Materials by design

Soft & complex media

Glasses & metastable liquids

Publications [Google Scholar]

55. P. T. Cummings, C. McCabe, C. R. Iacovella, A. Ledeczi,  E. Jankowski, A. Jayaraman, J. C. Palmer, E. J. Maginn, S. C. Glotzer, J. A. Anderson, J. I. Siepmann, J. Potoff,  R. A. Matsumoto, J. B. Gilmer, R. S. DeFever, R. Singh, and B. Crawford, Open‐source molecular modeling software in chemical engineering focusing on the molecular simulation design framework. AIChE Journal, 67, e17206 (2021).

54. D. Mangal, J. C. Palmer, and J. C. Conrad, Nanoparticle dispersion in porous media: effects of hydrodynamic interactions and dimensionality. AIChE Journal, 67, e17147 (2021).

53. R. Sosa, X. Geng, A. Agarwal, J. C. Palmer, J. C. Conrad, M. Reynolds, and J. D. Rimer, Acidic polysaccharides as green alternatives for barite scale dissolution. ACS Central Science, 12, 55434-55443 (2020).

52. M. Warzecha, L. Verma, B. Johnston, J. C. Palmer, A. J. Florence, and P. G. Vekilov, Olanzapine crystal symmetry originates in preformed centrosymmetric solute dimers. Nature Chemistry, 12, 914-920 (2020).

51. H. Dai, Y. Shen, T. Yang, C. Lee, D. Fu, A. Agarwal, T. Thanh Le, M. Tsapatsis, J. Palmer, B. M. Weckhuysen, P. J. Dauenhauer, X. Zou, and J. D. Rimer, Finned zeolite catalysts.  Nature Materials, 19, 1074-1080 (2020).

50. Y. Long, J. C. Palmer, B. Coasne, M. Śliwińska-Bartkowiak, and K. E. Gubbins. Reply to the ‘Comment on “Pressure enhancement in carbon nanopores: a major confinement effect”’ by D. van Dijk, Phys. Chem. Chem. Phys., 2020, 22, DOI: 10.1039/C9CP02890K. Physical Chemistry Chemical Physics, 22, 9826-9830 (2020) .

49. R. Roberts, N. Marioni, J. C. Palmer, and J. C. Conrad, Dynamics of polydisperse hard-spheres under strong confinement. Molecular Physics, 118, e1728407 (2020).

48.   M. Kumar, Z. J. Berkson, R. J. Clark, Y. Shen, N. A. Prisco, H. Zheng, J. C. Palmer, B. F. Chmelka, and J. D. Rimer, Crystallization of mordenite platelets using cooperative organic structure-directing agents. Journal of the American Chemical Society, 141, 20155-20165 (2019).

47. R. Roberts, R. Poling-Skutvik, J. C. Conrad, and J. C. Palmer, Tracer transport in attractive and repulsive supercooled liquids and glasses. Journal of Chemical Physics (invited article for Emerging Investigator issue),  151, 194501 (2019)

46. R. Poling-Skutvik, R. C. Roberts, A. H. Slim, S. Narayanan, R. Krishnamoorti, J. C. Palmer, and J. C. Conrad. Structure dominates localization of tracers within aging nanoparticle glasses. Journal of Physical Chemistry Letters, 10, 1784-1789 (2019)

45. W. Qin, A. Agarwal, M. Choudhary, J. C Palmer, and J. D. Rimer, Molecular modifiers suppress nonclassical pathways of zeolite crystallization. Chemistry of Materials, 9, 3228-3238 (2019)

44. F. Ricci, J. C. Palmer, Y. Goswami, S. Sastry, C. A. Angell, and P. G. Debenedetti. A computational investigation of the thermodynamics of the Stillinger-Weber family of models at supercooled conditions. Molecular Physics (invited article), 117, 3254-3268  (2019)

43. R. S. Singh, Jeremy C. Palmer, Athanassios Z. Panagiotopoulos, and P. G. Debenedetti,Thermodynamic analysis of the stability of planar interfaces between coexisting phases and its application to supercooled water. Journal of Chemical Physics (invited article), 150, 224503 (2019)

42. M. P. Howard, A. Nikoubashman, and J. C Palmer, Modeling hydrodynamic interactions in soft materials with multiparticle collision dynamics. Current Opinion in Chemical Engineering (invited review), 23, 34-43 (2019)

41. J. C. Palmer, From water’s ephemeral dance, a new order merges. Proceedings of the National Academy of Sciences (invited commentary), 116, 1829-1831 (2019)

40. R. Chen, R. Poling-Skutvik, M. P. Howard, A. Nikoubashman, S. A. Egorov, J. C. Conrad and J. C. Palmer, Influence of polymer flexibility on nanoparticle dynamics in semidilute solutions. Soft Matter (invited article for Emerging Investigators issue), 15, 1260-1268 (2019)

39. J. C. Palmer, P. H. Poole, F. Sciortino and P. G. Debenedetti, Advances in computational studies of the liquid-liquid transition in water and water-like models. Chemical Reviews (invited article), 118, 9129-9151 (2018)

38. K. Olafson, R. J. Clark, P. G. Vekilov, J. C. Palmer and J. D. Rimer, Structuring of organic solvents at solid interfaces and ramifications for antimalarial adsorption on β-hematin crystals. ACS Applied Materials and Interfaces, 10, 29288-29298 (2018)

37. R. Roberts, R. Poling-Skutvik, J. C. Palmer and J. C. Conrad, Tracer transport probes relaxation and structure of attractive and repulsive glassy liquids. Journal of Physical Chemistry Letters, 9, 3008-3013 (2018)

36. R. Chen, R. Poling-Skutvik, A. Nikoubashman, M. P. Howard, J. C. Conrad and J. C. Palmer, Coupling of nanoparticle dynamics to polymer center-of-mass motion in semidilute polymer solutions. Macromolecules, 51, 1865 – 1872 (2018)

34. J. Guo, R. S. Singh and J. C. Palmer, Anomalous scattering in supercooled ST2 water. Molecular Physics (invited article), 116, 1953-1964 (2018)

33. J. Guo, A. Haji-Akbari and J. C. Palmer, Hybrid Monte Carlo with LAMMPS.  Journal of Theoretical and Computational Chemistry (invited article), 17, 1840002 (2018)

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. Molecular Systems Design & Engineering (invited article), 3, 159 – 170 (2018)

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, 148, 137101 (2018)

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

Software resources:

 

• Our group is a proud contributor to the Molecular Simulation Design Framework - a multi-institutional, NSF-sponsored  initiative to develop software tools that aid in enhancing the reproducibility of molecular simulation research
• Force field parameterization toolkit - python-based package to optimize force field parameter using gradient-free numerical optimization methods.  The parameters can be optimized to match ab initio data, equations of state, structural quantities, or any experimental observable that can computed in simulation.
• Structural order parameters for supercooled liquids - fortran routines wrapped through a python interface for computing various order parameters that are commonly used in studies of supercooled liquids.
• Kinetic Monte Carlo (kMC) simulations of molecular transport in zeolites - python routines to build and simulation kMC models to study molecular transport in zeolites.
• Multiparticle collision dynamics (MPCD) of polymer-colloid systems with LAMMPS - modified LAMMPS routines to couple polymers to an MPCD solvent.  Example inputfiles from some of our published studies are included.
• Hybrid Monte Carlo with LAMMPS - python script for performing hybrid Monte Carlo simulations in the isothermal-isobaric ensemble with LAMMPS.  Example inputfiles and validation tests are included, along with 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: