Files
lammps/doc/src/Bibliography.rst
Axel Kohlmeyer 8f366268bb whitespace
2024-08-15 22:55:07 -04:00

1734 lines
55 KiB
ReStructuredText

Bibliography
************
**(Abascal1)**
Abascal, Sanz, Fernandez, Vega, J Chem Phys, 122, 234511 (2005)
**(Abascal2)**
Abascal, J Chem Phys, 123, 234505 (2005)
**(Ackland)**
Ackland, Jones, Phys Rev B, 73, 054104 (2006).
**(Ackland1)**
Ackland, Condensed Matter (2005).
**(Ackland2)**
Ackland, Mendelev, Srolovitz, Han and Barashev, Journal of Physics: Condensed Matter, 16, S2629 (2004).
**(Addington)**
Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018).
**(Adhikari et al.)**
Adhikari, R., Stratford, K., Cates, M. E., and Wagner, A. J., Fluctuating lattice Boltzmann, Europhys. Lett. 71 (2005) 473-479.
**(Afshar)**
Afshar, F. Schmid, A. Pishevar, S. Worley, Comput Phys Comm, 184, 1119-1128 (2013).
**(Agnolin and Roux 2007)**
Agnolin, I. & Roux, J-N. (2007). Internal states of model isotropic granular packings. I. Assembling process, geometry, and contact networks. Phys. Rev. E, 76, 061302.
**(Ahrens-Iwers2022)**
Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022).
**(Ahrens-Iwers)**
Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).
**(Aktulga)**
Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012).
**(Albe)**
J.\ Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003).
**(Albe1)**
K.\ Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002).
**(Allen)**
Allen and Germano, Mol Phys 104, 3225-3235 (2006).
**(AllenTildesley)**
Allen and Tildesley, Computer Simulation of Liquids, Oxford University Press (1987)
**(Allinger)**
Allinger, Yuh, Lii, JACS, 111(23), 8551-8566 (1989),
**(Andersen)**
H.\ Andersen, J of Comp Phys, 52, 24-34 (1983).
**(Anderson)**
Anderson, Mukherjee, Critchley, Ziegler, and Lipton "POEMS: Parallelizable Open-source Efficient Multibody Software ", Engineering With Computers (2006).
**(Appshaw)**
Appshaw, Seddon, Hanna, Soft. Matter,18, 1747(2022).
**(Avendano)**
C.\ Avendano, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011).
**(Axilrod)**
Axilrod and Teller, J Chem Phys, 11, 299 (1943); Muto, Nippon Sugaku-Buturigakkwaishi 17, 629 (1943).
**(Babadi)**
Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
**(Babadi2)**
Babadi and Ejtehadi, EPL, 77 (2007) 23002.
**(Baczewski)**
A.D. Baczewski and S.D. Bond, J. Chem. Phys. 139, 044107 (2013).
**(Bal)**
K.\ M Bal and E. C. Neyts, J. Chem. Phys. 141, 204104 (2014).
**(Ball)**
Ball and Melrose, Physica A, 247, 444-472 (1997).
**(Ballenegger)**
Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107 (2009).
**(Barrat)**
Barrat and Rodney, J. Stat. Phys, 144, 679 (2011).
**(Barrett)**
Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012).
**(Barros)**
Barros, Sinkovits, Luijten, J. Chem. Phys, 140, 064903 (2014)
**(Bartok)**
Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
**(Bartok2010)**
Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
**(Bartok2013)**
Bartok, Kondor, Csanyi, Phys Rev B, 87, 184115 (2013).
**(Bartok_PhD)**
A Bartok-Partay, PhD Thesis, University of Cambridge, (2010).
**(Baskes)**
Baskes, Phys Rev B, 46, 2727-2742 (1992).
**(Baskes2)**
Baskes, Phys Rev B, 75, 094113 (2007).
**(Beck)**
Beck, Molecular Physics, 14, 311 (1968).
**(Becton)**
Becton, Averett, Wang, Biomech. Model. Mechanobiology, 18, 425-433(2019).
**(Behler and Parrinello 2007)**
Behler, J.; Parrinello, M. Phys. Rev. Lett. 2007, 98 (14), 146401.
**(Bennet)**
Bennet, J Comput Phys, 22, 245 (1976)
**(Berardi)**
Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998). Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
**(Berendsen)**
Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984).
**(Berendsen2)**
Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
**(Bessarab)**
Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, 335-347 (2015).
**(Beutler)**
Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem Phys Lett, 222, 529 (1994).
**(Bird)**
G.\ A. Bird, "Molecular Gas Dynamics and the Direct Simulation of Gas Flows" (1994).
**(Bitzek)**
Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, 97, 170201 (2006).
**(Bolintineanu1)**
Bolintineanu, Lechman, Plimpton, Grest, Phys Rev E, 86, 066703 (2012).
**(Bolintineanu2)**
Bolintineanu, Grest, Lechman, Pierce, Plimpton, Schunk, Comp Particle Mechanics, 1, 321-356 (2014).
**(Bomont)**
Bomont, Bretonnet, J. Chem. Phys. 124, 054504 (2006).
**(Bond)**
Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).
**(Boone)**
Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).
**(BoreschKarplus)**
Boresch and Karplus, J Phys Chem A, 103, 103 (1999).
**(Botu1)**
V.\ Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).
**(Botu2)**
V.\ Botu and R. Ramprasad, Phys. Rev. B, 92(9), 094306 (2015).
**(Botu3)**
V.\ Botu, R. Batra, J. Chapman and R. Ramprasad, https://arxiv.org/abs/1610.02098 (2016).
**(Branicio2009)**
Branicio, Rino, Gan and Tsuzuki, J. Phys Condensed Matter 21 (2009) 095002
**(Brennan)**
Brennan, J Chem Phys Lett, 5, 2144-2149 (2014).
**(Brenner)**
Brenner, Shenderova, Harrison, Stuart, Ni, Sinnott, J Physics: Condensed Matter, 14, 783-802 (2002).
**(Brilliantov)**
Brilliantov, Spahn, Hertzsch, Poschel, Phys Rev E, 53, p 5382-5392 (1996).
**(Brooks)**
Brooks, Brooks, MacKerell Jr., J Comput Chem, 30, 1545 (2009).
**(Brooks)**
Brooks, et al, J Comput Chem, 30, 1545 (2009).
**(Brown)**
Brown et al. International Tables for Crystallography Volume C: Mathematical and Chemical Tables, 554-95 (2004).
**(Buck)**
Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 (2006).
**(Bulacu)**
Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292
**(Bussi)**
G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
**(Bussi1)**
Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)
**(Bussi2)**
Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)
**(COMB_1)**
J.\ Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
**(COMB_2)**
T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
**(COMB3)**
T.\ Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek, Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, 255-279 (2013).
**(Calhoun)**
A.\ Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996).
**(Campana)**
C.\ Campana and M. H. Muser, Phys. Rev. B [74], 075420 (2006).
