Palmer Group @ UH

     Condensed Matter Theory & Simulation

Materials by design

Soft & complex media

Glasses & metastable liquids

Jeremy C. Palmer

Assistant Professor

Molecular simulation &

statistical mechanics

jcpalmer at

Jennifer Bernard

Undergraduate Researcher

Dynamics of confined glasses




Group Alumni


Undergraduate Researchers

Jose Sachango

Macy Samz

Katherine Stewart


Minh Vo

Postdoctoral Associate

Particle transport

in confined media

 mdvo4 at

Renjie Chen

Ph.D. Candidate

Particle transport in

polymer matrices

rchen8 at

Ryan Roberts

Ph.D. Candidate

Simulation & experiment of colloidal glasses

 mdvo4 at

Ankur Agarwal

Ph.D. Candidate

Computational design of zeolite catalysts

  aagarwal6 at

Deepak Mangal

Ph.D. Candidate

Enhanced particle separation using depletants

 dmangal at

Jingxiang Guo

Ph.D. Candidate

Crystal nucleation

with rare-event methods

 jguo10 at

R. John Clark

Ph.D. Candidate

Crystal design with

growth modifiers

 rjclark2 at

Publications [Google Scholar]

34. M. D. Vo,  R. Poling-Skutvik, J. D. C. Jacob, J. Conrad and J. C. Palmer, Modeling confined particle transport through post arrays with Lagrangian particle tracking, submitted to AIChE Journal (invited article) (2017) [preprint]

33. J. Guo, A. Haji-Akbari and J. C. Palmer, Hybrid Monte Carlo with LAMMPS, submitted to Journal of Theoretical and Computational Chemistry (invited article) (2017) [preprint]

32. A. Chawla, R. Li, R. Jain, R. J. Clark, J. Sutjianto, J. C. Palmer and J. D. Rimer, Synergistic effects of inorganic and organic structure-directing agents in ZSM-5 crystallization, submitted to Molecular Systems Design & Engineering (invited article) (2017)

31. J.C. Palmer, A. Haji-Akbari, R. Singh, F. Martelli, R. Car, A.Z. Panagiotopoulos and P.G. Debenedetti, Comment on "The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water" [Parts I and II: J. Chem. Phys. 135, 134503 (2011); J. Chem. Phys. 138, 214504 (2013)], Journal of Chemical Physics, in press (2017)

30. S. He,  J. C. Palmer, and G. Qin. A non-equilibrium molecular dynamics study of methane transport in clay nano-pores. Microporous and Mesoporous Materials, 249, 88-96 (2017)

29. R. Chen, E. Lascaris, and J. C. Palmer. Liquid–liquid phase transition in an ionic model of silica. Journal of Chemical Physics, 146, 234503 (2017)

28. R. S. Singh, J. C. Palmer, P. D. Pudney, P. K. Paul, C. Johannessen, P. G. Debenedetti, J. Raut, K. L., M. Noro, and D. Tiemessen. Molecular modeling and structural characterization of a high glycine–tyrosine hair keratin associated protein. Physical Chemistry Chemical Physics, 19, 8575-8583 (2017)

27. H. Pathak, J. C. Palmer, D. Schlesinger, K. T. Wikfeldt, J. A. Sellberg, L. G. M. Pettersson, and A .Nilsson. The structural validity of various thermodynamical models of supercooled water. Journal of Chemical Physics, 145, 134507 (2016)

26. J. C. Palmer, R. S. Singh, R. Chen, F. Martelli, and P. G. Debenedetti. Density and bond-orientational relaxations in supercooled water. Molecular Physics, 114, 2580-2585 (2016)

25. S. B. Kim, J. C. Palmer, and P. G. Debenedetti. Computational investigation of cold denaturation in the trp-cage miniprotein. Proceedings of the National Academy of Sciences, 113, 8991-8996 (2016)

24. J. C. Palmer, F. Martelli, Y. Liu, R. Car, A. Z. Panagiotopoulos, and P. G. Debenedetti. Palmer et al. reply. Nature, 531, E2-E3 (2016)

23. S. B. Kim, J. C. Palmer, and P. G. Debenedetti. A Computational Study of the Effect of Matrix Structural Order on Water Sorption by Trp-Cage Miniproteins. Journal of Physical Chemistry B, 119, 1847-1856 (2015)

22. J. C. Palmer, and P. G. Debenedetti. Recent Advances in Molecular Simulation: A Chemical Engineering Perspective. AIChE Journal, 61, 370-383 (2015)

21. J. C. Palmer, F. Martelli, Y. Liu, R. Car, A. Z. Panagiotopoulos, and P. G. Debenedetti. Metastable Liquid-Liquid Transition in a Molecular Model of Water. Nature, 510, 385-388 (2014)

20. V. Holten, J. C. Palmer, P. H. Poole. P. G. Debenedetti, and M. A. Anisimov. Two-State Thermodynamic Model of the ST2 Model for Supercooled Water. Journal of Chemical Physics, 140, 104502 (2014)

19. J. C. Palmer, R. Car, and P. G. Debenedetti. The liquid-Liquid Transition in Supercooled ST2 Water:  A Comparison Between Umbrella Sampling and Well-Tempered Metadynamics. Faraday Discussion, 167, 77-94, (2013)

18. S. O. Diallo, M. Jazdzewska, J. C. Palmer, E. Mamontov, K. E. Gubbins, and M. Sliwińska-Bartkowiak. Dynamics of Nanoconfined Water Under Pressure. Physical Review E, 88, 022316 (2013)

