Last Name

Dirk Gillespie

TitleAssociate Professor
InstitutionRush University, Rush Medical College
DepartmentPhysiology and Biophysics
Address1750 West Harrison St
Chicago IL 60612
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    My ORCID is 0000-0003-0802-5352.
    My Scopus ID is 7201826968.

    Research Areas:
    Cardiac excitation/contraction coupling, calcium-induced calcium release, calcium channel selectivity, nanofluidics, classical density functional theory of electrolytes.

    My Faculty Profile at Rush University Medical Center:

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    PhD, Rush University
    MS, Northwestern University
    BA, Johns Hopkins University

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Fill M, Gillespie D. Ryanodine Receptor Open Times Are Determined in the Closed State. Biophys J. 2018 Oct 02; 115(7):1160-1165. PMID: 30220413.
      View in: PubMed
    2. Voukadinova A, Valiskó M, Gillespie D. Assessing the accuracy of three classical density functional theories of the electrical double layer. Phys Rev E. 2018 Jul; 98(1-1):012116. PMID: 30110825.
      View in: PubMed
    3. Zsolnay V, Fill M, Gillespie D. Sarcoplasmic Reticulum Ca2+ Release Uses a Cascading Network of Intra-SR and Channel Countercurrents. Biophys J. 2018 01 23; 114(2):462-473. PMID: 29401443.
      View in: PubMed
    4. Chou KH, McCallum C, Gillespie D, Pennathur S. An Experimental Approach to Systematically Probe Charge Inversion in Nanofluidic Channels. Nano Lett. 2018 02 14; 18(2):1191-1195. PMID: 29266955.
      View in: PubMed
    5. Ható Z, Valiskó M, Kristóf T, Gillespie D, Boda D. Multiscale modeling of a rectifying bipolar nanopore: explicit-water versus implicit-water simulations. Phys Chem Chem Phys. 2017 Jul 21; 19(27):17816-17826. PMID: 28657634.
      View in: PubMed
    6. McCallum C, Pennathur S, Gillespie D. Two-Dimensional Electric Double Layer Structure with Heterogeneous Surface Charge. Langmuir. 2017 06 13; 33(23):5642-5651. PMID: 28525283.
      View in: PubMed
    7. Manno C, Figueroa LC, Gillespie D, Fitts R, Kang C, Franzini-Armstrong C, Rios E. Calsequestrin depolymerizes when calcium is depleted in the sarcoplasmic reticulum of working muscle. Proc Natl Acad Sci U S A. 2017 01 24; 114(4):E638-E647. PMID: 28069951.
      View in: PubMed
    8. Berti C, Zsolnay V, Shannon TR, Fill M, Gillespie D. Sarcoplasmic reticulum Ca2+, Mg2+, K+, and Cl- concentrations adjust quickly as heart rate changes. J Mol Cell Cardiol. 2017 02; 103:31-39. PMID: 27914790.
      View in: PubMed
    9. Loessberg-Zahl J, Janssen KG, McCallum C, Gillespie D, Pennathur S. (Almost) Stationary Isotachophoretic Concentration Boundary in a Nanofluidic Channel Using Charge Inversion. Anal Chem. 2016 06 21; 88(12):6145-50. PMID: 27268953.
      View in: PubMed
    10. Roth R, Gillespie D. Shells of charge: a density functional theory for charged hard spheres. J Phys Condens Matter. 2016 06 22; 28(24):244006. PMID: 27116385.
      View in: PubMed
    11. Berti C, Furini S, Gillespie D. PACO: PArticle COunting Method To Enforce Concentrations in Dynamic Simulations. J Chem Theory Comput. 2016 Mar 08; 12(3):925-9. PMID: 26891893.
      View in: PubMed
    12. Friedrich, L. Gillespie, D. Improving charge-sensitive biomolecule sensors with the right choice of electrolyte. Sensors and Actuators B: Chemical. 2016; 230:281-288.
    13. Z. Ható, D. Boda, D. Gillespie, J. Vrabec, G. Rutkai, T. Kristóf. Simulation study of a rectifying bipolar ion channel: Detailed model versus reduced model. Condensed Matter Physics. 2016; 19:13802.
    14. Gillespie D. Algorithm for the Time-Propagation of the Radial Diffusion Equation Based on a Gaussian Quadrature. PLoS One. 2015; 10(7):e0132273. PMID: 26208111; PMCID: PMC4514844.