**(Cao1)**
J.\ Cao and B. Berne, J Chem Phys, 99, 2902 (1993).
**(Cao2)**
J.\ Cao and G. Voth, J Chem Phys, 100, 5093 (1994).
**(Caro)**
A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)
**(CasP)**
CasP webpage: http://www.casp-program.org/
**(Cawkwell2012)**
A.\ M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012).
**(Cercignani)**
C.\ Cercignani and M. Lampis. Trans. Theory Stat. Phys. 1, 2, 101 (1971).
**(Cerda)**
Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
**(Ceriotti)**
M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
**(Ceriotti1)**
Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6, 1170-80 (2010)
**(Ceriotti2)**
Ceriotti, Bussi and Parrinello, Phys Rev Lett 103, 030603 (2009)
**(Cerutti)**
Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory and Computation 5, 2322 (2009)
**(Chen)**
J Chen, D Tzou and J Beraun, Int. J. Heat Mass Transfer, 49, 307-316 (2006).
**(Chenoweth_2008)**
Chenoweth, van Duin and Goddard, Journal of Physical Chemistry A, 112, 1040-1053 (2008).
**(Clarke)**
Clarke and Smith, J Chem Phys, 84, 2290 (1986).
**(Clavier)**
G. Clavier, N. Desbiens, E. Bourasseau, V. Lachet, N. Brusselle-Dupend and B. Rousseau, Mol Sim, 43, 1413 (2017).
**(Clemmer)**
Clemmer and Robbins, Phys. Rev. Lett. (2022).
**(Clemmer1)**
Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).
**(Clemmer2)**
Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
**(Coleman)**
Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013).
**(Colliex)**
Colliex et al. International Tables for Crystallography Volume C: Mathematical and Chemical Tables, 249-429 (2004).
**(Cooke)**
"Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)"
**(Cornell)**
Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
**(Cundall, 1987)**
Cundall, P. A. Distinct Element Models of Rock and Soil
**(Curk1)**
T. Curk, J. Yuan, and E. Luijten, JCP 156 (2022).
**(Curk2)**
T. Curk and E. Luijten, PRL 126 (2021)
**(Cusentino)**
Cusentino, Wood, Thompson, J Phys Chem A, 124, 5456, (2020)
**(Daivis and Todd)**
Daivis and Todd, J Chem Phys, 124, 194103 (2006).
**(Daivis and Todd)**
Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).
**(Dammak)**
Dammak, Chalopin, Laroche, Hayoun, and Greffet, Phys Rev Lett, 103, 190601 (2009).
**(Darden)**
Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
**(Davidchack)**
R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
**(Daw1)**
Daw, Baskes, Phys Rev Lett, 50, 1285 (1983). Daw, Baskes, Phys Rev B, 29, 6443 (1984).
**(Daw2)**
M.\ S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984).
**(de Buyl)**
de Buyl, Colberg and Hofling, Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
**(Deissenbeck)**
Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021).
**(de Koning)**
de Koning and Antonelli, Phys Rev E, 53, 465 (1996).
**(DeVane)**
Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
**(Deserno)**
Deserno and Holm, J Chem Phys, 109, 7694 (1998).
**(Destree)**
M.\ Destree, F. Laupretre, A. Lyulin, and J.-P. Ryckaert, J Chem Phys, 112, 9632 (2000).
**(Dickel)**
Dickel, Francis, and Barrett, Computational Materials Science 171 (2020): 109157.
**(Dietz)**
Dietz and Hoy, J. Chem Phys, 156, 014103 (2022).
**(Dobson)**
Dobson, J Chem Phys, 141, 184103 (2014).
**(Drautz)**
Drautz, Phys Rev B, 99, 014104 (2019).
**(Duffy)**
D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, 016207-016218 (2007).
**(Dufils)**
Dufils *et al.*, Phys. Rev. Letters 123, 195501 (2019).
**(Dullweber)**
Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997).
**(Dunn1)**
Dunn and Noid, J Chem Phys, 143, 243148 (2015).
**(Dunn2)**
Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).
**(Dunweg)**
Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
**(EcheverriRestrepo)**
Echeverri Restrepo, Andric, Comput Mater Sci, 218, 111978 (2023).
**(EDIP)**
J F Justo et al, Phys Rev B 58, 2539 (1998).
**(Eike)**
Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006).
**(Elliott)**
Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api <https://openkim.org/kim-api>`_ (2011) doi: `https://doi.org/10.25950/FF8F563A <https://doi.org/10.25950/FF8F563A>`_
**(Ellis)**
Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, Phys Rev B, 104, 035120, (2021)
**(Emmrich)**
Emmrich, Weckner, Commun. Math. Sci., 5, 851-864 (2007),
**(Elstner)**
M.\ Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998).
**(Erdmann)**
U.\ Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, Eur. Phys. J. B 15, 105-113, 2000.
**(Eshelby)**
J.D. Eshelby, Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]
**(Espanol and Revenga)**
Espanol, Revenga, Physical Review E, 67, 026705 (2003).
**(Espanol1997)**
Espanol, Europhys Lett, 40(6): 631-636 (1997). DOI:10.1209/epl/i1997-00515-8
**(Evans and Morriss)**
Evans and Morriss, Phys Rev A, 30, 1528 (1984).
**(Evans)**
Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).
**(Everaers)**
Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003).
**(Faken)**
Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
**(Falk)**
Falk and Langer PRE, 57, 7192 (1998).
**(Fath)**
Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).
**(Feng1)**
Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C. 127(18), 8704-8713 (2023).
**(Feng2)**
Z. Feng, ..., and W. Ouyang, Langmuir 39(50), 18198-18207 (2023).
**(Fennell)**
C.\ J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006).
**(Feynman)**
R.\ Feynman and A. Hibbs, Chapter 7, Quantum Mechanics and Path Integrals, McGraw-Hill, New York (1965).
**(Fichthorn)**
Fichthorn, Balankura, Qi, CrystEngComm, 18(29), 5410-5417 (2016).
**(Fily)**
Y.\ Fily and M.C. Marchetti, Phys. Rev. Lett. 108, 235702, 2012. Default
**(Fincham)**
Fincham, Mackrodt and Mitchell, J Phys Condensed Matter, 6, 393-404 (1994).
**(Finnis1)**
Finnis, Sinclair, Philosophical Magazine A, 50, 45 (1984).
**(Finnis2)**
M.\ W. Finnis, A. T. Paxton, M. Methfessel, and M. van Schilfgarde, Phys. Rev. Lett., 81, 5149 (1998).
**(Fiorin)**
Fiorin, Klein, Henin, Mol. Phys., DOI:10.1080/00268976.2013.813594
**(Fox)**
Fox, O'Keefe, Tabbernor, Acta Crystallogr. A, 45, 786-93 (1989).
**(Fraige)**
F.\ Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds, Particuology, 6, 455 (2008).
