Department of Chemistry



Rob D Coalson



Chevron Science Center
219 Parkman Avenue

Pittsburgh, PA 15260

Research Overview

Theoretical/Computational Studies of Structure/Function Relations in Nanopores:

The Nuclear Pore Complex. 

The Nuclear Pore Complex (NPC) perforates the nuclear membrane and allows the flow of large biomolecules between the nucleoplasm and the cytoplasm in eukaryotic cells.  It is the largest protein complex in the cell.  Its detailed structure has not yet been fully elucidated, but it is known that the pore region is lined with natively unfolded nucleoporin proteins. These proteins extend into the center of the pore in a polymer brush configuration. They form a tight barrier to the passage of large biomolecules.  The amino acid sequence of the natively unfolded nucleoporins includes hydrophobic repeat segments.  These hydrophobic segments bind transiently to hydrophobic grooves on the outside of special globular receptor proteins (Nuclear Transport Factors [NTFs]), which also bind biomolecules (“cargoes”) waiting to be transported into/out of the nucleus.  Transient binding of the nucleoporin (nup) strands to the receptor protein NTFs allows the NTFs (with cargo attached) to transport through the NPC in a selective and efficient way.  The exact mechanism of the transport process is not known.  We use coarse-grained models to investigate basic physico-chemical models of NPC function.  These include bead-spring models of the nup chains that are grafted to the inside of the NPC pore and interact with spherical NTFs.  Coarse-grained MD simulations of these systems yield insight into the way the receptor proteins interact with the nup filiaments, such as inducing morphology changes in the nup brush and diffusing through the brush barrier from one side of the NPC to the other.  In addition, coarse-grained statistical mechanical models including Flory-Huggins and Self-Consistent Field Theories are utilized to assess trends in relevant equilibrium aspects of NPC function.

Smart Nanoparticle/Polymer Brush Composites. 

The biological NPC inspires design of synthetic polymer brush systems in which the brush morphology is modified upon binding of nanoparticles that attract to brush monomers.  In the context of an inside-grafted cylindrical brush (directly analogous to the NPC), binding of attractive nanoparticles to the polymer strands causes partial compression of the polymer brush (retraction toward the binding surface).  This opens up space along the center of the channel.  Analyte molecules small enough to fit through the opening can diffuse through the pore.  The flow of larger analyte molecules is blocked.  The degree of retraction of the brush can be precisely controlled by the concentration of nanoparticles in solution.   In this way, a size-selective molecular sieve can be generated, with an easily controllable aperture size.  We seek next to incorporate chemical features of the analyte molecules, in addition to their geometric size, into the sieving process.

Biological Ion Channels. 

These are proteins that span cytoplasmic membranes (e.g., the outer cell membrane).  They are responsible for the selective passage of ions from one side of the membrane to the other.  Structural details of many ion channels are available from X-ray and cryo-electron microscopy experiments.  We are interested in studying the gating and ion permeation properties of specific channels based on specific structural data, using large-scale MD simulations as well as coarse-grained electrostatic methods (e.g., Poisson-Nernst-Planck theory) and discrete state kinetic models.  In addition, we seek to understand general, universal properties of ion permeation that are shared by all ion channels, regardless of their structural details.  For example: statistics of ion permeation events, which are constrained by non-equilibrium fluctuation theorems.

Research Related Software Repository

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Dr. Coalson's complete publication list can be found here . Clickable links to recent publications are provided below.


  • NSF Presidential Young Investigator, 1986-91
  • Alfred P. Sloan Foundation Fellow, 1989-91
  • Camille and Henry Dreyfus Teacher-Scholar, 1990-94
  • Chancellor's Distinguished Research Award (Junior Scholar Category), University of Pittsburgh, 1995
  • Fellow, American Physical Society, 1999
  • Chancellor's Distinguished Research Award (Senior Scholar Category), University of Pittsburgh, 2006


