Atomistic molecular dynamics simulations on the interaction of TEMPO-oxidized cellulose nanofibrils in water

Surface modification effects on nanocellulose – molecular dynamics simulations using umbrella sampling and computational alchemy

“…Reasons for the discrepancy may be different interaction potentials and different choices of reaction coordinates, but also very likely different fibrillar geometries. These results, however, are in sharp contrast to the work by Paajanen et al (60), who reports overall repulsion, also between unmodified fibrils. This is difficult to rationalize since native CNF is known to form stable aggregates.…”

A novel supra coarse-grained model for cellulose

“…2 The non-bonded interactions in our model are fitted to reproduce the potential of mean forces (PMF) obtained from the AA-MD simulations. The atomistic PMF are obtained from umbrella sampling simulations which will be reported elsewhere and are similar to those reported by Paajanen et al (2016), where two fibrils were simulated in water. It should be noted that the atomistic PMF are obtained for CNC with crosssection of 18 chains and they are normalized per unit surface area (projected surface area) of CNC.…”

“…Finally, to obtain the PMF we use the Weighted Histogram Analysis Method (WHAM) implemented in GROMACS (Hub et al 2010). For a more detailed discussion of the umbrella sampling simulations please see (Paajanen et al 2016). The results from the AA and CG-MD are presented in Fig.…”

“…Cellulose has been the subject of many molecular simulation studies. Some of these studies focus only at the surface phenomena and modifications of CNC, (Chen et al 2017;Zhou et al 2015;Bergenstråhle et al 2008;Paajanen et al 2016;Chundawat et al 2011) while many others simulate whole CNC, both at atomistic (Chen et al 2017;Zhou et al 2015;Bergenstråhle et al 2008;Paajanen et al 2016;Chundawat et al 2011;Matthews et al 2006;Conley et al 2016;Oehme et al 2015;Djahedi et al 2015;Paajanen et al 2019;Ciesielski et al 2019) and coarsegrained representations (López et al 2009;Wohlert and Berglund 2011;López et al 2015;Mehandzhiyski and Zozoulenko 2019;Glass et al 2012;Fan and Maranas 2015;Markutsya et al 2013;Shishehbor et al 2018;Shishehbor and Zavattieri 2019;Ramezani and Golchinfar 2019;Srinivas et al 2011;Poma et al 2015Poma et al , 2016Poma et al , 2017. All-atom molecular dynamics (AA-MD) studies are able to simulate the crystal structure of cellulose in a perfect agreement with the experimental crystal structure of different cellulose allomorphs and provide a detailed atomistic picture for the structure and dynamics of CNC (Chundawat et al 2011).…”

Chirality and bound water in the hierarchical cellulose structure

“…This includes studies on the crystal structure of cellulose microfibrils (Matthews et al 2006;Wada et al 2011;Oehme et al 2015bOehme et al , 2018, and, as mentioned before, various aspects of the microfibril twist (Yui et al 2006;Matthews et al 2006;Yui and Hayashi 2007;Paavilainen et al 2011;Hadden et al 2013;Bu et al 2015;Conley et al 2016;Kannam et al 2017). Other studies have looked at the interactions of microfibrils with water (Yui et al 2006;Bergenstråhle et al 2008;Maurer et al 2013;Kulasinski et al 2015Kulasinski et al , 2017Lindh et al 2016;O'Neill et al 2017), their response to elevated temperatures (Matthews et al 2011(Matthews et al , 2012bZhang et al 2011); their mechanical properties (Paavilainen et al 2012;Saitoh et al 2013;Molnár et al 2018), aggregation and disintegration (Oehme et al 2015a;Paajanen et al 2016;Silveira et al 2016), chemical modification (Wada et al 2011;Paajanen et al 2016), enzymatic degradation (Beckham et al 2011;Orłowski et al 2015), and dissolution in ionic liquids (Gross et al 2011;Uto et al 2018); the pyrolytic degradation of cellulose (Zheng et al 2016;Paajanen and Vaari 2017); and radiation-induced defects (Polvi et al 2012;…”