**(Freitas)**
Freitas, Asta, and de Koning, Computational Materials Science, 112, 333 (2016).
**(Frenkel)**
Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
**(Fu)**
Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017).
**(Gao)**
Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
**(Gingrich)**
Gingrich, `MSc thesis` <https://gingrich.chem.northwestern.edu/papers/ThesiswCorrections.pdf>` (2010).
**(Gissinger2017)**
Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
**(Gissinger2020)**
Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).
**(Gissinger)**
Jacob R. Gissinger, Scott R. Zavada, Joseph G. Smith, Josh Kemppainen, Ivan Gallegos, Gregory M. Odegard, Emilie J. Siochi, and Kristopher E. Wise, Carbon, 202, 336-347 (2023).
**(Gissinger2024)**
J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
**(Gloor)**
Gloor, J Chem Phys, 123, 134703 (2005)
**(Glosli)**
Glosli, unpublished, 2005. Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference Series, 46, 254 (2006).
**(Goff)**
Goff, Zhang, Negre, Rohskopf, Niklasson, Journal of Chemical Theory and Computation 19, no. 13 (2023).
**(Goldman1)**
Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009)
**(Goldman2)**
Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner, J. Phys. Chem. C, 117, 7885 (2013).
**(Grime)**
Grime and Voth, to appear in J Chem Theory & Computation (2014).
**(Grimme)**
Grimme, J Comput Chem, 27(15), 1787-1799 (2006).
**(Gronbech-Jensen1)**
Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511 (2019)
**(Gronbech-Jensen2)**
Gronbech-Jensen and Farago, Mol Phys, 111, 983 (2013)
**(Gronbech-Jensen3)**
Hayre, and Farago, Comp Phys Comm, 185, 524 (2014)
**(Groot)**
Groot and Warren, J Chem Phys, 107: 4423-4435 (1997). DOI:10.1063/1.474784
**(Guenole)**
Guenole, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek, Comput Mater Sci, 175, 109584 (2020).
**(Gullet)**
Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). DOI:10.2172/918395
**(Guo)**
Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
**(Gupta)**
Gupta ,Phys Rev. B, 23, 6265-6270 (1981).
**(Hardy)**
David Hardy thesis: Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006).
**(Hardy2)**
Hardy, Stone, Schulten, Parallel Computing, 35, 164-177 (2009).
**(Hecht)**
Hecht, Harting, Ihle, Herrmann, Phys Rev E, 72, 011408 (2005).
**(Henkelman1)**
Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000).
**(Henkelman2)**
Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000).
**(Henkes)**
Henkes, S, Fily, Y., and Marchetti, M. C. Phys. Rev. E, 84, 040301(R), 2011.
**(Henrich)**
O.\ Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
**(Herman)**
M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).
**(Hess)**
Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.
**(Heyes)**
Heyes, Phys Rev B, 49, 755 (1994).
**(Hijazi)**
M.\ Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018)
**(Hockney)**
Hockney and Eastwood, Computer Simulation Using Particles, Adam Hilger, NY (1989).
**(Holian)**
Holian and Ravelo, Phys Rev B, 51, 11275 (1995).
**(Hone)**
T.\ Hone, P. Rossky, G. Voth, J Chem Phys, 124, 154103 (2006).
**(Hoover)**
Hoover, Phys Rev A, 31, 1695 (1985).
**(Huang)**
Huang, Zhang, Yuan, Gao, Zhang, Nano Lett. 13, 4546(2013).
**(Huang2014)**
X. Huang, "Exploring critical-state behavior using DEM", Doctoral dissertation, Imperial College. (2014). https://doi.org/10.25560/25316
**(Hu)**
Hu, and Adams J. Comp. Physics, 213, 844-861 (2006).
**(Hu)**
Hu, J. Chem. Theory Comput. 10, 5254 (2014).
**(Hummer)**
Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)
**(Hunt)**
Hunt, Mol Simul, 42, 347 (2016).
**(Ikeshoji)**
Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).
**(Ikeshoji2)**
Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
**(Ilie)**
Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015).
**(In 't Veld)**
In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
**(IPI)**
`https://ipi-code.org/ <https://ipi-code.org/>`
**(IPI-CPC)**
Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
**(Isele-Holder)**
Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).
**(Isele-Holder2)**
Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail, J Chem Theory Comput 9, 5412 (2013).
**(Ismail)**
Ismail, Tsige, In 't Veld, Grest, Molecular Physics (accepted) (2007).
**(Ivanov)**
Ivanov, Uzdin, Jonsson. arXiv preprint arXiv:1904.02669, (2019).
**(Izrailev)**
Izrailev, Stepaniants, Isralewitz, Kosztin, Lu, Molnar, Wriggers, Schulten. Computational Molecular Dynamics: Challenges, Methods, Ideas, volume 4 of Lecture Notes in Computational Science and
**(Izvekov)**
Izvekov, Voth, J Chem Phys 123, 134105 (2005).
**(Jadhao)**
Jadhao, Solis, Olvera de la Cruz, J Chem Phys, 138, 054119 (2013)
**(Janssens)**
Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature Materials, 5, 124-127 (2006).
**(Jaramillo-Botero)**
Jaramillo-Botero, Su, Qi, Goddard, Large-scale, Long-term Non-adiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments, J Comp
**(Jarzynski)**
Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)
**(Jiang)**
Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011).
**(Jiang1)**
Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011).
**(Jiang2)**
J.-W. Jiang, Nanotechnology 26, 315706 (2015).
**(Jiang3)**
J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019).
**(Johnson et al, 1971)**
Johnson, K. L., Kendall, K., & Roberts, A. D. (1971). Surface energy and the contact of elastic solids. Proc. R. Soc. Lond. A, 324(1558), 301-313.
**(Jones)**
Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.
**(Jonsson)**
Jonsson, Mills and Jacobsen, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti, and Coker World Scientific, Singapore, 1998, p 385.
**(Jorgensen)**
Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983).
**(Jusufi)**
Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112, 13783 (2008).
**(Kamberaj)**
Kamberaj, Low, Neal, J Chem Phys, 122, 224114 (2005).
**(Katsura)**
H.\ Katsura, N. Nagaosa, A.V. Balatsky. Phys. Rev. Lett., 95(5), 057205. (2005)
**(Kelchner)**
Kelchner, Plimpton, Hamilton, Phys Rev B, 58, 11085 (1998).
**(Khrapak)**
Khrapak, Chaudhuri, and Morfill, J Chem Phys, 134, 054120 (2011).
**(Kim)**
Kim, Keyes, Straub, J Chem. Phys, 132, 224107 (2010).
**(Klapp)**
Klapp, Schoen, J Chem Phys, 117, 8050 (2002).
**(Kolafa)**
Kolafa and Perram, Molecular Simulation, 9, 351 (1992).