    15. Gillespie, D. A review of steric interactions of ions: Why some theories succeed and others fail to acount for ion size. Microfluidics and Nanofluidics. 2015; 18:717-738.
    16. Gillespie D, Xu L, Meissner G. Selecting ions by size in a calcium channel: the ryanodine receptor case study. Biophys J. 2014 Nov 18; 107(10):2263-73. PMID: 25418295; PMCID: PMC4241444.
    17. Gillespie D. Restoring the consistency with the contact density theorem of a classical density functional theory of ions at a planar electrical double layer. Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Nov; 90(5-1):052134. PMID: 25493766.
      View in: PubMed
    18. Peyser A, Gillespie D, Roth R, Nonner W. Domain and interdomain energetics underlying gating in Shaker-type Kv channels. Biophys J. 2014 Oct 21; 107(8):1841-1852. PMID: 25418165.
      View in: PubMed
    19. Berti C, Furini S, Gillespie D, Boda D, Eisenberg RS, Sangiorgi E, Fiegna C. Three-Dimensional Brownian Dynamics Simulator for the Study of Ion Permeation through Membrane Pores. J Chem Theory Comput. 2014 Aug 12; 10(8):2911-26. PMID: 26588267.
      View in: PubMed
    20. D. Boda, É. Csányi, D. Gillespie and T. Kristóf. Dynamic Monte Carlo simulation of coupled transport through a narrow multiply-occupied pore. Journal of Chemical Physics. 2014; 118:700-707.
    21. D. Boda, R. Kovács, D. Gillespie, T. Kristóf. Selective transport through a model calcium channel studied by Local Equilibrium Monte Carlo simulations coupled to the Nernst-Planck equation. Journal of Molecular Liquids. 2014; 189:100-112.
    22. Gillespie D. Computing the partition function, ensemble averages, and density of states for lattice spin systems by sampling the mean. J Comput Phys. 2013 Oct 01; 250:1-12. PMID: 23935210.
      View in: PubMed
    23. Guo T, Nani A, Shonts S, Perryman M, Chen H, Shannon T, Gillespie D, Fill M. Sarcoplasmic reticulum K(+) (TRIC) channel does not carry essential countercurrent during Ca(2+) release. Biophys J. 2013 Sep 03; 105(5):1151-60. PMID: 24010658; PMCID: PMC3762336.
    24. Boda D, Henderson D, Gillespie D. The role of solvation in the binding selectivity of the L-type calcium channel. J Chem Phys. 2013 Aug 07; 139(5):055103. PMID: 23927288.
      View in: PubMed
    25. Gillespie D, Pennathur S. Separation of ions in nanofluidic channels with combined pressure-driven and electro-osmotic flow. Anal Chem. 2013 Mar 05; 85(5):2991-8. PMID: 23368674.
      View in: PubMed
    26. Gillespie D, Fill M. Pernicious attrition and inter-RyR2 CICR current control in cardiac muscle. J Mol Cell Cardiol. 2013 May; 58:53-8. PMID: 23369697; PMCID: PMC3628281.
    27. Hoffmann J, Gillespie D. Ion correlations in nanofluidic channels: effects of ion size, valence, and concentration on voltage- and pressure-driven currents. Langmuir. 2013 Jan 29; 29(4):1303-17. PMID: 23286510; PMCID: PMC3558667.
    28. Berti C, Gillespie D, Bardhan JP, Eisenberg RS, Fiegna C. Comparison of three-dimensional poisson solution methods for particle-based simulation and inhomogeneous dielectrics. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jul; 86(1 Pt 1):011912. PMID: 23005457.
      View in: PubMed
    29. Guo T, Gillespie D, Fill M. Ryanodine receptor current amplitude controls Ca2+ sparks in cardiac muscle. Circ Res. 2012 Jun 22; 111(1):28-36. PMID: 22628577; PMCID: PMC3417769.
    30. Gillespie D, Chen H, Fill M. Is ryanodine receptor a calcium or magnesium channel? Roles of K+ and Mg2+ during Ca2+ release. Cell Calcium. 2012 Jun; 51(6):427-33. PMID: 22387011; PMCID: PMC3361554.
