References
- Germann TC, Kadau K. Trillion-atom molecular dynamics becomes a reality. J Mod Phys C. 2008;19(9):1315–1319.
- Dubbeldam D, Calero S, Ellis DE, et al. RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials. Mol Simul. 2016;42(2):81–101.
- Hall SR, Allen FH, Brown ID. The crystallographic information file (CIF) -- a new standard archive file for crystallography. Acta Crystallogr A. 1991;47:655–685.
- Kozlkova B, Krone M, Falk M, et al. Visualization of biomolecular structures: State of the art revisited. Comput Graph Forum. 2017;36(8):178–204.
- Schrödinger LLC. The PyMOL molecular graphics system, version 1.8; 2015 Nov.
- Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graphics. 1996;14(1):33–38.
- Pettersen EF, Goddard TD, Huang CC, et al. UCSF chimera-a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612.
- Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006;34(4):255–261.
- Macrae CF, Edgington PR, McCabe P, et al. Mercury: visualization and analysis of crystal structures. J Appl Crystallogr. 2006;39(3):453–457.
- Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci. 1995;20(9):374–376.
- Akkermans RLC, Spenley NA, Robertson SH. Monte carlo methods in materials studio. Mol Simulat. 2013;39(14–15):1153–1164.
- Palmer D, Conley M. Crystalmaker; 2007.
- Hanwell MD, Curtis DE, Lonie DC, et al. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminform. 2012;4(1):1–17.
- Momma K, Izumi F. Vesta 3 for three-dimensional visualization of crystal, volumetric and morphology data. J Appl Crystallogr. 2011;44(6):1272–1276.
- Le Muzic M, Autin L, Parulek J, et al. cellVIEW: a tool for illustrative and multi-scale rendering of large biomolecular datasets. In: B\"{u}hler K, Linsen L, John NW, editors. Eurographics workshop on visual computing for biology and medicine; 2015. p. 61–70.
- Grottel S, krone M, Muller C, et al. Megamol-a prototyping framework for particle-based visualization. IEEE Trans Vis Comput Graph. 2015;21(2):201–214.
- Tarini M, Cignoni P, Montani C. Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Trans Visual Comput Graphics. 2006;12:1237–1244.
- Stone JE, Hardy DJ, Ufimtsev IS, et al. Gpu-accelerated molecular modeling coming of age. J Mol Graphics Model. 2010;29(2):116–125.
- Wright RS, Haemel N, Sellers G, et al. OpenGL superbible: comprehensive tutorial and reference. 5th ed. Boston, MA: Addison-Wesley Professional; 2011.
- Movania MM. OpenGL development Cookbook. Birmingham, UK: Packt Publishing; 2013.
- Lo RCH, Lo WCY. OpenGL data visualization Cookbook. Birmingham, UK: Packt Publishing; 2015.
- Scarpino M. OpenCL in action: how to accelerate graphics and computation. Shelter Island (NY): Manning Publications; 2011.
- Munshi A, Gaster BR, Mattson TG, et al. OpenCL programming guide. Boston, MA: Pearson Education Inc; 2012.
- Gaster BR, Howes L, Kaeli DR, et al. Heterogeneous computing with OpenCL. Waltham (MA): Elsevier; 2013.
- Tay R. OpenCL parallel programming development Cookbook. Birmingham, UK: Packt Publishing; 2013.
- Kaeli D, Mistry P, Schaa D, et al. Heterogeneous computing with OpenCL 2.0. Waltham (MA): Elsevier; 2015.
- Buck EM, Yacktman DA. Cocoa design patterns. Boston (MA): Pearson Education Inc; 2010.
- Chisnall D. Cocoa programming developer’s handbook. Ann Arbor (MA): Pearson Education Inc; 2010.
- Hillegass A, Preble A, Chandler N. Cocoa programming for OSX. 5th ed. Indianapolis (IN): Pearson Education Inc.; 2015.
- Anderson F. XCode 6 start to finish: iOS and OS X development. Ann Arbor (MA): Pearson Education Inc.; 2015.