**(Kolmogorov)**
A.\ N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
**(Kong)**
L.T. Kong, G. Bartels, C. Campana, C. Denniston, and Martin H. Muser, `Computer Physics Communications [180](6):1004-1010 (2009). <https://doi.org/10.1016/j.cpc.2008.12.035>`_
**(Kong2011)**
L.T. Kong, `Computer Physics Communications [182](10):2201-2207, (2011). <https://doi.org/10.1016/j.cpc.2011.04.019>`_
**(Kremer)**
Kremer, Grest, J Chem Phys, 92, 5057 (1990).
**(Kuhn and Bagi, 2005)**
Kuhn, M. R., & Bagi, K. (2004). Contact rolling and deformation in granular media. International journal of solids and structures, 41(21), 5793-5820.
**(Kumagai)**
T.\ Kumagai, S. Izumi, S. Hara, S. Sakai, Comp. Mat. Science, 39, 457 (2007).
**(Kumar)**
Kumar and Higdon, Phys Rev E, 82, 051401 (2010).
**(Kumar)**
Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008)
**(Lafourcade)**
Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica, `Comp. Mat. Science, 230, 112534 (2023) <https://doi.org/10.1016/j.commatsci.2023.112534>`_
**(Lamoureux and Roux)**
G.\ Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
**(Lamoureux)**
Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003).
**(Landsgesell)**
J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, Macromolecules 53, 3007-3020 (2020).
**(Larentzos1)**
J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, Comput. Phys. Commun., 185, 1987-1998 (2014).
**(Larentzos2)**
J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014).
**(Larsen)**
Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
**(Lebedeva1)**
I.\ V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
**(Lebedeva2)**
I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Physica E: 44, 949-954 (2012)
**(Lechman)**
Lechman, et al, in preparation (2010).
**(Lee)**
Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000).
**(Lee2)**
Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001).
**(Lee2020)**
C.W. Lee, et al. (2020) Physical Review B, 102(2), 024107.
**(Lenart)**
Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007).
**(Lenosky)**
Lenosky, Sadigh, Alonso, Bulatov, de la Rubia, Kim, Voter, Kress, Modelling Simulation Materials Science Engineering, 8, 825 (2000).
**(Leven1)**
I.\ Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
**(Leven2)**
I.\ Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
**(Li2013_POF)**
Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI:10.1063/1.4812366.
**(Li2014_JCP)**
Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014). DOI:10.1016/j.jcp.2014.02.003.
**(Li2015_CC)**
Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015). DOI:10.1039/C5CC01684C.
**(Li2015_JCP)**
Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015). DOI:10.1063/1.4923254.
**(Liang)**
Liang, Phillpot, Sinnott Phys. Rev. B79 245110, (2009), Erratum: Phys. Rev. B85 199903(E), (2012)
**(Lisal)**
M.\ Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011).
**(Liu1)**
L.\ Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal of Physical Chemistry A, 115, 11016-11022 (2011).
**(Liu2)**
Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8) 2798 (2009)
**(Los and Fasolino)**
J.\ H. Los and A. Fasolino, Phys. Rev. B 68, 024107 (2003).
**(Los2017)**
J.\ H. Los et al. "Extended Tersoff potential for boron nitride: Energetics and elastic properties of pristine and defective h-BN", Phys. Rev. B 96 (184108), 2017.
**(Luding, 2008)**
Luding, S. (2008). Cohesive, frictional powders: contact models for tension. Granular matter, 10(4), 235.
**(Lysogorskiy)**
Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
**(Lysogorskiy21)**
Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
**(Lysogorskiy23)**
Lysogorskiy, Bochkarev, Mrovec, Drautz, Phys Rev Mater, 7, 043801 (2023) / arXiv:2212.08716 (2022).
**(Maaravi)**
T.\ Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
**(MacKerell)**
MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
**(Mackay and Denniston)**
Mackay, F. E., and Denniston, C., Coupling MD particles to a lattice-Boltzmann fluid through the use of conservative forces, J. Comput. Phys. 237 (2013) 289-298.
**(Mackay et al.)**
Mackay, F. E., Ollila, S.T.T., and Denniston, C., Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid, Computer Physics Communications 184 (2013) 2021-2031.
**(Magda)**
Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985); erratum in JCP 84, 2901 (1986).
**(Maginn)**
Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, 260, 218-231 (2007).
**(Mahoney)**
Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000)
**(Malolepsza)**
Malolepsza, Secor, Keyes, J Phys Chem B 119 (42), 13379-13384 (2015).
**(Mandadapu)**
Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115. Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
**(Mandelli_1)**
D. Mandelli, W. Ouyang, M. Urbakh, and O. Hod, ACS Nano 13(7), 7603-7609 (2019).
**(Maras)**
Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp Phys Comm, 205, 13-21 (2016).
**(Marrink)**
Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).
**(Marshall, 2009)**
Marshall, J. S. (2009). Discrete-element modeling of particulate aerosol flows. Journal of Computational Physics, 228(5), 1541-1561.
**(Martyna1992)**
Martyna, Klein, Tuckerman, J Chem Phys, 97, 2635 (1992); Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117.
**(Martyna1994)**
Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
**(Martyna2)**
G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999).
**(Mason)**
J.\ K. Mason, Acta Cryst A65, 259 (2009).
**(Mattice)**
Mattice, Suter, Conformational Theory of Large Molecules, Wiley, New York, 1994.
**(Maxwell)**
J.C. Maxwell, Philos. Tans. Royal Soc. London, 157: 49-88 (1867).
**(Mayergoyz)**
I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009)
**(Mayo)**
Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909 (1990).
**(Mees)**
M.\ J. Mees, G. Pourtois, E. C. Neyts, B. J. Thijsse, and A. Stesmans, Phys. Rev. B 85, 134301 (2012).
**(Mei)**
Mei, Davenport, Fernando, Phys Rev B, 43 4653 (1991)
**(Melchor)**
Gonzalez-Melchor, Mayoral, Velazquez, and Alejandre, J Chem Phys, 125, 224107 (2006).
**(Meloni)**
Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
**(Meremianin)**
Meremianin, J. Phys. A, 39, 3099 (2006).
**(Mezei)**
Mezei, J Chem Phys, 86, 7084 (1987)
**(Mickel)**
W.\ Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
**(Mie)**
G.\ Mie, Ann Phys, 316, 657 (1903).
**(Milano)**
G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).
**(Miller1)**
T.\ F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
**(Miller2)**
Miller, Tadmor, Gibson, Bernstein and Pavia, J Chem Phys, 144, 184107 (2016).
**(Minary)**
Minary, Martyna, and Tuckerman, J Chem Phys, 18, 2510 (2003).
**(Mindlin and Deresiewicz, 1953)**
Mindlin, R.D., & Deresiewicz, H (1953). Elastic Spheres in Contact under Varying Oblique Force. J. Appl. Mech., ASME 20, 327-344.