“Dynamics of relaxation and dressing of a quenched Bose polaron,” Boyanovsky D, Jasnow D, Wu XL, Coalson RD PHYSICAL REVIEW A 2019, 100 4, 043617-21
“The Role of Cohesiveness on the Selective Permeability of Spatial Assemblies of FG Nucleoporins,” Zilman A, Vovk A, Gu C, Coalson RD BIOPHYSICAL JOURNAL 2019, 116 7, 1204-1215
“Controlling the Surface Properties of Polymer Coated Colloids via Targeted Nanoparticles,” Ozmaian M, Freitas BA, Coalson RD JOURNAL OF PHYSICAL CHEMISTRY B 2019, 123 1, 258-265
“Calculating Tracer Currents through Narrow Ion Channels: Beyond the Independent Particle Model,” Jasnow D, Coalson RD JOURNAL OF PHYSICS: CONDENSED MATTER 2018, 30 29, 294002:1-11
“Effects of Cross-linking on Partitioning of Nanoparticles into a Polymer Brush: Coarse-grained Simulations test Simple Approximate Theories,” Zilman A, Ozmaian M, Nasrabad AE, Jasnow D, Coalson RD JOURNAL OF PHYSICAL CHEMISTRY 2018, 148 2, 024902:1-12
“Free Energy of Nanoparticle Binding to Multivalent Polymeric Substrates,” Zilman A, Jasnow D, Gu C, Coalson RD JOURNAL OF PHYSICAL CHEMISTRY B 2017, 121 26, 6425-6435
“Precise Control of Polymer Coated Nanopores by Nanoparticle Additives: Insights from Computational Modeling,” Zilman A, Nasrabad AE, Jasnow D, Coalson RD JOURNAL OF PHYSICAL CHEMISTRY 2016, 145 6, 64901-64915
“Simple Biophysics Underpins Collective Conformations of the Intrinsically Disordered Proteins of the Nuclear Pore Complex,” Zilman A, Vovk A, Opferman MG, Lim RYH, Kapinos LE, Jasnow D, Gu C, Coalson RD E LIFE SCIENCES 2016, 1-29
“Computational Study of Water and Ion Permeability in a Model of Claudin,” Yu ASL, Laghaei R, Coalson RD,  PROTEINS (STRUCTURE FUNCTION & BIOINFORMATICS) 2016, 84 3, 305-315
“A Polymer-Brush-Based Nanovalve Controlled by Nanoparticle Additives: Design Principles,” Zilman A, Jasnow D, Nasrabad AE, Coalson RD JOURNAL OF PHYSICAL CHEMISTRY B 2015, 119 35, 11858-11866
“Calculation of Iron Transport through Human H-chain Ferritin,” Laghaei, R, Kowallis, W, Evans, DG, Coalson, RD JOURNAL OF PHYSICAL CHEMISTRY A 2014, 118 35, 7442-7453
“Morphology of Polymer Brushes Infiltrated by Attractive Nanoinclusions of Various Sizes,” Opferman MG, Coalson RD, Jasnow D, Zilman A LANGMUIR 2013, 29 27, 8584-8591
“Metal binding sites of human H-chain ferritin and iron transport mechanism to the ferroxidase sites: A molecular dynamics simulation study,” Laghaei R, Evans DG, Coalson, RD PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 2013, 81, 1042-1050
“Langevin Dynamics Simulation of 3D Colloidal Crystal Vacancies and Phase Transitions,” Laghaei R, Asher SA, Coalson RD Journal of Physical Chemistry B 2013, 117 17, 5271-5279
“Surface plasmon polaritons and optical transmission through a vortex lattice in a film of type-II superconductor,” Berman OL, Lozovik YE, Kolesnikov AA, Bogdanova MV, Coalson RD JOURNAL OF THE OPTICAL SOCIETY OF AMERICA B-OPTICAL PHYSICS 2013, 30, 909-913
“Energetics and Ion permeation Characteristics in a Glutamate-Gated Chloride (GluCl) Receptor Channel,” Cheng MH, Coalson RD JOURNAL OF PHYSICAL CHEMISTRY B 2012, 116, 13637-13643
“Response of Rotation-Translation Blocked Proteins Using Langevin Dynamics on a Locally Harmonic Landscape,” Manson AC, Coalson RD JOURNAL OF PHYSICAL CHEMISTRY B 2012, 116, 12142-12158
“Morphological control of grafted polymer films via attraction to small nanoparticle inclusions,” Opferman MG, Coalson RD, Jasnow D, Zilman A PHYSICAL REVIEW E 2012, 86, 031806
“Physical Modeling of the Conformational Dynamics of the Flexible Unfolded Proteins of the Nuclear Pore Complex,” Zilman A, Opferman M, Coalson R, Jasnow D, Welch P BIOPHYSICAL JOURNAL 2012, 102, 526A-526A