- Mathias M, Gallagher J. Swift programming: the Big Nerd Ranch guide. Indianapolis (IN): Pearson Education; 2016.
- Nahavandipoor V. Concurrent programming in Mac OS X and iOS. Sebastopol (CA): O’Reilly Media Inc.; 2011.
- Chung YG, Camp J, Haranczyk M, et al. Computation-ready, experimental metal-organic frameworks: a tool to enable high-throughput computation of nanoporous crystals. Chem Mater. 2014;26(21):6185–6192.
- Nazarian D, Camp JS, Sholl DS. A comprehensive set of high-quality point charges for simulations of metal-organic frameworks. Chem Mat. 2016;28(3):785–793.
- Baerlocher Ch, McCusker LB, Olson DH. Atlas of zeolite framework types. 6th ed. Amsterdam: Elsevier Science; 2007.
- Callaway J, Cummings M, Deroski B, et al. Protein data bank contents guide: atomic coordinate entry format description. New York (NY): Brookhaven National Laboratory; 1996.
- Kuipers JB. Quaternions and rotation sequences. New Jersey, USA: Princeton University Press; 2002.
- Krone M, Friess F, Scharnowski K, et al. Molecular surface maps. IEEE Trans Visual Comput Graphics. 2017;23(1):701–710.
- Snurr RQ, Bell AT, Theodorou DN. Prediction of adsorption of aromatic-hydrocarbons in silicalite from grand-canonical monte-carlo simulations with biased insertions. J Phys Chem. 1993;97(51):13742–13752.
- Dubbeldam D, Calero S, Maesen TLM, Smit B. Understanding the window effect in zeolite catalysis. Angew Chem Int Ed. 2003;42(31):3624–3626.
- Akenine-Müller T, Haines E, Hoffman N. Real-time rendering. Boca Raton (FL): CRC Press; 2008.
- Easdon R. Ambient occlusion and shadows for molecular graphics [PhD thesis]. Norwich, UK: University of East Anglia; 2013.
- Ferey G, Mellot-Draznieks C, Serre C, Millange F, Dutour J, Surble S, Margiolaki I. A chromium terephthalate-based solid with unusually large pore volumes and surface area. Science. 2005;309:2040–2042.
- Giacovazzo C, Monaco HL, Artioli G, et al. Fundamentals of crystallography. New York (NY): Oxford University Press; 2002.
- Hahn T. International tables for crystallography. In: Volume A: space group symmetry: space group symmetry v.A. IUCr Series. International tables of crystallography. Wiley-Blackwell; Corrected Reprint 2005.
- Rhodes G. Crystallography made crystal clear. Burlington (MA): Elsevier; 2006.
- Rupp B. Biomolecular crystallography: principles, practice and application to structural biology. New York (NY): Taylor and Francis group; 2010.
- Julian MM. Foundations of crystallography with computer applications. Boca Raton (FL): Taylor and Francis group; 2015.
- Niggli P. Krystallographische und strukturtheoretische Grundbegriffe. Vol. 1. Krauchenwies, Germany: Akademische verlagsgesellschaft mbh; 1928.
- Burgers WG. On the process of transition of the cubic-body-centered modification into the hexagonal-close-packed modification of zirconium. Physica. 1934;1(7–12):561–586.
- Krivy I, Gruber B. A unified algorithm for determining the reduced (niggli) cell. Acta Crystallogra Sect A: Crystal Phys Diffr Theor General Crystallogr. 1976;32(2):297–298.
- Grosse-Kunstleve RW, Sauter NK, Adams PD. Numerically stable algorithms for the computation of reduced unit cells. Acta Crystallogr A. 2004;60:1–6.
- Santoro A, Mighell AD. Determination of reduced cells. Acta Crystallogra Sect A: Crystal Phys Diffr Theor General Crystallogr. 1970;26(1):124–127.
- Düren T, Sarkisov L, Yaghi OM, et al. Design of new materials for methane storage. Langmuir. 2004;20:2683–2689.
- Duren T, Millange F, Ferey G, et al. Calculating geometric surface areas as a characterization tool for metal-organic frameworks. J Phys Chem C. 2007;111(42):15350–15356.
