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Molecular Simulations Research Group
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Publications

2018

  • P Chen, Y Ogawa, Y Nishiyama, AE Ismail, and K Mazeau. (2018). Iα to Iβ mechano-conversion and amorphization in native cellulose simulated by crys- tal bending. Cellulose, 25, 4435. DOI: 10.1007/s10570-018-1860-x (2018).
  • J Chapman, AE Ismail, and CZ Dinu. Industrial Applications of Enzymes: Re- cent Advances, Techniques, and Outlooks. Catalysts, 8, 238. DOI: 10.3390/ catal8060238 (2018). (Invited)
  • D Fabregat Traver, AE Ismail, and P Bientinesi. Accelerating molecular dynam- ics codes by performance and accuracy modeling. Journal of Computational Science, 27, 77. DOI: 10.1016/j.jocs.2018.05.004 (2018).

2017

  • BC Rinderspacher, JP Bardhan, AE Ismail. Theory of wavelet-based coarse-graining hierarchies for molecular dynamics. Phys. Rev. E. DOI  10.1103/physreve.96.013301 (2017).
  • P Chen, Y Nishiyama, J Wohlert, A Lu, K Mazeau, and AE Ismail. Translational Entropy and Dispersion Energy Jointly Drive the Adsorption of Urea on Cellulose. J. Phys. Chem. B. DOI  10.1021/acs.jpcb.6b11914 (2017).
  • W McDoniel, M Höhnerbach, R Canales, AE Ismail, P Bientinesi. LAMMPS’ PPPM Long-Range Solver for the Second Generation Xeon Phi. Lecture Notes in Computer Science. DOI  10.1007/978-3-319-58667-0_4 (2017).

2016

  • RE Isele-Holder and AE Ismail. Requirements for the Formation and Shape of Microscopic Precursors in Droplet Spreading. Langmuir,  32, 4472-4478 (2016)
  • RE Isele-Holder and AE Ismail. Classification of precursors in nanoscale droplets. Phys. Rev. E. DOI  10.1103/PhysRevE.93.043319 (2016)
  • D Fabregat Travers, AE Ismail, and P Bientinesi. Accelerating scientific codes by performance and accuracy modeling. ArXiv preprint  arXiv:1608.04694. (2016)
  • P Chen, Y Ogawa, N Yoshiharu, AE Ismail, and K Mazeau. Linear, non-linear and plastic bending deformation of cellulose nanocrystals. Phys. Chem. Chem. Phys. DOI 
    10.1039/C6CP00624H
  • M. Höhnerbach, A E. Ismail, and P. Bientinesi. The Tersoff many-body potential: Sustainable performance through vectorization. Supercomputing 2015.
  • C. R. Iacovella, C. Klein, J. Sallai, and A. E. Ismail. “Validation of Computational Models and Codes” in Introduction to Technical and Scientific Computing, F. Willmore, E. Jankowski, and C. Colina, eds. CRC Press, 2016.

2015

  • BD Rabideau and AE Ismail. Effect of Water Content in N‑Methylmorpholine N‑Oxide/Cellulose Solutions on Thermodynamics, Structure, and Hydrogen Bonding. J. Phys. Chem. B. DOI  10.1021/acs.jpcb.5b07500 (2015).
  • MG Schmidt, AE Ismail, and RA Sauer. A continuum mechanical surrogate model for atomic beam structures. Int. J. Multiscale Comput. Eng. In press.
  • P Springer, AE Ismail, P Bientinesi. A Scalable, Linear-Time Dynamic Cutoff Algorithm for Molecular Dynamics. High Performance Computing: 30th International Conference, ISC High Performance 2015 . Lecture Notes in Computer Science, Vol. 9137, Frankfurt, Germany, 12-16 July 2015.
  • BC Rinderspacher, JP Bardhan, AE Ismail. Diffusion Wavelet Decomposition for Coarse-Graining of Polymer Chains. Materials Research Society Symposium Proceedings. Vol. 1753, DOI 10.1557/opl.2015.106 (2015).
  • M Carballo Pacheco, AE Ismail, and B Strodel. Oligomer Formation of Toxic and Functional Amyloid Peptides Studied with Atomistic Simulations. J. Phys. Chem. B. DOI: 10.1021/acs.jpcb.5b04822 (2015).
  • RE Isele-Holder, B Berkels, and AE Ismail. Smoothing of contact lines in spreading droplets by trisiloxane surfactants and its relevance for superspreading. Soft Matter, 11, 4527 (2015).
  • M Döntgen, M Przybylski-Freund, LC Kröger, WA Kopp, AE Ismail, and K Leonhard. Automated discovery of reaction pathways, rate constants and transition states using reactive molecular dynamics simulations.  J. Chem. Theory Comput., DOI: 10.1021/acs.jctc.5b00201 (2015).
  • BD Rabideau and AE Ismail. Mechanisms of hydrogen bond formation between ionic liquids and cellulose and the influence of water content.  Phys. Chem. Chem. Phys., DOI:  10.1039/c4cp04060k (2015). 

