Vikram Krishnamurthy

Summary

Affiliation: University of British Columbia
Country: Canada

Publications

  1. doi request reprint Engineering aspects of biological ion channels--from biosensors to computational models for permeation
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, V6T 1Z4, Canada
    Protoplasma 249:S3-9. 2012
  2. ncbi request reprint Adaptive learning algorithms for nernst potential and I-V curves in nerve cell membrane ion channels modeled as hidden Markov models
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, Canada
    IEEE Trans Nanobioscience 2:266-78. 2003
  3. ncbi request reprint Dynamic ion channel activation scheduling in patch clamp on a chip
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    IEEE Trans Nanobioscience 3:217-24. 2004
  4. ncbi request reprint Brownian dynamics simulation for modeling ion permeation across bionanotubes
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    IEEE Trans Nanobioscience 4:102-11. 2005
  5. ncbi request reprint Controlled hidden markov models for dynamically adapting patch clamp experiment to estimate Nernst potential of single-ion channels
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada
    IEEE Trans Nanobioscience 5:115-25. 2006
  6. ncbi request reprint Adaptive Brownian dynamics simulation for estimating potential mean force in ion channel permeation
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada
    IEEE Trans Nanobioscience 5:126-38. 2006
  7. doi request reprint Semi-Markov models for brownian dynamics permeation in biological ion channels
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada
    IEEE/ACM Trans Comput Biol Bioinform 8:273-81. 2011
  8. doi request reprint A molecular machine biosensor: construction, predictive models and experimental studies
    Sahar Moradi-Monfared
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, Canada
    Biosens Bioelectron 34:261-6. 2012
  9. ncbi request reprint Adaptive Brownian dynamics for shape estimation of sodium ion channels
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada
    J Nanosci Nanotechnol 7:2273-82. 2007
  10. doi request reprint Free energy calculations of gramicidin dimer dissociation
    Surajith N Wanasundara
    Department of Electrical and Computer Engineering, University of British Columbia, 5500 2332 Main Mall, Vancouver, BC, V6T 1Z4 Canada
    J Phys Chem B 115:13765-70. 2011

Collaborators

  • Shin Ho Chung
  • William Hoiles
  • Bruce Cornell
  • Sahar Moradi-Monfared
  • Surajith N Wanasundara
  • Matthew Hoyles
  • Jin Aun Ng
  • Rini Gupta
  • Charles Cranfield
  • Charles G Cranfield
  • Taira Vora
  • May Siksik

Detail Information

Publications14

  1. doi request reprint Engineering aspects of biological ion channels--from biosensors to computational models for permeation
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, V6T 1Z4, Canada
    Protoplasma 249:S3-9. 2012
    ..We describe our recent research in these areas, potential challenges and possible solutions...
  2. ncbi request reprint Adaptive learning algorithms for nernst potential and I-V curves in nerve cell membrane ion channels modeled as hidden Markov models
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, Canada
    IEEE Trans Nanobioscience 2:266-78. 2003
    ..Numerical examples illustrate the performance of the algorithms on computer-generated synthetic data...
  3. ncbi request reprint Dynamic ion channel activation scheduling in patch clamp on a chip
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    IEEE Trans Nanobioscience 3:217-24. 2004
    ..Numerical examples using state-of-the-art algorithms developed recently in artificial intelligence and operations research are presented to illustrate these dynamic ion channel (macromolecule) activation scheduling algorithms...
  4. ncbi request reprint Brownian dynamics simulation for modeling ion permeation across bionanotubes
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    IEEE Trans Nanobioscience 4:102-11. 2005
    ..We illustrate how BD simulations are used to unravel the permeation dynamics in two biological ion channels-the KcsA K+ channel and CIC Cl- channel...
  5. ncbi request reprint Controlled hidden markov models for dynamically adapting patch clamp experiment to estimate Nernst potential of single-ion channels
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada
    IEEE Trans Nanobioscience 5:115-25. 2006
    ..We illustrate the efficiency of the algorithms for the experimentally determined current voltage curve of a bi-ionic single potassium ion channel...
  6. ncbi request reprint Adaptive Brownian dynamics simulation for estimating potential mean force in ion channel permeation
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada
    IEEE Trans Nanobioscience 5:126-38. 2006
    ..Numerical simulations on the gramicidin ion channel show that the algorithm yields the potential of mean force profile that accurately reproduces experimental observations...
  7. doi request reprint Semi-Markov models for brownian dynamics permeation in biological ion channels
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada
    IEEE/ACM Trans Comput Biol Bioinform 8:273-81. 2011
    ..Numerical studies on the simulation of gramicidin A ion channels are presented...
  8. doi request reprint A molecular machine biosensor: construction, predictive models and experimental studies
    Sahar Moradi-Monfared
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, Canada
    Biosens Bioelectron 34:261-6. 2012
    ....
  9. ncbi request reprint Adaptive Brownian dynamics for shape estimation of sodium ion channels
    Vikram Krishnamurthy
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver V6T 1Z4, Canada
    J Nanosci Nanotechnol 7:2273-82. 2007
    ..Brownian dynamics simulations emulate the propagation of individual ions through the sodium channel nanotube at a femto time second time scale and Angstrom unit (10(-10) meter) spatial scale...
  10. doi request reprint Free energy calculations of gramicidin dimer dissociation
    Surajith N Wanasundara
    Department of Electrical and Computer Engineering, University of British Columbia, 5500 2332 Main Mall, Vancouver, BC, V6T 1Z4 Canada
    J Phys Chem B 115:13765-70. 2011
    ....
  11. pmc The Effect of Tethers on Artificial Cell Membranes: A Coarse-Grained Molecular Dynamics Study
    William Hoiles
    Department of Electrical and Computer Engineering, The University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 11:e0162790. 2016
    ....
  12. pmc An engineered membrane to measure electroporation: effect of tethers and bioelectronic interface
    William Hoiles
    Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, British Columbia, Canada
    Biophys J 107:1339-51. 2014
    ..To validate the accuracy of the two-level model, the predicted current is compared with experimentally measured current for different tethering densities. ..
  13. pmc Brownian dynamics theory for predicting internal and external blockages of tetraethylammonium in the KcsA potassium channel
    Matthew Hoyles
    Research School of Biological Sciences, The Australian National University, Canberra, Australia
    Biophys J 94:366-78. 2008
    ....
  14. ncbi request reprint Estimating the dielectric constant of the channel protein and pore
    Jin Aun Ng
    Research School of Biological Sciences, Australian National University, Canberra, Australia
    Eur Biophys J 37:213-22. 2008
    ..From the algorithm we obtain an optimum value of 2 for the protein dielectric constant and 64 for the pore dielectric constant...