- Sarkisov L, Harrison A. Computational structure characterisation tools in application to ordered and disordered porous materials. Mol Phys. 2011;37(15):1248–1257.
- Walton KS, Snurr RQ. Applicability of the bet method for determining surface areas of metal-organic frameworks. J Am Chem Soc. 2007;129:8552–8556.
- de Lange MF, Lin L-C, Gascon J, et al. Assessing the surface area of porous solids: Limitations, probe molecules, and methods. Langmuir. 2016;32(48):12664–12675.
- Bai P, Tsapatsis M, Siepmann JI. TraPPE-zeo: transferable potentials for phase equilibria force field for all-silica zeolites. J Phys Chem C. 2013;117:24375–24387.
- Talu O, Myers AL. Molecular simulation of adsorption: gibbs dividing surface and comparison with experiment. AIChE J. 2001;47:1160–1168.
- Gelb LD, Gubbins KE. Pore size distributions in porous glasses: a computer simulation study. Langmuir. 1999;15:305–308.
- Serrano DP, Aguado J, Morales G, et al. Molecular and meso-and macroscopic properties of hierarchical nanocrystalline zsm-5 zeolite prepared by seed silanization. Chem Mater. 2009;21(4):641–654.
- Wang H, Pinnavaia TJ. Zsm-5 with intracrystal mesopores for catalytic cracking. Stud Surface Sci Catal. 2007;170:1529–1534.
- Probing Intrazeolite Space, Abrams L, Corbin DR. J Incl Phenom Mol Recognit Chem. 1995;21:1–46.
- Wilmer CE, Leaf M, Lee CY, et al. Large-scale screening of hypothetical metal-organic frameworks. Nat Chem. 2012;4(2):83–89.
- Colon YJ, Snurr RQ. High-throughput computational screening of metal-organic frameworks. Chem. Soc. Rev. 2014;43:5735–5749.
- Yazaydin AO, Snurr RQ, Park T-H, et al. Screening of metal-organic frameworks for carbon dioxide capture from flue gas using a combined experimental and modeling approach. J Am Chem Soc. 2009;131(51):18198–18199.
- Bae YS, Snurr RQ. Development and evaluation of porous materials for carbon dioxide separation and capture. Angew Chem Int Ed. 2011;50(49):11586–11596.
- Krishna R, Calero S, Smit B. Investigation of entropy effects during sorption of mixtures of alkanes in MFI zeolite. Chem Eng J. 2002;88(1–3):81–94.
- Dubbeldam D, Krishna R, Calero S, et al. Computer-assisted screening of ordered crystalline nanoporous adsorbents for separation of alkane isomers. Angew Chem Int Ed. 2012;51(47):11867–11871.
- Torres-Knoop A, Krishna R, Dubbeldam D. Separating xylene isomers by commensurate stacking of p-xylene within channels of MAF-X8. Angew Chem Int Ed. 2014;53(30):7774–7778.
- Torres-Knoop A, Heinen J, Krishna R, et al. Entropic separation of styrene/ethylbenzene mixtures by exploitation of subtle differences in molecular configurations in ordered crystalline nanoporous adsorbents. Langmuir. 2015;31(12):3771–3778.
- Haldoupis E, Nair S, Sholl DS. Finding MOFs for highly selective CO2/N2 adsorption using materials screening based on efficient assignment of atomic point charges. J Am Chem Soc. 2012;134(9):4313–4323.
- Matito-Martos I, Martin-Calvo A, Gutiérrez-Sevillano JJ, et al. Zeolite screening for the separation of gas mixtures containing so2, co2 and co. Phys Chem Chem Phys. 2014;16:19884–19893.
- Wu D, Wang C, liu B, et al. Large-scale computational screening of metal-organic frameworks for CH2/H2 separation. AIChE J. 2012;58(7):2078–2084.
- Chui SS-Y, Lo SM-F, Charmant JPH, et al. A chemically functionalizable nanoporous material [Cu3(TMA)2(H2O)3]n. Science. 1999;283(5405):1148–1150.