“Molecular Dynamics and Brownian Dynamics Investigation of Ion Permeation and Anesthetic Halothane Effects on a Proton-Gated Ion Channel,” Cheng MHY, Coalson RD, Tang P Journal of the American Chemical Society 2010, 132, 16442-16449
“Calcium Inhibits Paracellular Sodium Conductance through Claudin-2 by Competitive Binding,” Yu ASL, Cheng MH, Coalson RD Journal of Biological Chemistry 2010, 285, 37060-37069
“The Electrostatics of VDAC: Implications for Selectivity and Gating,” Choudhary OP, Ujwal R, Kowallis W, Coalson RD, Abramson J, Grabe M JOURNAL OF MOLECULAR BIOLOGY 2010, 396, 580-592
“Effectiveness of Perturbation Theory Approaches for Computing Non-Condon Electron Transfer Dynamics in Condensed Phases,” Cook WR, Coalson RD, Evans DG JOURNAL OF PHYSICAL CHEMISTRY B 2009, 113, 11437-11447
“Dynamic Linear Response Theory for Conformational Relaxation of Proteins,” Author(s): Essiz SG, Coalson RD JOURNAL OF PHYSICAL CHEMISTRY B 2009, 113, 10859-10869
“Molecular Basis for Cation Selectivity in Claudin-2-based Paracellular Pores: Identification of an Electrostatic Interaction Site,” Yu ASL, Cheng MH, Angelow S, Gunzel D, Kansawa SA, Schneeberger EE, Fromm M, Coalson RD JOURNAL OF GENERAL PHYSIOLOGY 2009, 133, 111-127
“Discrete-state model of coupled ion permeation and fast gating in ClC chloride channels,” Coalson RD JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL 2009, 41, 115001
“In Silico Models for the Human alpha 4 beta 2 Nicotinic Acetylcholine Receptor,” Haddadian EJ, Cheng MHY, Coalson RD, Xu Y, Tang P JOURNAL OF PHYSICAL CHEMISTRY B 2008, 112, 13981-13990
“Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds,” Cheng MH, Coalson RD, Cascio M, Kurnikova M JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN 2008, 22, 563-570
“Partitioning of a polymer chain between a confining cavity and a gel,” Tsonchev S, Coalson RD, Duncan A PHYSICAL REVIEW E 2007, 76, 041804, Part 1
“Langevin dynamics of molecules with internal rigid fragments in the harmonic regime,” Essiz SG, Coalson RD JOURNAL OF CHEMICAL PHYSICS 2007, 127, 104109
“Water and Deuterium oxide Permeability Through Aquaporin : MD Predictions and Experimental Verification,” Zeidel ML, Mathai JC, Mamonov AB, Coalson RD JOURNAL OF GENERAL PHYSIOLOGY 2007, 130 1, 111-116
“Modeling the Fast Gating Mechanism in ClC Chloride Channel,” Mamonov AB, Dukes JW, Coalson RD, Cheng RD JOURNAL OF PHYSICAL CHEMISTRY B 2007, 111 21, 5956-5965
“Homology Modeling and Molecular Dynamics Simulations of the a1 Glycine Receptor Reveals Different States of the Channel,” Coalson RD, Cheng MH, Cascio M PROTEINS (STRUCTURE FUNCTION & BIOINFORMATICS) 2007, 68 2, 581-593
“Poisson-Nernst-Planck Theory of Ion Permeation through Biological Channel,” Kurnikova MG, Coalson RD BIOLOGICAL MEMBRANE ION CHANNELS 2007, 449-484
“Superconducting Photonic Crystals: Numerical Calculations of the Band Structure,” Lozovik YE, Eiderman SL, Coalson RD, Berman OL PHYSICAL REVIEW B 2006, 74, 092505:1-3
“Unfolding of Alanine-based Peptides using Electron Spin Resonance Distance Measurement,” Yonkunas M, Saxena S, Jun S, Coalson RD, Becker JS BIOCHEMISTRY 2006, 45 38, 11666-11673
“Condensed-phase Relaxation of Multilevel Quantum Systems. I. An Exactly Solvable Model,” Peter S, Evans DG, Coalson RD JOURNAL OF PHYSICAL CHEMISTRY B 2006, 110 38, 18758-18763
“Phase transitions of Indirect Excitons in Coupled Quantum Wells: The Role of Disorder,” Snoke DW, Lozovik YE, Coalson RD, Berman OL PHYSICA E 2006, 34 1-2, 268-271
“Superfluidity of Dirty Indirect Excitons and Magnetoexcitons in a Two-dimensional Trap,” Snoke DW, Lozovik YE, Coalson RD. Berman OL PHYSICAL REVIEW B 2006, 73 23, 235352:1-5