2014

  • RE Isele-Holder, AE Ismail. Atomistic Potentials for Trisiloxane, Alkyl Ethoxylate, and Perfluoroalkane-Based Surfactants with TIP4P/2005 and Application to Simulations at the Air–Water Interface. J. Phys. Chem. B, 118, 9284-9297 (2014).
  • MG Schmidt, RA Sauer, AE Ismail. Multiscale treatment of mechanical contact problems involving thin polymeric layers. Model. Simul. Mater. Sci. Eng., 22 045012 (2014).
  • KM Salerno, AE Ismail, JMD Lane, and GS Grest. Coating thickness and coverage effects on the forces between silica nanoparticles in water. J. Chem. Phys., 140, 194904 (2014).
  • BD Rabideau, A Agarwal, and AE Ismail. The Role of the Cation in the Solvation of Cellulose by Imidazolium-Based Ionic Liquids.  J. Phys. Chem. B, DOI: 10.1021/jp4115755 (2014).
  • D Tameling, P Springer, P Bientinesi, AE Ismail. Multilevel summation for dispersion: A linear-time algorithm for r^-6 potentials. J. Chem. Phys.,  140, 024105 (2014).

2013

  • RE Isele-Holder, W Mitchell, JR Hammond, A Kohlmeyer, and AE Ismail. Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation.  J. Chem. Theory Comput., DOI: 10.1021/ct4004614 (2013).
  • BD Rabideau, A Agarwal, and AE Ismail. Observed Mechanism for the Breakup of Small Bundles of Cellulose Iɑ and Iβ in Ionic Liquids from Molecular Dynamics Simulations.  J. Phys. Chem. B, DOI:  10.1021/jp310225t (2013).
  • AA Niazi, BD Rabideau, and AE Ismail. Effects of Water Concentration on the Structural and Diffusion Properties of Imidazolium-Based Ionic Liquid-Water Mixtures.  J. Phys. Chem. B, DOI: 10.1021/jp3080496 (2013). 

2012

  • RE Isele-Holder, WL Mitchell, and AE Ismail. Development and implementation of a particle-particle particle mesh method for dispersion interactions. J. Chem. Phys.,  137, 174107 (2012).
  • BL Peters, JMD Lane, AE Ismail, and GS Grest. Fully-atomistic simulations of the response of silica nanoparticle coatings to alkane solvents. Langmuir, 28, 17443 (2012).
  • BD Rabideau and AE Ismail. The Effects of Chloride Binding on the Behavior of Cellulose-Derived Solutes in the Ionic Liquid 1-Butyl-3-methyl-imidazolium Chloride. J. Phys. Chem. B. 116, 9732 (2012).
  • RE Isele-Holder, BD Rabideau, and AE Ismail. Definition and Computation of Intermolecular Contact in Liquids using Additively Weighted Voronoi Tessellation. J. Phys. Chem. A, 116, 4657 (2012).

2011

  • AE Ismail, F Pierce, GS Grest. Diffusion of small penetrants in polybutadienes. Mol. Phys., 109, 2025 (2011).