**(Mindlin, 1949)**
Mindlin, R. D. (1949). Compliance of elastic bodies in contact. J. Appl. Mech., ASME 16, 259-268.
**(Miron)**
R.\ A. Miron and K. A. Fichthorn, J Chem Phys, 119, 6210 (2003).
**(Mishin)**
Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 (2005).
**(Mitchell and Fincham)**
Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993).
**(Mitchell2011)**
Mitchell. A non-local, ordinary-state-based viscoelasticity model for peridynamics. Sandia National Lab Report, 8064:1-28 (2011).
**(Mitchell2011a)**
Mitchell. A Nonlocal, Ordinary, State-Based Plasticity Model for Peridynamics. Sandia National Lab Report, 3166:1-34 (2011).
**(Miyazaki)**
Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020).
**(Mniszewski)**
S.\ M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C. Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015).
**(Monaghan)**
Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983).
**(Monti)**
Monti, Clemmer, Srivastava, Silbert, Grest, and Lechman, Phys. Rev. E, (2022).
**(Moore)**
Moore, J Chem Phys, 144, 104501 (2016).
**(Mori)**
Y.\ Mori, Y. Okamoto, J. Phys. Soc. Jpn., 7, 074003 (2010).
**(Moriarty1)**
Moriarty, Physical Review B, 38, 3199 (1988).
**(Moriarty2)**
Moriarty, Physical Review B, 42, 1609 (1990). Moriarty, Physical Review B 49, 12431 (1994).
**(Moriarty3)**
Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang, Journal of Materials Research, 21, 563 (2006).
**(Morris)**
Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).
**(Moustafa)**
Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
**(Muller-Plathe1)**
Muller-Plathe, J Chem Phys, 106, 6082 (1997).
**(Muller-Plathe2)**
Muller-Plathe, Phys Rev E, 59, 4894-4898 (1999).
**(Murdick)**
D.A. Murdick, X.W. Zhou, H.N.G. Wadley, D. Nguyen-Manh, R. Drautz, and D.G. Pettifor, Phys. Rev. B, 73, 45206 (2006).
**(Murty)**
M.V.R. Murty, H.A. Atwater, Phys Rev B, 51, 4889 (1995).
**(Nakano)**
A.\ Nakano, Computer Physics Communications, 104, 59-69 (1997).
**(Neelov)**
Neelov, Holm, J Chem Phys 132, 234103 (2010)
**(Nelson)**
Nelson, Halperin, Phys Rev B, 19, 2457 (1979).
**(Nettleton)**
Nettleton and Green, J Chem Phys, 29, 6 (1958).
**(Neyts)**
E.\ C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 (2013).
**(Nguyen2023)**
Nguyen, Physical Review B, 107(14), 144103, (2023).
**(Nguyen2024)**
Nguyen, Journal of Computational Physics, 113102, (2024).
**(Nguyen and Rohskopf)**
Nguyen and Rohskopf, Journal of Computational Physics, 480, 112030, (2023).
**(Nguyen and Sema)**
Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
**(NguyenTD)**
Nguyen, Li, Bagchi, Solis, Olvera de la Cruz, Comput Phys Commun 241, 80-19 (2019)
**(Nicholson and Rutledge)**
Nicholson and Rutledge, J Chem Phys, 145, 244903 (2016).
**(Niklasson2002)**
A.\ M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002).
**(Niklasson2008)**
A.\ M. N. Niklasson, Phys. Rev. Lett., 100, 123004 (2008).
**(Niklasson2014)**
A.\ M. N. Niklasson and M. Cawkwell, J. Chem. Phys., 141, 164123, (2014).
**(Niklasson2017)**
A.\ M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
**(Nitol)**
Nitol, Dickel, and Barrett, Computational Materials Science 188 (2021): 110207.
**(Noid)**
Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J Chem Phys 128, 134105 (2008).
**(Nordlund95)**
Nordlund, Kai. Computational materials science 3.4 (1995): 448-456.
**(Nordlund98)**
Nordlund, Kai, et al. Physical Review B 57.13 (1998): 7556.
**(Norman)**
G E Norman, S V Starikov, V V Stegailov et al., Contrib. Plasma Phys., 53, 129-139 (2013).
**(Noskov)**
Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005).
**(Nurdin)**
Nurdin and Schotte Phys Rev E, 61(4), 3579 (2000)
**(O'Connor)**
O'Connor et al., J. Chem. Phys. 142, 024903 (2015).
**(O'Hearn)**
O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1--C22 (2020).
**(Okabe)**
T.\ Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001).
**(Ollila et al.)**
Ollila, S.T.T., Denniston, C., Karttunen, M., and Ala-Nissila, T., Fluctuating lattice-Boltzmann model for complex fluids, J. Chem. Phys. 134 (2011) 064902.
**(Omelyan)**
Omelyan, Mryglod, and Folk. Phys. Rev. Lett. 86(5), 898. (2001).
**(OPLS-AA96)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).
**(Oppelstrup)**
Oppelstrup, unpublished, 2015. Oppelstrup and Moriarty, to be published.
**(Orsi)**
Orsi & Essex, The ELBA force field for coarse-grain modeling of lipid membranes, PloS ONE 6(12): e28637, 2011.
**(Otis R. Walton)**
Walton, O.R., Personal Communication
**(Ouldridge)**
T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
**(Ouldridge-DPhil)**
T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
**(Ouyang1)**
W.\ Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).
**(Ouyang2)**
W.\ Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
**(Ouyang_1)**
W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
**(Ouyang6)**
W. Ouyang, O. Hod, and R. Guerra, J. Chem. Theory Comput. 17, 7215 (2021).
**(Ouyang7)**
W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).
**(Palkar)**
Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022
**(Paquay)**
Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
**(Park)**
Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
**(Parks)**
Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008).
**(Parrinello)**
Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
**(PASS)**
PASS webpage: https://www.sdu.dk/en/DPASS
**(Paula Leite2016)**
Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126, 044509 (2016).
**(Paula Leite2017)**
Paula Leite, Santos-Florez, and de Koning, Phys Rev E, 96, 32115 (2017).
**(Pavlov1)**
D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
**(Pavlov2)**
Pavlov, Galigerov, Kolotinskii, Nikolskiy, Stegailov, "GPU-based Molecular Dynamics of Fluid Flows: Reaching for Turbulence", Int. J. High Perf. Comp. Appl., (2024)
**(Pearlman)**
Pearlman, J Chem Phys, 98, 1487 (1994)
**(Pedersen)**
Pedersen, J. Chem. Phys., 139, 104102 (2013).
**(Pedone)**
A. Pedone, G. Malavasi, M. C. Menziani, A. N. Cormack, and U. Segre, J. Phys. Chem. B, 110, 11780 (2006)
**(Peng)**
Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 (1996).
**(Perram)**
Perram and Rasmussen, Phys Rev E, 54, 6565-6572 (1996).
