Publications

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1. Type Label Framework for Bonded Force Fields in LAMMPS., J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M.-K. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, E. Tadmor, J. Phys. Chem B, 128, 3282 (2024) (Link) (Preprint)

2. LAMMPS - A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. A.P. Thompson, H.M. Aktulga, R. Berger, D.S. Bolintineanu , W.M. Brown, P.S. Crozier, P.J. in ’t Veld, A. Kohlmeyer, S.G. Moore, T.D. Nguyen, R. Shan, M. Stevens, J. Tranchida, C. Trott, S.J. Plimpton, Comp. Phys. Comm, 271, 10817 (2022) (Link)

3. TopoGromacs: Automated Topology Conversion from CHARMM to Gromacs within VMD, J.V. Vermaas, D.J. Hardy, J.E. Stone, E. Tajkhorshid, and A. Kohlmeyer, J. Chem. Inf. Model. 56(6), 1112-1116 (2016). (Link)

4. Surfactin at the Water/Air Interface and in Solution, J. Iglesias-Fernandez, Leonardo Darre, Axel Kohlmeyer, Robert K Thomas, Hsin-Hui Shen, Carmen Domene, Langmuir 31, 11079-11104 (2015). (Link)

5. Molecular dynamics simulations and neutron reflectivity as an effective approach to characterize biological membranes and related macromolecular assemblies, Leonardo Darre, Javier Iglesias-Fernandez, Axel Kohlmeyer, Hanna Wacklin, Carmen Domene, J. Chem. Theory Comput. 11, 4875-4884 (2015). (Link)

6. Hybrid parallelization of the LIGGGHTS open-source DEM code, R. Berger, C. Kloss, A. Kohlmeyer, S. Pirker, Powder Technology 278, 234-247 (2015). (Link)

7. Reconsidering Dispersion Potentials: Reduced Cutoffs in Mesh-Based Ewald Solvers Can Be Faster Than Truncation, R. Isele-Holder, W. Mitchell, J. Hammond, A. Kohlmeyer, A.E. Ismail, J. Chem. Theory Comput. 9, 5412-5420 (2013). (Link)

8. Advanced Techniques for Scientific Programming and Collaborative Development of Open Source Software Packages at the International Centre for Theoretical Physics (ICTP), I. Girotto, A Kohlmeyer, D. Grellscheid, S.T. Brown, arXiv: 1309.5377,(2013). (Link)

9. Self-Assembly of Charged Surfactants: Full Comparison of Molecular Simulations and Scattering Experiments, A. Jusufi, A. Kohlmeyer, M. Sztucki, T. Narayanan, M. Ballauff, Langmuir 28(51), 17632-17641 (2012). (Link)

10. Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh, W.M. Brown, A. Kohlmeyer, S.J. Plimpton, A.N. Tharrington, Comp. Phys. Comm. 183(3), 449-459 (2012). (Link)

11. Micellization studied by GPU-accelerated coarse-grained molecular dynamics, B.G. Levine , D.N. LeBard , R.H. DeVane , W. Shinoda , A. Kohlmeyer, M.L. Klein, J. Chem. Theory Comput. 7(12), 4135-4145 (2011). (Link)

12. Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units: Radial Distribution Function Histogramming, B.G. Levine, J.E. Stone, A. Kohlmeyer, J. Comput. Phys. 230(9), 3556-3569 (2011) (Link)

13. Immersive Molecular Visualization and Interactive Modeling with Commodity Hardware, J. E. Stone, A. Kohlmeyer, K. L. Vandivort, and K. Schulten, Lecture Notes in Computer Science, 6454 382-393 (2010), (Link)

14. Ab initio molecular dynamics study of supercritical carbon dioxide including dispersion corrections , S. Balasubramanian, A. Kohlmeyer, M. L. Klein, Journal of Chemical Physics 131, 144506 (2009). (Link)

15. Free energy landscape of a DNA-carbon nanotube hybrid using replica exchange molecular dynamics, R. R. Johnson, A. Kohlmeyer, A. T. C. Johnson, M. L. Klein, Nano Letters 9(2), 537541 (2009). (Link)

16. Probing peptide nanotube self-assembly at a liquid-liquid interface with coarse-grained molecular dynamics, E. Khurana, R. H. DeVane, A. Kohlmeyer, M. L. Klein, Nano Letters 8 , 3626-3630 (2008). (Link)

17. X-ray diffraction and computation yield the structure of alkanethiols on gold(111), A. Cossaro, R.Mazzarello, R. Rousseau, L. Casalis, A. Verdini, A. Kohlmeyer, L. Floreano, S. Scandolo, A. Morgante, M.L. Klein, G. Scoles, Science 321, 943-946 (2008). (Link)

18. First principles calculation of phonon dispersion, thermodynamic properties and B1-to-B2 phase transition of lighter alkali hydrides., W. Yu, C. Jin, A. Kohlmeyer, J. Phys.: Condens. Matter 19, 086209 (2007). (Link)

19. Benchmark Analysis of 64-bit Servers for Linux Clusters for Application in Molecular Modeling, S. Cozzini, A. Kohlmeyer, R. Rousseau, Proceedings of the 7th LCI International Conference on Clusters (2006). (Link)

20. Inverse Temperature Transition of Biomimetic Elastin Model: Reactive Flux Analysis of Folding/Unfolding and Its Coupling to Solvent Dielectric Relaxation, M Baer, E. Schreiner, A. Kohlmeyer, R. Rousseau, D. Marx, J. Phys. Chem. B 110, 3576-3587 (2006). (Link)

21. Carbon monoxide reaction with UO2(111) single crystal surfaces: A theoretical and experimental study, S.D. Senanayake, A. Soon, A. Kohlmeyer, T. Soehnel, H. Idriss, J. Vac. Sci. Technol. A 23, 1078-1084 (2005), (Link)

22. Temperature Dependent Conformational Transitions and Hydrogen Bond Dynamics of the Elastin-Like Octapeptide GVG(VPGVG): a Molecular Dynamics Study, R. Rousseau, E. Schreiner, A. Kohlmeyer, D. Marx, Biophys. J. 86, 1393-1407 (2004) (Link)

23. Folding and Unfolding of an Elastinlike Oligopeptide: "Inverse Temperature Transition" Reentrance, and Hydrogen-Bond Dynamics., E. Schreiner, Ch. Nicolini, B. Ludolph, R. Ravindra, N. Otte, A. Kohlmeyer, R. Rousseau, R. Winter, D. Marx, Phys. Rev. Lett. 92, 148101 (2004). (Link)

24. Orientational correlations near interfaces. Computer simulations of water and electrolyte solutions in confined environments, A. Kohlmeyer, C. Hartnig, E. Spohr, J. Mol Liquids 78, 233-253 (1998), (Link)

25. Computersimulations of electrochemical systems, P.A. Bopp, A. Kohlmeyer, E. Spohr, Electrochim. Acta 43 (19-20), 2911-2918 (1998) (Link)

26. Long-range structures in bulk water, A. Kohlmeyer, W. Witschel, E. Spohr, Z. Naturforsch. 52a, 432-434, (1997). (Link)

27. Molecular dynamics simulations of water/metal and water/vacuum interfaces with a polarizable water model, A. Kohlmeyer, W. Witschel, E. Spohr, Chem. Phys.213, 211-216 (1996). (Link)