- Heinen J, Burtch N, Guerra CF, et al. Predicting multicomponent adsorption isotherms in open-metal site materials using force field calculations based on energy decomposed density functional theory. Chem - A Eur J. 2016;22(50):18045–18050.
- Vicent-Luna JM, Dubbeldam D, Gomez-Alvarez P, et al. Microscopic assembly of aqueous solutions of ionic liquids. Chem Phys Chem. 2016;17(3):380–386.
- Rahbari A, Poursaeidesfahani A, Torres-Knoop A, et al. Chemical potentials of water, methanol, carbon dioxide, and hydrogen sulfide at low temperatures using continuous fractional component gibbs ensemble Monte Carlo. Mol Simulat. 2017;44(5):405–414.
- Dinca M, Choi HJ, Long JR. Broadly hysteretic H2 adsorption in the microporous metal-organic framework Co(1,4-benzenedipyrazolate). J Am Chem Soc. 2008;130:7848–7850.
- Torres-Knoop A, Balestra SRG, Krishna R, et al. Entropic separations of mixtures of aromatics by selective face-to-face molecular stacking in one-dimensional channels of metal-organic frameworks and zeolites. Chem Phys Chem. 2015;16(3):532–535.
- Torres-Knoop A, Dubbeldam D. Exploiting large-pore metal-organic frameworks for separations using entropic molecular mechanisms. Chem Phys Chem. 2015;16(10):2046–2067.
- Dubbeldam D, Snurr RQ. Recent developments in the molecular modeling of diffusion in nanoporous materials. Mol Simulat. 2007;33(4–5):305–325.
- Clark LA, Ye GT, Gupta A, et al. Diffusion mechanisms of normal alkanes in faujasite zeolites. J Chem Phys. 1999;111(3):1209–1222.
- Rost RJ, Licea-Kane B. OpenGL shading language. Boston (MA): Pearson Education Inc.; 2010.
- Bailey M, Cunningham S. Graphics shaders: theory and practice. 2nd ed. Boca Raton (FL): Taylor and Francis group; 2012.
- Wolf D. OpenGL 4 shading language Cookbook. Birmingham, UK: Packt Publishing; 2013.
- Pharr M, Jakob W, Humphreys G. Physically based rendering: from theory to implementation. Burlington (MA): Morgan Kaufmann; 2016.
- Phong BT. Illumination for computer-generated images [PhD thesis]. The University of Utah; 1973. AAI7402100.
- McReynolds T, Blythe D. Advanced graphics programming using OpenGL. San Francisco (CA): Elsevier; 2005.
- Maciel PWC, Shirley P. Visual navigation of large environments using textured clusters. Proceedings of the 1995 symposium on Interactive 3D graphics. Monterey, CA, USA: ACM; 1995. p. 95–102.
- Shade J, Lischinski D, Salesin DH, et al. Hierarchical image caching for accelerated walkthroughs of complex environments. Proceedings of the 23rd annual conference on Computer graphics and interactive techniques; New York, USA: ACM; 1996.
- Bajaj C, Djeu P, Siddavanahalli V, et al. Texmol: interactive visual exploration of large flexible multi-component molecular complexes. Visualization, 2004. IEEE; Austin, TX, USA: IEEE; 2004.
- Lengyel E. Mathematics for 3D game programming & computer graphics. Boston (MA): Charles River Media; 2004.
- Roth SD. Ray casting for modeling solids. Computer graphics and image processing. 1982;18(2):109–144.
- Gumhold S. Splatting illuminated ellipsoids with depth correction. In: Proceedings of International Workshop on Vision, Modeling, and Visualization; Munich, Germany; 2003. p. 245–252.
- Sigg C, Weyrich T, Botsch M, et al. GPU-based ray-casting of quadratic surfaces. In: Proceedings of the 3rd Eurographics/IEEE VGTC Conference on Point-Based Graphics, pages 59–65, Aire-la-Ville, Switzerland; Switzerland: Eurographics Association; 2006.
- Bagur PD, Shivashankar N, Natarajan V. Improved quadric surface impostors for large bio-molecular visualization. In: The Eighth Indian Conference on Vision, Graphics and Image Processing, ICVGIP ’12, Mumbai, India, 16--19 December, 2012; 2012. p. 33.
