Lokendra Poudel Ph.D.

Biography

I am a postdoctoral fellow at Center for Quantitative Medicine at UConn Health, under the supervision of Prof. Reinhard Laubenbacher. My research focuses on to build and validate computational model of the “battle over iron” between host and fungus during the innate immune response to Aspergillus, incorporating multi-scales modelling.

My doctoral researches focused on atomistic modelling and simulation to understand the electronic structure, partial charge distribution, hydrogen bonding in complex biomolecules such as DNA, RNA, Protein, Viruses, Drug-DNA complex etc. using first-principles methods that are based on density functional theory (DFT).

Research Skills and Interests

  • Field of expertise in atomistic modeling and investigations of complex and large biomolecules using first-principles method from state of art density functional theory (DFT) and ab initio molecular dynamics (AIMD) and classical molecular dynamics (CMD) theory.
  • Experienced with DFT packages for simulation of Vienna ab initio Simulation Package (VASP), Orthogonal Linear Combination of Atomic Orbital (OLCAO), and Gaussian Package for geometry optimization, electronic structure calculation such as density of states, partial charge distribution, nature of bonding including hydrogen bonding network.
  • Experienced with molecular dynamic (MD) simulation packages of Nanoscale Molecular dynamics (NAMD) and AMBER for free binding energy calculation and non-bonded interaction (electrostatic and vdW) energies calculation of complex biosystem.

Education

Ph.D., Physics, University of Missouri-Kansas City, Kansas City, Missouri, USA
2014-2018
Dissertation titled ‘Deciphering of packing signal hypothesis in bacteriophage RNA recognition by the MS2 capsid protein in virus assembly

M.S., Physics, University of Missouri-Kansas City, Kansas City, Missouri, USA
2012-2014
Thesis titled ‘Electronic structure and partial charge distribution of doxorubicin under different molecular environments

Publications

  1. Jawad, Bahaa, Lokendra Poudel, Rudolf Podgornik, Nicole F. Steinmetz, and Wai-Yim Ching. "Molecular Mechanism and Binding Free Energy of Doxorubicin intercalation in DNA." Physical Chemistry Chemical Physics7 (2019):3877-3893.
  2. Poudel, Lokendra, Candan Tamerler, Anil Misra, and Wai-Yim Ching. "Atomic-Scale Quantification of Interfacial Binding Between Peptides and Inorganic Crystals: The Case of Calcium Carbonate Binding Peptide on Aragonite." The Journal of Physical Chemistry C 51 (2017) 28354-28363.
  3. Poudel, Lokendra, Reidun Twarock, Nicole F. Steinmetz, Rudolf Podgornik, and Wai- Yim Ching. "Impact of Hydrogen Bonding in Binding Site Between Capsid Protein and MS2 Bacteriophage ssRNA." The Journal of Physical Chemistry B 26 (2017) 6321-6330.
  4. Poudel, Lokendra, Rudolf Podgornik, and Wai-Yim Ching. "The Hydration Effect and Selectivity of Alkali-Metal Ions on Polyethylene Glycol (PEG) Models in Cyclic and Linear Topology." The Journal of Physical Chemistry A 24 (2017): 4721-4731.
  5. Poudel, Lokendra, Nicole F. Steinmetz, Roger H. French, V. Adrian Parsegian, Rudolf Podgornik, and Wai-Yim Ching. "Implication of the solvent effect, metal ions and topology in the electronic structure and hydrogen bonding of human telomeric G-quadruplex DNA." Physical Chemistry Chemical Physics 31 (2016): 21573-21585.
  6. Poudel, Lokendra, Amy M. Wen, Roger H. French, V. Adrian Parsegian, Rudolf Podgornik, Nicole F. Steinmetz, and Wai‐ Yim Ching. "Electronic structure and partial charge distribution of doxorubicin in different molecular environments." ChemPhysChem 7 (2015): 1451-1460.
  7. Dryden, Daniel M., Jaime C. Hopkins, Lin K. Denoyer, Lokendra Poudel, Nicole F. Steinmetz, Wai-Yim Ching, Rudolf Podgornik, Adrian Parsegian, and Roger H. French. "van der Waals interactions on the mesoscale: Open-science implementation, anisotropy, retardation, and solvent effects." Langmuir 37 (2015): 10145-10153.
  8. Schimelman, Jacob B., Daniel M. Dryden, Lokendra Poudel, Katherine E. Krawiec, Yingfang Ma, Rudolf Podgornik, V. Adrian Parsegian et al. "Optical properties and electronic transitions of DNA oligonucleotides as a function of composition and stacking sequence." Physical Chemistry Chemical Physics 6 (2015): 4589-4599.
  9. Poudel, Lokendra, Paul Rulis, Lei Liang, and W. Y. Ching. "Electronic structure, stacking energy, partial charge, and hydrogen bonding in four periodic B-DNA models." Physical Review E 90.2 (2014): 022705.