and diffusivities.
Paper ↗Cite
@article{panigrahy2023pccp, title = {Structure, energetics and dynamics in crowded amino acid solutions: a molecular dynamics study}, author = {S. Panigrahy and R. Sahu and S. K. Reddy and D. Nayar}, journal = {Physical Chemistry Chemical Physics}, volume = {25}, pages = {5430–5442}, year = {2023}, doi = {10.1039/d2cp04238j}, }
In preparation
Effect of mixed molecular crowding environment on the conformational properties of ss-DNA
S. Panigrahy, D. Nayar
Manuscript in preparation
Crowder chemistry, not just excluded volume, decides whether a DNA strand extends, stiffens or folds.
Effect of size on stability of citrate adsorbed to gold nanoparticle: assessing polarized and non-polarized models
S. Panigrahy, D. Nayar
Manuscript in preparation
Metal polarizability switches citrate from non-specific coating to facet-selective binding on {111}.
Also on OpenReview.