**(Petersen)**
Petersen, J Chem Phys, 103, 3668 (1995).
**(Petersen)**
Petersen, Lechman, Plimpton, Grest, in' t Veld, Schunk, J Chem Phys, 132, 174106 (2010).
**(Pettifor_1)**
D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 59, 8487 (1999).
**(Pettifor_2)**
D.G. Pettifor and I.I. Oleinik, Phys. Rev. Lett., 84, 4124 (2000).
**(Pettifor_3)**
D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 (2002).
**(PFC)**
PFC Particle Flow Code 6.0 Documentation. Itasca Consulting Group.
**(Phillips)**
C.\ L. Phillips, J. A. Anderson, S. C. Glotzer, Comput Phys Comm, 230, 7191-7201 (2011).
**(Piaggi)**
Piaggi and Parrinello, J Chem Phys, 147, 114112 (2017).
**(Pisarev)**
V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, 475401 (2014).
**(Plimpton)**
Plimpton and Knight, JPDC, 147, 184-195 (2021).
**(PLUMED)**
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Pollock)**
Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
**(Ponder)**
Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
**(Popov1)**
A.M. Popov, I. V. Lebedeva, A. A. Knizhnik, Y. E. Lozovik and B. V. Potapkin, Chem. Phys. Lett. 536, 82-86 (2012).
**(Price1)**
Price and Brooks, J Chem Phys, 121, 10096 (2004).
**(Price2)**
Price, Stone and Alderton, Mol Phys, 52, 987 (1984).
**(QEq/Fire)**
T.-R. Shan, A. P. Thompson, S. J. Plimpton, in preparation
**(Qi)**
Qi and Reed, J. Phys. Chem. A 116, 10451 (2012).
**(Ramirez)**
J.\ Ramirez, S.K. Sukumaran, B. Vorselaars and A.E. Likhtman, J. Chem. Phys. 133, 154103 (2010).
**(Rappe)**
Rappe and Goddard III, Journal of Physical Chemistry, 95, 3358-3363 (1991).
**(Ravelo)**
Ravelo, Holian, Germann and Lomdahl, Phys Rev B, 70, 014103 (2004).
**(ReaxFF)**
A.\ C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J Physical Chemistry, 105, 9396-9049 (2001)
**(Rector)**
Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
**(Ree)**
Ree, Journal of Chemical Physics, 73, 5401 (1980).
**(Reed)**
Reed, Fried, and Joannopoulos, Phys. Rev. Lett., 90, 235503 (2003).
**(Reed2)**
Reed, J. Phys. Chem. C, 116, 2205 (2012).
**(Rick)**
S.\ W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141 (1994).
**(Rick2)**
S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
**(Roberts)**
R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning. `<http://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_
**(Rohart)**
Rohart and Thiaville, Physical Review B, 88(18), 184422. (2013).
**(Rosenberger)**
Rosenberger, Sanyal, Shell and van der Vegt, Journal of Chemical Physics, 2019, 151 (4), 044111.
**(Rubensson)**
E.\ H. Rubensson, A. M. N. Niklasson, SIAM J. Sci. Comput. 36 (2), 147-170, (2014).
**(Rutherford)**
A M Rutherford and D M Duffy, J. Phys.: Condens. Matter, 19, 496201-496210 (2007).
**(Ryckaert)**
J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen, J of Comp Phys, 23, 327-341 (1977).
**(SMTB-Q_1)**
N.\ Salles, O. Politano, E. Amzallag, R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
**(SMTB-Q_2)**
E.\ Maras, N. Salles, R. Tetot, T. Ala-Nissila, H. Jonsson, J. Phys. Chem. C 2015, 119, 10391-10399
**(SMTB-Q_3)**
R.\ Tetot, N. Salles, S. Landron, E. Amzallag, Surface Science 616, 19-8722 28 (2013)
**(SRIM)**
SRIM webpage: http://www.srim.org/
**(SW)**
F.\ H. Stillinger, and T. A. Weber, Phys. Rev. B, 31, 5262 (1985).
**(SWM4-NDP)**
Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys Let, 418, 245-249 (2006)
**(Sadigh)**
B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
**(Sadigh1)**
B. Sadigh, P. Erhart, A. Stukowski, A. Caro, E. Martinez, and L. Zepeda-Ruiz, Phys. Rev. B **85**, 184203 (2012)
**(Sadigh2)**
B. Sadigh and P. Erhart, Phys. Rev. B **86**, 134204 (2012)
**(Safran)**
Safran, Statistical Thermodynamics of Surfaces, Interfaces, And Membranes, Westview Press, ISBN: 978-0813340791 (2003).
**(Salanne)**
Salanne, Rotenberg, Jahn, Vuilleumier, Simon, Christian and Madden, Theor Chem Acc, 131, 1143 (2012).
**(Salerno)**
Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).
**(Sanyal1)**
Sanyal and Shell, Journal of Chemical Physics, 2016, 145 (3), 034109.
**(Sanyal2)**
Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693.
**(Scalfi)**
Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020).
**(Schelling)**
Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).
**(Scherer1)**
C. Scherer and D. Andrienko, Phys. Chem. Chem. Phys. 20, 22387-22394 (2018).
**(Scherer2)**
C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194-3204 (2020).
**(Schlitter1)**
Schlitter, Swegat, Mulders, "Distance-type reaction coordinates for modelling activated processes", J Molecular Modeling, 7, 171-177 (2001).
**(Schlitter2)**
Schlitter and Klahn, "The free energy of a reaction coordinate at multiple constraints: a concise formulation", Molecular Physics, 101, 3439-3443 (2003).
**(Schmid)**
S.\ Bureekaew, S. Amirjalayer, M. Tafipolsky, C. Spickermann, T.K. Roy and R. Schmid, Phys. Status Solidi B, 6, 1128 (2013).
**(Schneider)**
Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
**(Schratt & Mohles)**
Schratt, Mohles. Comp. Mat. Sci. 182 (2020) 109774 ----------
**(Schroeder)**
Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010).
**(Seleson 2010)**
Seleson, Parks, Int J Mult Comp Eng 9(6), pp. 689-706, 2011.
**(Semaev)**
Semaev, Cryptography and Lattices, 181 (2001).
**(Seo)**
Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019).
**(Sheppard)**
Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 (2008). See ref 1 in this paper for original reference to Qmin in Jonsson, Mills, Jacobsen.
**(Shi)**
Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.
**(Shinoda)**
Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
**(Shinoda)**
Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
**(Shire)**
Shire, Hanley and Stratford, Comp. Part. Mech., (2020).
**(Sides)**
Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42, 199-208 (2004).
**(Siepmann)**
Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995).
**(Silbert)**
Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev E, 64, p 051302 (2001).