    31. Berti C, Gillespie D, Eisenberg RS, Fiegna C. Particle-based simulation of charge transport in discrete-charge nano-scale systems: the electrostatic problem. Nanoscale Res Lett. 2012 Feb 16; 7:135. PMID: 22338640; PMCID: PMC3395871.
    32. Boda D, Gillespie D. Steady-State Electrodiffusion from the Nernst-Planck Equation Coupled to Local Equilibrium Monte Carlo Simulations. J Chem Theory Comput. 2012 Mar 13; 8(3):824-9. PMID: 26593344.
      View in: PubMed
    33. Gillespie D. High energy conversion efficiency in nanofluidic channels. Nano Lett. 2012 Mar 14; 12(3):1410-6. PMID: 22300476.
      View in: PubMed
    34. Csányi E, Boda D, Gillespie D, Kristóf T. Current and selectivity in a model sodium channel under physiological conditions: Dynamic Monte Carlo simulations. Biochim Biophys Acta. 2012 Mar; 1818(3):592-600. PMID: 22080102; PMCID: PMC3273597.
    35. Boda D, Henderson D, Eisenberg B, Gillespie D. A method for treating the passage of a charged hard sphere ion as it passes through a sharp dielectric boundary. J Chem Phys. 2011 Aug 14; 135(6):064105. PMID: 21842924; PMCID: PMC3170393.
    36. Gillespie D. Free-Energy Density Functional of Ions at a Dielectric Interface. J Phys Chem Lett. 2011 May 19; 2(10):1178-82. PMID: 26295322.
      View in: PubMed
    37. Gillespie D, Khair AS, Bardhan JP, Pennathur S. Efficiently accounting for ion correlations in electrokinetic nanofluidic devices using density functional theory. J Colloid Interface Sci. 2011 Jul 15; 359(2):520-9. PMID: 21531429.
      View in: PubMed
    38. Krauss D, Eisenberg B, Gillespie D. Selectivity sequences in a model calcium channel: role of electrostatic field strength. Eur Biophys J. 2011 Jun; 40(6):775-82. PMID: 21380773; PMCID: PMC3124256.
    39. Boda D, Giri J, Henderson D, Eisenberg B, Gillespie D. Analyzing the components of the free-energy landscape in a calcium selective ion channel by Widom's particle insertion method. J Chem Phys. 2011 Feb 07; 134(5):055102. PMID: 21303162; PMCID: PMC3045419.
    40. Gillespie D. Toward making the mean spherical approximation of primitive model electrolytes analytic: an analytic approximation of the MSA screening parameter. J Chem Phys. 2011 Jan 28; 134(4):044103. PMID: 21280683.
      View in: PubMed
    41. Malasics A, Boda D, Valiskó M, Henderson D, Gillespie D. Simulations of calcium channel block by trivalent cations: Gd(3+) competes with permeant ions for the selectivity filter. Biochim Biophys Acta. 2010 Nov; 1798(11):2013-21. PMID: 20696128; PMCID: PMC2946232.
    42. Krauss D, Gillespie D. Sieving experiments and pore diameter: it's not a simple relationship. Eur Biophys J. 2010 Oct; 39(11):1513-21. PMID: 20458579.
      View in: PubMed
    43. Gillespie D. Analytic theory for dilute colloids in a charged slit. J Phys Chem B. 2010 Apr 01; 114(12):4302-9. PMID: 20210321.
      View in: PubMed
    44. Knepley MG, Karpeev DA, Davidovits S, Eisenberg RS, Gillespie D. An efficient algorithm for classical density functional theory in three dimensions: ionic solutions. J Chem Phys. 2010 Mar 28; 132(12):124101. PMID: 20370108; PMCID: PMC2856503.
    45. Gillespie D, Giri J, Fill M. Reinterpreting the anomalous mole fraction effect: the ryanodine receptor case study. Biophys J. 2009 Oct 21; 97(8):2212-21. PMID: 19843453; PMCID: PMC2764102.
    46. Malasics A, Gillespie D, Nonner W, Henderson D, Eisenberg B, Boda D. Protein structure and ionic selectivity in calcium channels: selectivity filter size, not shape, matters. Biochim Biophys Acta. 2009 Dec; 1788(12):2471-80. PMID: 19818330; PMCID: PMC2789594.