17. Y. Long, J. C. Palmer, B. Coasne, M. M Sliwinska-Bartkowiak, G. Jackson, E. A. Müller, and K. E. Gubbins. On the Molecular Origin of High-Pressure Effects in Nanoconfinement: The Role of Surface Chemistry and Roughness. Journal of Chemical Physics, 139, 144701 (2013)

16. Y. Liu, J. C. Palmer, A. Z. Panagiotopoulos, and P. G. Debenedetti. Liquid-Liquid Transition in ST2 Water.  Journal of Chemical Physics, 137, 214505 (2012)

15. J. C. Palmer and P. G. Debenedetti. Computer Simulation of Water Sorption on Flexible Protein Crystals.  Journal of Physical Chemistry Letters, 3, 2713-2718 (2012)

14. Y. Long, M. Sliwińska-Bartkowiak, H. Drozdowski, M. Kempiński, K. A. Phillips, J. C Palmer, and K. E Gubbins. High Pressure Effect In Nanoporous Carbon Materials: Effects of Pore Geometry. Colloids and Surfaces A, 437, 33-41 (2012)

13. K. A. Phillips, J. C. Palmer, and K. E. Gubbins. Analysis of the Solvation Structure of Rubidium Bromide under Nanoconfinement. Molecular Simulation,  38, 1209-1220 (2012)

12. M. Sliwińska-Bartkowiak, H. Drozdowski, M. Kempinski, M. Jazdzewska, Y. Long,  J. C. Palmer,  and K. E. Gubbins. Structural Analysis of Water and Carbon Tetrachloride Adsorbed in Activated Carbon Fibres.  Physical Chemistry Chemical Physics, 14, 7145-7153 (2012)

11. Y. Long, J. C. Palmer, B. Coasne, M. Sliwińska-Bartkowiak, and K. E. Gubbins. Under Pressure: Quasi-High Pressure Effects in Nanopores. Microporous and Mesoporous Materials, 154, 19-23 (2012)

10. J. C. Palmer and K. E. Gubbins. Atomistic Models for Disordered Nanoporous Carbons Using Reactive Force Fields. Microporous and Mesoporous Materials, 154, 24-37 (2012)

9. Y. Long, J. C. Palmer, B. Coasne, M. Sliwińska-Bartkowiak, and K. E. Gubbins. Pressure Enhancement in Nanopores: A Major Confinement Effect. Physical Chemistry Chemical Physics, 13, 17163-17170 (2011)

8. J. C. Palmer, J. D. Moore, J. K. Brennan, and K. E. Gubbins. Simulating Local Adsorption Isotherms in Models of Complex Porous Materials: A Direct Assessment of the Slit Pore Model. Journal of Physical Chemistry Letters, 2, 165-169 (2011)

7. J. C. Palmer, J. D. Moore, T. J. Roussel, J. K. Brennan, and K. E. Gubbins. Adsorptive Behavior of CO2, CH4 and Their Mixtures in Carbon Nanospace: A Molecular Simulation Study. Physical Chemistry Chemical Physics, 13, 3985-3996 (2011)

6. J. C. Palmer, J. D. Moore, J. K. Brennan, and K. E. Gubbins. Adsorption and Diffusion of Argon in Disordered Nanoporous Carbons. Adsorption, 17, 189-199 (2011)

5. K. E. Gubbins, Y-C Liu, J. D. Moore, and J. C. Palmer. The Role of Molecular Modeling in Confined Systems: Impacts and Prospects.  Physical Chemistry Chemical Physics, 13, 58-85 (2011)

4. J. D. Moore, J. C. Palmer, Y-C Liu, T. J. Roussel, J. K. Brennan, and K. E. Gubbins. Adsorption and Diffusion of Argon Confined in Ordered and Disordered Microporous Carbons. Applied Surface Science, 256, 5131-5136 (2010)

3. J. C. Palmer, A. Llobet, S-H Yeon, J. E. Fischer, Y. Shi, Y. Gogotsi, and K. E. Gubbins. Modeling the Structural Evolution of Carbide-Derived Carbons Using Quenched Molecular Dynamics. Carbon, 48, 1116-1123 (2010)

2. J. C. Palmer, J. K. Brennan, M. M. Hurley, A. Balboa, and K. E. Gubbins. Detailed Structural Models for Activated Carbons from Molecular Simulation. Carbon, 47, 2904-2913 (2009)

1. J. C. Palmer, S. K. Jain, K. E. Gubbins, J. E. Fischer, R. Dash, and Y. Gogotsi. Hybrid Reverse Monte Carlo Simulations of Microporous Carbons, In: S. Kaskel, P. Llewellyn, F. Rodriguez-Reinoso and N. Seaton, eds., Characterization of Porous Solids VIII: Proceedings of the 8th International Symposium on the Characterization of Porous Solids, Cambridge: RSC (2008), pp. 56-63

Resources (Under construction)

  • Hybrid Monte Carlo with LAMMPS - python script for performing hybrid Monte Carlo simulations in the isothermal-isobaric ensemble with LAMMPS.  Details of the code will be documented in a forthcoming publication. Example inputfiles and validation tests will also be included shortly.  We will also release a version of the code to perform umbrella sampling.
  • Hybrid Monte Carlo code for rigid bodies - fortran code (hosted at Princeton) to perform hybrid Monte Carlo simulations of rigid bodies using a quaternion based molecular dynamics integrator.  The example inputs can be used to reproduce the free energy surfaces for ST2 water model reported in Ref. 21.


  • Computing resources:


    NSF MRI Cluster @ UH