**(Silbert, 2001)**
Silbert, L. E., Ertas, D., Grest, G. S., Halsey, T. C., Levine, D., & Plimpton, S. J. (2001). Granular flow down an inclined plane: Bagnold scaling and rheology. Physical Review E,
**(Silling 2000)**
Silling, J Mech Phys Solids, 48, 175-209 (2000).
**(Silling 2005)**
Silling Askari, Computer and Structures, 83, 1526-1535 (2005).
**(Silling 2007)**
Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007).
**(Singh)**
Singh and Warner, Acta Mater, 58, 5797-5805 (2010),
**(Singraber, Behler and Dellago 2019)**
Singraber, A.; Behler, J.; Dellago, C. J., Chem. Theory Comput. 2019, 15 (3), 1827-1840
**(Singraber et al 2019)**
Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C., J. Chem. Theory Comput. 2019, 15 (5), 3075-3092.
**(Sirk1)**
Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J Chem Phys, 136 (13) 134903, 2012.
**(Sirk2)**
Sirk, Moore, Brown, J Chem Phys, 138, 064505 (2013).
**(Skomski)**
Skomski, R. (2008). Simple models of magnetism. Oxford University Press.
**(Snodin)**
B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
**(Son)**
Son, McDaniel, Cui and Yethiraj, J Phys Chem Lett, 10, 7523 (2019).
**(Srivastava)**
Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417 (2005).
**(Steinbach)**
Steinbach, Brooks, J Comput Chem, 15, 667 (1994).
**(Steinhardt)**
P.\ Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
**(Steward)**
Stewart, Spearot, Modelling Simul. Mater. Sci. Eng. 21, 045003, (2013).
**(Stewart2018)**
J.A. Stewart, et al. (2018) Journal of Applied Physics, 123(16), 165902.
**(Stiles)**
Stiles , Hubbard, and Kayser, J Chem Phys, 77, 6189 (1982).
**(Stillinger)**
Stillinger, Weber, Phys. Rev. B 31, 5262 (1985).
**(Stoddard)**
Stoddard and Ford, Phys Rev A, 8, 1504 (1973).
**(Streitz)**
F.\ H. Streitz, J. W. Mintmire, Phys Rev B, 50, 11996-12003 (1994).
**(Strong)**
Strong and Eaves, J. Phys. Chem. B 121, 189 (2017).
**(Stuart)**
Stuart, Tutein, Harrison, J Chem Phys, 112, 6472-6486 (2000).
**(Stukowski)**
Stukowski, Sadigh, Erhart, Caro; Modeling Simulation Materials Science & Engineering, 7, 075005 (2009).
**(Su)**
Su and Goddard, Excited Electron Dynamics Modeling of Warm Dense Matter, Phys Rev Lett, 99:185003 (2007).
**(Sulc1)**
P.\ Sulc, F. Romano, T. E. Ouldridge, et al., J. Chem. Phys. 140, 235102 (2014).
**(Sulc2)**
P.\ Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
**(Sun)**
Sun, J. Phys. Chem. B, 102, 7338-7364 (1998).
**(Surblys2019)**
Surblys, Matsubara, Kikugawa, Ohara, Phys Rev E, 99, 051301(R) (2019).
**(Surblys2021)**
Surblys, Matsubara, Kikugawa, Ohara, J Appl Phys 130, 215104 (2021).
**(Sutmann)**
Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
**(Sutmann)** G. Sutmann. ScaFaCoS - a Scalable library of Fast Coulomb Solvers for particle Systems.
In Bajaj, Zavattieri, Koslowski, Siegmund, Proceedings of the Society of Engineering Science 51st Annual Technical Meeting. 2014.
**(Swinburne)**
Swinburne and Marinica, Physical Review Letters, 120, 1 (2018)
**(Tadmor)**
Tadmor, Elliott, Sethna, Miller and Becker, JOM, 63, 17 (2011). doi: `https://doi.org/10.1007/s11837-011-0102-6 <https://doi.org/10.1007/s11837-011-0102-6>`_
**(Tainter 2011)**
Tainter, Pieniazek, Lin, and Skinner, J. Chem. Phys., 134, 184501 (2011)
**(Tainter 2015)**
Tainter, Shi, and Skinner, 11, 2268 (2015)
**(Tang and Toennies)**
J Chem Phys, 80, 3726 (1984).
**(Tee)**
Tee and Searles, J. Chem. Phys. 156, 184101 (2022).
**(Templeton2010)**
Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
**(Templeton2011)**
Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
**(tenWolde)**
P.\ R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
**(Tersoff_1)**
J.\ Tersoff, Phys Rev B, 37, 6991 (1988).
**(Tersoff_2)**
J.\ Tersoff, Phys Rev B, 38, 9902 (1988).
**(Tersoff_3)**
J.\ Tersoff, Phys Rev B, 39, 5566 (1989); errata (PRB 41, 3248)
**(Theodorou)**
Theodorou, Suter, Macromolecules, 18, 1206 (1985).
**(Thole)**
Chem Phys, 59, 341 (1981).
**(Thompson1)**
Thompson, Plimpton, Mattson, J Chem Phys, 131, 154107 (2009).
**(Thompson2)**
Thompson, Swiler, Trott, Foiles, Tucker, J Comp Phys, 285, 316 (2015).
**(Thornton et al, 2013)**
Thornton, C., Cummins, S. J., & Cleary, P. W. (2013). An investigation of the comparative behavior of alternative contact force models during inelastic collisions. Powder
**(Thornton, 1991)**
Thornton, C. (1991). Interparticle sliding in the presence of adhesion. J. Phys. D: Appl. Phys. 24 1942
**(To)**
Q.D. To, V.H. Vu, G. Lauriat, and C. Leonard. J. Math. Phys. 56, 103101 (2015).
**(Todd)**
B.\ D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", Phys. Rev. E 52, 1627 (1995).
**(Toukmaji)**
Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113, 10913 (2000).
**(Toxvaerd)**
Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011).
**(Tranchida)**
Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018).
**(Tribello)**
G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
**(Tsuji et al, 1992)**
Tsuji, Y., Tanaka, T., & Ishida, T. (1992). Lagrangian numerical simulation of plug flow of cohesionless particles in a horizontal pipe. Powder technology, 71(3),
**(Tsuzuki)**
Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007).
**(Tuckerman1)**
M.\ Tuckerman and B. Berne, J Chem Phys, 99, 2796 (1993).
**(Tuckerman2)**
Tuckerman, Alejandre, Lopez-Rendon, Jochim, and Martyna, J Phys A: Math Gen, 39, 5629 (2006).
**(Tuckerman3)**
Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990 (1992).
**(Tuckerman4)**
Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, 106, 5615 (1997).
**(Tyagi)**
Tyagi, Suzen, Sega, Barbosa, Kantorovich, Holm, J Chem Phys, 132, 154112 (2010)
**(Ulomek)**
Ulomek, Brien, Foiles, Mohles, Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007
**(Vaiwala)**
Vaiwala, Jadhav, and Thaokar, J Chem Phys, 146, 124904 (2017).