    47. Bardhan JP, Eisenberg RS, Gillespie D. Discretization of the induced-charge boundary integral equation. Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Jul; 80(1 Pt 1):011906. PMID: 19658728; PMCID: PMC3700357.
    48. Boda D, Valiskó M, Henderson D, Eisenberg B, Gillespie D, Nonner W. Ionic selectivity in L-type calcium channels by electrostatics and hard-core repulsion. J Gen Physiol. 2009 May; 133(5):497-509. PMID: 19398776; PMCID: PMC2712969.
    49. He Y, Gillespie D, Boda D, Vlassiouk I, Eisenberg RS, Siwy ZS. Tuning transport properties of nanofluidic devices with local charge inversion. J Am Chem Soc. 2009 Apr 15; 131(14):5194-202. PMID: 19317490; PMCID: PMC2714767.
    50. Boda D, Valiskó M, Henderson D, Gillespie D, Eisenberg B, Gilson MK. Ions and inhibitors in the binding site of HIV protease: comparison of Monte Carlo simulations and the linearized Poisson-Boltzmann theory. Biophys J. 2009 Feb 18; 96(4):1293-306. PMID: 19217848; PMCID: PMC2717253.
    51. Gillespie D, Fill M. Intracellular calcium release channels mediate their own countercurrent: the ryanodine receptor case study. Biophys J. 2008 Oct; 95(8):3706-14. PMID: 18621826; PMCID: PMC2553138.
    52. Gillespie D, Boda D. The anomalous mole fraction effect in calcium channels: a measure of preferential selectivity. Biophys J. 2008 Sep 15; 95(6):2658-72. PMID: 18515379; PMCID: PMC2527270.
    53. Gillespie D, Boda D, He Y, Apel P, Siwy ZS. Synthetic nanopores as a test case for ion channel theories: the anomalous mole fraction effect without single filing. Biophys J. 2008 Jul; 95(2):609-19. PMID: 18390596; PMCID: PMC2440478.
    54. Malasics A, Gillespie D, Boda D. Simulating prescribed particle densities in the grand canonical ensemble using iterative algorithms. J Chem Phys. 2008 Mar 28; 128(12):124102. PMID: 18376903.
      View in: PubMed
    55. Roth R, Gillespie D, Nonner W, Eisenberg RE. Bubbles, gating, and anesthetics in ion channels. Biophys J. 2008 Jun; 94(11):4282-98. PMID: 18234836; PMCID: PMC2480679.
    56. Boda D, Nonner W, Henderson D, Eisenberg B, Gillespie D. Volume exclusion in calcium selective channels. Biophys J. 2008 May 01; 94(9):3486-96. PMID: 18199663; PMCID: PMC2292364.
    57. A. Singer, D. Gillespie, J. Norbury, R.S. Eisenberg. Singular perturbation analysis of the steady state Poisson-Nernst-Planck system: Applications to ion channels. European Journal of Applied Mathematics. 2008; 19:541-560.
    58. Gillespie D. Energetics of divalent selectivity in a calcium channel: the ryanodine receptor case study. Biophys J. 2008 Feb 15; 94(4):1169-84. PMID: 17951303; PMCID: PMC2212702.
    59. Boda D, Nonner W, Valiskó M, Henderson D, Eisenberg B, Gillespie D. Steric selectivity in Na channels arising from protein polarization and mobile side chains. Biophys J. 2007 Sep 15; 93(6):1960-80. PMID: 17526571; PMCID: PMC1959557.
    60. Boda D, Valiskó M, Eisenberg B, Nonner W, Henderson D, Gillespie D. Combined effect of pore radius and protein dielectric coefficient on the selectivity of a calcium channel. Phys Rev Lett. 2007 Apr 20; 98(16):168102. PMID: 17501467.
      View in: PubMed
    61. M. Valiskó, D. Boda, D. Gillespie. Selective adsorption of ions with different diameter and valence at highly-charged interfaces. Journal of Physical Chemistry C. 2007; 111:15575-15585.
    62. Miedema H, Vrouenraets M, Wierenga J, Gillespie D, Eisenberg B, Meijberg W, Nonner W. Ca2+ selectivity of a chemically modified OmpF with reduced pore volume. Biophys J. 2006 Dec 15; 91(12):4392-400. PMID: 16997866; PMCID: PMC1779923.
