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Wonpil Im

Associate Professor
Primary office:
(785) 864-1993
200E MRB

Theoretical/computational methods to chemical and physical problems in biology and material science.

The research programs in our group focus on the applications of theoretical/ computational methods to chemical and physical problems in biology and material science.

Specific research interests and projects are

  • peptide/protein interactions with/in biological membranes
  • transmembrane-induced signaling and regulation
  • NMR structure calculation and refinement 
  • glycan and glycoprotein structure and dynamics
  • protein translocation through molecular pores
  • ion channel activities such as ion permeation, selectivity, and gating
  • theoretical/methodological developments 

In addition, we are involved in developing the biomolecular simulation program CHARMM, and CHARMM-GUI.

Representative Publications

The complete list of publications is available at or check Google Scholar Citations at

  • S. Park, T. Kim, and W. Im (2012) Transmembrane Helix Assembly with Window Exchange Umbrella Sampling. Phys. Rev. Lett. 108:108102.
  • S. Jo and W. Im (2011) Transmembrane Helix Orientation and Dynamics: Insights from Ensemble Dynamics with Solid-State NMR Observables. Biophys. J. 100:2913-2922.
  • T. Rathinavelan, L. Zhang, W.L. Picking, D.D. Weis, R.N. De Guzman, and W. Im (2010) A Repulsive Electrostatic Mechanism for Protein Export through the Type III Secretion Apparatus. Biophys. J. 98:452-461.
  • W. Im, J. Lee, T. Kim, and H. Rui (2009) Novel Free Energy Calculations to Explore Mechanisms and Energetics of Membrane Protein Structure and Function. J. Comput. Chem. 30:1622-1633.
  • J. Lee and W. Im (2008) Transmembrane Helix Tilting: Insights from Calculating the Potential of Mean Force. Phys. Rev. Lett. 100:018103.
  • J. Lee and W. Im (2007) Implementation and Application of Helix-Helix Distance and Crossing Angle Restraint Potentials. J. Comput. Chem. 28:669–680.
  • W. Im, J. Chen, and C.L. Brooks III (2006) Peptide and Protein Folding and Conformational Equilibria: Theoretical Treatment of Electrostatics and Hydrogen Bonding with Implicit Solvent Models. Adv. Protein Chem. 72:173–198.
  • W. Im and C.L. Brooks III (2005) Interfacial Folding and Membrane Insertion of Synthetic Peptides Studied by Molecular Dynamics Simulations. Proc. Natl. Acad. Sci. USA 102:6771–6776.
  • W. Im and C.L. Brooks III (2004) De Novo Folding of Membrane Proteins: An Exploration of the Structure and NMR Properties of the fd Coat Protein. J. Mol. Biol. 337:513–519.
  • W. Im, M. Feig, and C.L. Brooks III (2003) An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane Proteins. Biophys. J. 85:2900–2918.
  • W. Im and B. Roux (2002) Ion Permeation and Selectivity of OmpF Porin: A Theoretical Study Based on Molecular Dynamics, Brownian Dynamics, and Continuum Electrodiffusion Theory. J. Mol. Biol. 322:851–869.
  • W. Im, S. Berneche, and B. Roux (2001) Generalized Solvent Boundary Potentials for Computer Simulations. J. Chem. Phys. 114:2924–2937.
  • W. Im, S. Seefeld and B. Roux (2000) Grand Canonical Monte Carlo - Brownian Dynamics Algorithm for Simulating Ion Channels. Biophys. J. 79:788–801.
  • M. Nina, W. Im, and B. Roux (1999) Optimized Atomic Radii for Protein Continuum Electrostatics Solvation Forces.Biophys. Chem. 78:89–96.
  • W. Im, D. Beglov, and B. Roux (1998) Continuum Solvation Model: Computation of Electrostatic Forces from Numerical Solutions to the Poisson-Boltzmann Equation. Comput. Phys. Comm. 111:59–75.
  • W. Im and Y. Won (1994) Molecular Dynamics Simulation on Thermodynamic and Structural Properties of Liquid Hydrocarbons : Normal Alkanes. bull. Korean Chem. Soc. 15:852–856.

Search PubMed for articles by Wonpil Im.

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