2010

  • MB Nemer, Y-L Xiong, AE Ismail, and J-H Jang. Solubility of Fe2(OH)3Cl (Pure-Iron End-Member of Hibbingite) in 0.1-5 m NaCl. Chem. Geol., 280, 26 (2010).
  • AE Ismail, JA Greathouse, PS Crozier, and SM Foiles. The Effect of Electron-Ion Coupling on Simulations of Radiation Damage in a Pyrochlore Wasteform. J. Phys.: Cond. Matt. 22, 225405 (2010).

  • Y Xiong, J Nowak, LH Brush, AE Ismail, and JL Long. Establishment of Uncertainty Ranges and Probability Distributions of Actinide Solu- bilities for Performance Assessment in the Waste Isolation Pilot Plant. Materials Research Society Symposium Proceedings, Vol. 1265: Scientific Basis for Nuclear Waste Management XXXIV. San Francisco, CA, 5-9 April 2010.

2009

  • JMD Lane, AE Ismail, ME Chandross, CD Lorenz, and GS Grest.Forces between functionalized silica nanoparticles in solution. Phys. Rev. E, 79, 050501R (2009).
  • AE Ismail, GS Grest, DR Heine, MJ Stevens, and M Tsige. Interfacial structure and dynamics of siloxane systems: PDMS-vapor and PDMS-water. Macromolecules, 42, 3186 (2009). 

2008

  • DJ Clayton and AE Ismail. Impact of Proposed Disturbed Rock Zone Conceptual Model Modifications to the 2007 Waste Isolation Pilot Plant Performance Assessment on Long-Term Repository Performance. Proceedings of the 2008 Waste Management Symposium. Phoenix, AZ, 25-28 February 2008.

2007

  • AE Ismail, M Tsige, PJ in 't Veld and GS Grest. Surface tension of normal and branched alkanes. Mol. Phys.,  105, 3155 (2007).
  • PJ in 't Veld, AE Ismail, and GS Grest. Application of Ewald summations to long-range dispersion forces. J. Chem. Phys.,  127, 144711 (2007).
  • AE Ismail, GS Grest, and MJ Stevens. Structure and dynamics of water near the interface with oligo(ethylene oxide) self-assembled monolayers. Langmuir, 23, 8508 (2007).

2006

  • AE Ismail, GS Grest, and MJ Stevens. Capillary waves at the liquid-vapor interface and the surface tension of water. J. Chem. Phys., 125, 014702 (2006). 

2005

  • AE Ismail, GC Rutledge, and G Stephanopoulos. Topological coarse-graining of polymer chains using Wavelet-Accelerated Monte Carlo. I. Freely-jointed chains. J. Chem. Phys., 122, 234901 (2005).
  • AE Ismail, G Stephanopoulos, and GC Rutledge. Topological coarse-graining of polymer chains using Wavelet-Accelerated Monte Carlo. II. Self-avoiding chains.  J. Chem. Phys.,  122, 234902 (2005).
  • AE Ismail, G Stephanopoulos, and GC Rutledge. Wavelet-Accelerated Monte Carlo sampling of polymer chains. J. Polym. Sci. B: Polym. Phys., 43, 897 (2005). (Invited)
  • AE Ismail, GC Rutledge, and G Stephanopoulos. Using wavelet transforms for multiresolution materials modeling. Comp. Chem. Eng., 29, 689 (2005). (Invited) 

2004

  • AE Ismail and M. Loewnberg. Long-time evolution of a drop size distribution by coalescence in a linear flow. Phys. Rev. E,  69, 046307 (2004). 

2003

  • AE Ismail, GC Rutledge, and G Stephanopoulos. Multiresolution analysis in statistical mechanics. I. Using wavelets to calculate thermodynamic properties. J. Chem. Phys.,  118, 4414 (2003).
  • AE Ismail, G Stephanopoulos, and GC Rutledge. Multiresolution analysis in statistical mechanics. II. The wavelet transform as a basis for Monte Carlo simulations on lattices. J. Chem. Phys.,  118, 4424 (2003).