**(Valone)**
Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
**(vanWijk)**
M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014)
**(Van Workum)**
K. Van Workum et al., J. Chem. Phys. 125 144506 (2006)
**(Vargas and McCarthy 2001)**
Vargas, W.L. and McCarthy, J.J. (2001).
**(Varshalovich)**
Varshalovich, Moskalev, Khersonskii, Quantum Theory of Angular Momentum, World Scientific, Singapore (1987).
**(Vashishta1990)**
P.\ Vashishta, R. K. Kalia, J. P. Rino, Phys. Rev. B 41, 12197 (1990).
**(Vashishta2007)**
P.\ Vashishta, R. K. Kalia, A. Nakano, J. P. Rino. J. Appl. Phys. 101, 103515 (2007).
**(Veld)**
In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
**(Verstraelen)**
Verstraelen, Ayers, Speybroeck, Waroquier, J. Chem. Phys. 138, 074108 (2013).
**(Volkov1)**
Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010).
**(Volkov2)**
Volkov, Simov and Zhigilei, APS Meeting Abstracts, Q31.013 (2008).
**(Voter1998)**
Voter, Phys Rev B, 57, 13985 (1998).
**(Voter2000)**
Sorensen and Voter, J Chem Phys, 112, 9599 (2000)
**(Voter2002)**
Voter, Montalenti, Germann, Annual Review of Materials Research 32, 321 (2002).
**(Voter2013)**
S.\ Y. Kim, D. Perez, A. F. Voter, J Chem Phys, 139, 144110 (2013).
**(Wagner)**
Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
**(Wang et al, 2015)**
Wang, Y., Alonso-Marroquin, F., & Guo, W. W. (2015). Rolling and sliding in 3-D discrete element models. Particuology, 23, 49-55.
**(Wang2020)**
X. Wang, S. Ramirez-Hinestrosa, J. Dobnikar, and D. Frenkel, Phys. Chem. Chem. Phys. 22, 10624 (2020).
**(Wang1)**
J.\ Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011).
**(Wang2)**
J.\ Wang, and A. Rockett, Phys. Rev. B, 43, 12571 (1991).
**(Wang3)**
Wang and Holm, J Chem Phys, 115, 6277 (2001).
**(Wang4)**
Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004).
**(Ward)**
D.K. Ward, X.W. Zhou, B.M. Wong, F.P. Doty, and J.A. Zimmerman, Phys. Rev. B, 85,115206 (2012).
**(Warren)**
Warren, Phys Rev E, 68, 066702 (2003).
**(Watkins)**
Watkins and Jorgensen, J Phys Chem A, 105, 4118-4125 (2001).
**(Weeks)**
Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)
**(WeinanE)**
E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
**(Wen)**
M.\ Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, 98, 235404 (2018)
**(Wennberg)**
Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013).
**(Wicaksono1)**
Wicaksono, Sinclair, Militzer, Computational Materials Science, 117, 397-405 (2016).
**(Wicaksono2)**
Wicaksono, figshare, https://doi.org/10.6084/m9.figshare.1488628.v1 (2015).
**(Winkler)**
Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015).
**(Wirnsberger)**
Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 (2015).
**(Wolf)**
D.\ Wolf, P. Keblinski, S. R. Phillpot, J. Eggebrecht, J Chem Phys, 110, 8254 (1999).
**(Wolff)**
Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
**(Wood)**
Wood and Thompson, J Chem Phys, 148, 241721, (2018)
**(Xie23)**
Xie, S.R., Rupp, M. & Hennig, R.G. Ultra-fast interpretable machine-learning potentials. npj Comput Mater 9, 162 (2023). https://doi.org/10.1038/s41524-023-01092-7
**(Yade-DEM)**
V. Smilauer et al. (2021), Yade Documentation 3rd ed.
**(Yanxon2020)**
Yanxon, Zagaceta, Tang, Matteson, Zhu, Mach. Learn.: Sci. Technol. 2, 027001 (2020).
**(Yeh)**
Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
**(Yuan2010a)**
Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010).
**(Yuan2010b)**
Yuan, Huang, Zhang, Soft. Matter, 6, 4571(2010).
**(Zagaceta2020)**
Zagaceta, Yanxon, Zhu, J Appl Phys, 128, 045113 (2020).
**(ZBL)**
J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges of Ions in Matter' Vol 1, 1985, Pergamon Press.
**(Zhang1)**
Zhang and Makse, Phys Rev E, 72, p 011301 (2005).
**(Zhang2)**
Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016).
**(Zhang3)**
Zhang, Glotzer, Nanoletters, 4, 1407-1413 (2004).
**(Zhang4)**
Zhang, J Chem Phys, 106, 6102 (1997).
**(Zhang5)**
Zhang, Lussetti, de Souza, Muller-Plathe, J Phys Chem B, 109, 15060-15067 (2005).
**(Zhigilei1)**
Volkov and Zhigilei, ACS Nano 4, 6187 (2010).
**(Zhigilei2)**
Volkov, Simov, Zhigilei, ASME paper IMECE2008, 68021 (2008).
**(Zhigilei3)**
Volkov, Zhigilei, J. Phys. Chem. C 114, 5513 (2010).
**(Zhigilei4)**
Wittmaack, Banna, Volkov, Zhigilei, Carbon 130, 69 (2018).
**(Zhigilei5)**
Wittmaack, Volkov, Zhigilei, Compos. Sci. Technol. 166, 66 (2018).
**(Zhigilei6)**
Wittmaack, Volkov, Zhigilei, Carbon 143, 587 (2019).
**(Zhigilei7)**
Volkov, Zhigilei, Phys. Rev. Lett. 104, 215902 (2010).
**(Zhigilei8)**
Volkov, Shiga, Nicholson, Shiomi, Zhigilei, J. Appl. Phys. 111, 053501 (2012).
**(Zhigilei9)**
Volkov, Zhigilei, Appl. Phys. Lett. 101, 043113 (2012).
**(Zhigilei10)**
Jacobs, Nicholson, Zemer, Volkov, Zhigilei, Phys. Rev. B 86, 165414 (2012).
**(Zhou1)**
Zhou, Saidi, Fichthorn, J Phys Chem C, 118(6), 3366-3374 (2014).
**(Zhou3)**
X.\ W. Zhou, M. E. Foster, R. E. Jones, P. Yang, H. Fan, and F. P. Doty, J. Mater. Sci. Res., 4, 15 (2015).
**(Zhou4)**
X.\ W. Zhou, M. E. Foster, J. A. Ronevich, and C. W. San Marchi, J. Comp. Chem., 41, 1299 (2020).
**(Zhu)**
Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).
**(Ziegler)**
J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
**(Zimmerman2004)**
Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319.
**(Zimmerman2010)**
Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
**(electronic stopping)**
Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29