👋🏽 I'm a postdoc inFerguson lab, PME @UChicago.

🔭 Active works

• development of ultra coarse-grained models and enhanced sampling methods using machine learning for studying phase transitions of chiral and large multi-molecular systems.

✔️ Completed works

• development and application of a novel machine learning (ML) based solution for tackling a grand challenge in water.Featured on TACC magazine -https://texascale.org/2022/powering-discoveries/ai-and-real-solutions-frontera/
• implementation of metadynamics inSSAGES andPySAGES. Link to paper:https://doi.org/10.48550/arXiv.2301.04835
• implementation of artificial neural network based CV inPLUMED for direct enhanced sampling along system and environmental variables (PINES). Link to paper:https://doi.org/10.48550/arXiv.2308.08680
• active learning of polarizable nanoparticle phase diagrams for the guided design of triggerable self-assembling superlattices.Link to published paper — featured in MSDE recent HOT 🔥 articles collection.
• permutationally invariant enhanced sampling method (PINES) [https://doi.org/10.1021/acs.jctc.3c00923].
• implementation of collective variables inPySAGES. Link to paper:https://doi.org/10.1038/s41524-023-01189-z
• Data-driven prediction of aIIbb3 integrin activation paths using manifold learning and deep generative modeling. [https://doi.org/10.1016/j.bpj.2023.12.009]

🕰️ Previously

• Graduate research atSarupria group, ChBE @Clemson.
  • Dissertation (PhD, 2019): Towards computer aided engineering of proteins and protein-surface complexes.
  • Thesis (MS, 2015): Understanding molecular interactions between proteins and carbon nanomaterials.
• Software developer inmscripts team at Exeter India @Banglore.

♾️ Interests

• Data-driven methods & applications.
• Statistical mechanics, enhanced sampling methods, probability, nonlinear dynamics.
• Modeling, numerical methods, computational design.
• Deep learning, coding, algorithms, network theory.

🗨 Reach out @

• ✉️sivadasetty@uchicago.edu
• LinkedIn

📜 Works

• Google Scholar
• ORCiD
• https://gist.github.com/sivadasetty

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1. Ferg-Lab/pinesFerg-Lab/pinesPublic

   Permutationally invariant networks for enhanced sampling (PINES)

   C++ 6

2. Ferg-Lab/activeLearningPFASLinearFerg-Lab/activeLearningPFASLinearPublic

   Data-driven discovery of linear molecular probes with optimal selective affinity for PFAS in water

   Jupyter Notebook 3 1

3. image_method_MICCoMimage_method_MICCoMPublic

   LAMMPS fix for calculating many-body forces using image method.

   C++ 1

4. SSAGESLabs/PySAGESSSAGESLabs/PySAGESPublic

   Python Suite for Advanced General Ensemble Simulations

   Python 77 27

5. containerscontainersPublic

   singularity definitions of GROMACS

   Shell 3 1

6. Ferg-Lab/integrin_molgenFerg-Lab/integrin_molgenPublic

   Deep generative modeling of large multi-molecular systems

   Jupyter Notebook 1