“Diffusion Constant of K+ inside Gramicidin A: a Comparative Study of Four Computational Methods,” Mamonov AB, Kurnikova MG, Coalson RD BIOPHYS CHEM 2006, 124 3, 268-278
“An Introduction to Simulation and Visualization of Biological Systems at Multiple Scales: A Summer Training Program for Interdisciplinary Research,” Stiles JR, Munshi R, Meirovitch H, Madura JD, Coalson RD, Bahar I BIOTECHNOL PROG 2006, 22 10785, 179-185
“Fast Fourier Transform Simulation Techniques for Coulomb Gases,” Sedgewick RD, Duncan A, Coalson RD COMPUTER PHYSICS COMMUNICATIONS 2006, 175 2, 73-77
“Local Simulation Algorithms for Coulomb Gases with Dynamical Dielectric Effects,” Sedgewick RD, Duncan A, Coalson RD PHYSICAL REVIEW E 2006, 016705:1-6
“Exact Solution of a Model of Condensed-Phase Electron Transfer with Non-Condon Effect,” Evans DG, Cook WR, Coalson RD CHEMICAL PHYSICS LETTERS 2006, 420 4-6, 362-366
“The Band Structure of Photonic Band-Gap Crystals with Superconducting Element,” Lozovik YE, Eiderman SL, Coalson RD, Berman OL AIP CONFERENCE PROCEEDINGS 2006, 850 1, 997-998
“The Role of the Dielectric Barrier in Narrow Biological Channels: a Novel Composite Approach to Modeling Single Channel Currents,” Nitzan A, Mamonov AB, Kurnikova MG, Coalson RD BIOPHYSICAL JOURNAL 2003, 84 6, 3646-3661
“Control of Electron Current by Double-Barrier Structures using Pulsed Laser Fields,” York JT, Dahnovsky Y, Coalson RD PHYSICAL REVIEW B 2002, 65 23, 235321
“3D Dynamic Monte Carlo Simulations of Driven Polymer Transport Through a Hole in a Wall,” Coalson RD, Chern S-S, Cárdenas AE,  JOURNAL OF CHEMICAL PHYSICS 2001, 115 16, 7772-7773
“A Dynamic Lattice Monte Carlo Model of Ion Transport in Inhomogeneous Dielectric Environments: Method and Implementation,” Nitzan A, Kurnikova MG, Graf P, Coalson RD JOURNAL OF PHYSICAL CHEMISTRY B 2000, 104 51, 12324-12338
“On the Reliability of Mean-Field Methods in Polymer Statistical Mechanics,” Tsonchev S, Duncan A, Coalson RD, Chern S-S JOURNAL OF CHEMICAL PHYSICS 2000, 113 18, 8381-8389
“Partitioning of a Polymer Chain Between Two Confining Cavities: The Role of Electrostatic Interactions,” Tsonchev S, Duncan A, Coalson RD PHYSICAL REVIEW E 2000, 62 1, 799-806
“3D Poisson-Nernst-Planck Theory Studies: Influence of Membrane Electrostatics on Gramicidin A Channel Conductance,” Kurnikova MG, Coalson RD, Cárdenas AE, BIOPHYSICAL JOURNAL 2000, 79 1, 80-93
“A Theoretical Description of Microdialysis with Mass Transport Coupled to Chemical Events,” Yang H, Peters J, Michael AC, Coalson RD, Chern S-S ANALYTICAL CHEMISTRY 2000, 72 9, 2042-2049
“Statistical Mechanics of Charged Polymers in Electrolyte Solutions: A Lattice Field Theory Approach,” Tsonchev S, Duncan A, Coalson RD PHYSICAL REVIEW E 1999, 60 4, 4257-4267
“Entropic Trapping of a Flexible Polymer in a Fixed Network of Random Obstacles,” Coalson RD. Chern S-S JOURNAL OF CHEMICAL PHYSICS 1999, 111 4, 1778-1781
“Rotational Relaxation of Ionic Molecules in Electrolyte Solutions: Anisotropy Relaxation and Molecular Dynamics Study,” Waldeck DH, Kurnikova MG, Coalson RD, Balabai N JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 1998, 120 31, 7944-7951
“Rotational Diffusion of Organic Solutes: The Role of Dielectric Friction in Polar Solvents and Electrolyte Solutions,” Waldeck DH, Sukharevsky A,  Strazisar B, Read I, Kurnikova M, Hartman RS, Coalson RD, Balabai N  1998, 77 1-3, 37-60
“Long-Range Electron Transfer Driven by Two Lasers: Induced Irradiance,” Lubchenko V, Dakhnovskii Y, Coalson RD JOURNAL OF CHEMICAL PHYSICS 1998, 109 2, 691-703
“Rotational Relaxation in Polar Solvents. Molecular Dynamics Study of Solute—Solvent Interaction,” Waldeck DH, Kurnikova MG, Coalson RD, Balabai N JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 1998, 120 24, 6121-6130