    63. Boda D, Valiskó M, Eisenberg B, Nonner W, Henderson D, Gillespie D. The effect of protein dielectric coefficient on the ionic selectivity of a calcium channel. J Chem Phys. 2006 Jul 21; 125(3):34901. PMID: 16863379.
      View in: PubMed
    64. Roth R, Gillespie D. Physics of size selectivity. Phys Rev Lett. 2005 Dec 09; 95(24):247801. PMID: 16384426.
      View in: PubMed
    65. Xu L, Wang Y, Gillespie D, Meissner G. Two rings of negative charges in the cytosolic vestibule of type-1 ryanodine receptor modulate ion fluxes. Biophys J. 2006 Jan 15; 90(2):443-53. PMID: 16239337; PMCID: PMC1367051.
    66. Gillespie D, Xu L, Wang Y, Meissner G. (De)constructing the ryanodine receptor: modeling ion permeation and selectivity of the calcium release channel. J Phys Chem B. 2005 Aug 18; 109(32):15598-610. PMID: 16852978.
      View in: PubMed
    67. Wang Y, Xu L, Pasek DA, Gillespie D, Meissner G. Probing the role of negatively charged amino acid residues in ion permeation of skeletal muscle ryanodine receptor. Biophys J. 2005 Jul; 89(1):256-65. PMID: 15863483; PMCID: PMC1366523.
    68. D. Gillespie, M. Valiskó, D. Boda. Density functional theory of the electrical double layer: the RFD functional. Journal of Physics: Condensed Matter. 2005; 17:6609-6626.
    69. D. Henderson, D. Gillespie, T. Nagy, D. Boda. Monte Carlo simulation of the electric double layer: dielectric boundaries and the effects of induced charge. Molecular Physics. 2005; 103:2851-2861.
    70. Nonner W, Peyser A, Gillespie D, Eisenberg B. Relating microscopic charge movement to macroscopic currents: the Ramo-Shockley theorem applied to ion channels. Biophys J. 2004 Dec; 87(6):3716-22. PMID: 15465857; PMCID: PMC1304885.
    71. Miedema H, Meter-Arkema A, Wierenga J, Tang J, Eisenberg B, Nonner W, Hektor H, Gillespie D, Meijberg W. Permeation properties of an engineered bacterial OmpF porin containing the EEEE-locus of Ca2+ channels. Biophys J. 2004 Nov; 87(5):3137-47. PMID: 15326033; PMCID: PMC1304784.
    72. Boda D, Gillespie D, Nonner W, Henderson D, Eisenberg B. Computing induced charges in inhomogeneous dielectric media: application in a Monte Carlo simulation of complex ionic systems. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Apr; 69(4 Pt 2):046702. PMID: 15169126.
      View in: PubMed
    73. D. Boda, T. Varga, D. Henderson, D.D. Busath, W. Nonner, D. Gillespie, B. Eisenberg. Monte Carlo simulation study of a system with a dielectric boundary: Application to calcium channel selectivity. Molecular Simulation. 2004; 30:89-96.
    74. Gillespie D, Nonner W, Eisenberg RS. Density functional theory of charged, hard-sphere fluids. Phys Rev E Stat Nonlin Soft Matter Phys. 2003 Sep; 68(3 Pt 1):031503. PMID: 14524773.
      View in: PubMed
    75. Gillespie D, Eisenberg RS. Physical descriptions of experimental selectivity measurements in ion channels. Eur Biophys J. 2002 Oct; 31(6):454-66. PMID: 12355255.
      View in: PubMed
    76. D. Gillespie, W. Nonner, R.S. Eisenberg. Coupling Poisson-Nernst-Planck and density functional theory to calculate ion flux. Journal of Physics: Condensed Matter. 2002; 14:12129-12145.
    77. D. Gillespie, W. Nonner, D. Henderson, R.S. Eisenberg. A physical mechanism for large-ion selectivity in ion channels. Physical Chemistry Chemical Physics. 2002; 4:4763-4769.
    78. W. Nonner, D. Gillespie, D. Henderson, B. Eisenberg. Ion accumulation in a biological calcium channel: effects of solvent and confining pressure. Journal of Physical Chemistry B. 2001; 105:6427-6436.
    79. D. Gillespie, R.S. Eisenberg. Modified Donnan potentials for ion transport through biological ion channels. Physical Review E. 2001; 62:061902.
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