I am a PhD student at the center for Biophysics and Quantitative Biology at the University of Illinois at Urbana-Champaign. I study antibiotic permeation through bacterial outer membrane porins using molecular dynamics simulations. Developing new antibiotics against Gram-negative bacteria is a huge challenge as drugs face barriers crossing the lipopolysaccharide-coated outer membrane. Our experimental collaborator Dr. Paul J. Hergenrother's group from UIUC has recently found that positively charged primary amine group enhances the permeation of drugs through porins of the outer membrane. I use free energy calculation methods such as Bias Exchange Umbrella Sampling to characterize the permeation mechanism of newly synthesized antibiotics through outer membrane porins.
I also study the binding of Hexokinase, a cytosolic protein, into the membrane using the Highly Mobile Membrane Mimetic (HMMM). Hexokinase binds to the mitochondrial membrane and then to VDAC on the membrane surface. This process plays a key role in the survival of cancer cells. I use Atomic Resolution Brownian Dyanmics (ARBD) to characterize the binding of Hexokianse to VDAC on the membrane surface. Experimental cell biology groups of Dr. Wai-Meng Kwok and Dr. Amadou Camara from Wisconsin Medical School help us to verify this computational model.

Home Department: Biophysics and Quantitative Biology

Office Address: Beckman Institute for Advanced Science and Technology, Room 3017, 405 N Mathews Ave, Urbana, IL 61801

Email Address: nhaloi2@illinois.edu




  • Molecular Dynamics techniques: BEUS, Force field development, HMMM, ARBD, SMD
  • Software Packages: NAMD, VMD, Gaussian09, AutoDock, HADDOCK2.2
  • Programming Skills: Tcl, Bash and Python. Good knowledge in Linux environment

Research Interests

  • Free energy calculation of drug permeation.

  • Protein-lipid interactions.

  • Protein-protein interactions.

Steered Molecular Dynamics

Publications during B.Tech

  • Mechanistic Insights into the Phosphatidylinositols Binding Properties of Pleckstrin Homology Domain of Lamellipodin
  • Gorai, S.; Paul, D.; Haloi, N.; Borah, R.; Santra, M. K.; Manna, D. Molecular BioSystems, 2016, 12:747-757

  • Role of Cationic Groove and Hydrophobic Residues in Phosphatidylinositol-Dependent Membrane-Binding Properties of Tks5-Phox Homology Domain
  • Gorai, S.; Paul, D.; Borah, R.; Haloi, N.; Santra, M. K.; Manna, D. Chemistry Select, 2018, 3(4):1205-1214