- Falk M, Grottel S, Krone M, et al. Interactive GPU-based visualization of large dynamic particle data. Synthesis Lectures on Visualization. October 2016;4(3):1–121.
- Toledo R, Lévy B. Extending the graphic pipeline with new gpu-accelerated primitives. Technical report. INRIA-ALICE; 2004.
- de Toledo R, Levy B, Paul JC. Iterative methods for visualization of implicit surfaces on GPU. In: Bebis G, Boyle R, Parvin B, Koracin D, Paragios N, Tanveer S-M, Ju T, Liu Z, Coquillart S, Cruz-Neira C, Müller T, Malzbender T, editors. Advances in visual computing. ISVC 2007. Vol. 4841, Lecture notes in computer science. Berlin, Heidelberg: Springer; 2007.
- Loop C, Blinn J. Real-time GPU rendering of piecewise algebraic surfaces. ACM Trans Graphics. 2006;25(3):664–670.
- Grottel S, Reina G, Ertl T. Optimized data transfer for time-dependent, GPU-based glyphs. Proc IEEE Pac Visual Symp. 2009;2009:65–72.
- Zhukov S, Iones A, Kronin G. An ambient light illumination model. In: Drettakis G, Max N, editors. Rendering techniques ’98. Eurographics. Vienna: Springer; 1998. p. 45–55.
- Landis H. Production-ready global illumination. Course notes on Renderman in production. SIGGRAPH 2002; 2002 Jul.
- Praun E, Hoppe H. Spherical parametrization and remeshing. ACM Trans Graphics. 2003;22(3):340–349.
- Lorensen WE, Cline HE. Marching cubes: a high resolution 3D surface construction algorithm. ACM Siggraph Comput Graphics. 1987;21(4):163–169.
- Montani C, Scateni R, Scopigno R. A modified look-up table for implicit disambiguation of marching cubes. Visual Comput. 1994;10(6):353–355.
- Smistad E, Elster AC, Lindseth F. Fast surface extraction and visualization of medical images using opencl and GPUs. The Joint Workshop on High Performance and Distributed Computing for Medical Imaging; 2011.
- Ziegler G, Tevs A, Theobalt C, et al. On-the-fly point clouds through histogram pyramids. 11th International Fall Workshop on Vision, Modeling and Visualization 2006 (VMV2006); 2006. p. 137–144.
- Dyken C, Ziegler G, Theobalt C, et al. High-speed marching cubes using histopyramids. Comput Graphics Forum. 2008;27(8):2028–2039.
- Cozzi P, Riccio C. OpenGL insights. Boca Raton (FL): Taylor and Francis group; 2012.
- Green C. Improved alpha-tested magnification for vector textures and special effects. ACM SIGGRAPH 2007 courses; New York (NY): ACM; 2007. p. 9–18.
- Hannemann A, Hundt R, Schon JC, et al. A new algorithm for space-group determination. J Appl Crystallogr. 1998;31:922–928.
- Delaunay B. Neue darstellung der geometrischen kristallographie. Z Kristallographie-Cryst Mater. 1933;84(1–6):109–149.
- Le Page Y. Computer derivation of the symmetry elements implied in a structure description. J Appl CrystallogR. 1987;20(3):264–269.
- Lebedev AA, Vagin AA, Murshudov GN. Intensity statistics in twinned crystals with examples from the PDB. Acta Crystallogra Sect D: Biol Crystallogr. 2006;62(1):83–95.
- Grosse-Kunstleve RW. Algorithms for deriving crystallographic space-group information. Acta Crystallogr A. 1999;55(2):383–395.
- Storjohann A. Computation of Hermite and Smith normal forms of matrices [PhD thesis]. Waterloo (ON): University of Waterloo; 1994.
- Wan Z. Computing the smith forms of integer matrices and solving related problems [PhD thesis]. Newark, Delaware, USA: University of Delaware; 2005.
- Fontein F. Aspects of computer algebra. Zurich, Switzerland: Spring Semester; 2013.