Our materials projects were motivated by questions from our partners in industry and engineering. For example, knowledge of the pKa’s of surfactants in various environments would be valuable for detergent formulation; however, the lack of structure makes the problem extremely challenging if possible at all for traditional structure-based continuum methods. We published the first study showing that the pKa's of surfactant micelles can be accurately calculated using hybrid-solvent CpHMD. Later, we also published the first study that calculates surfactant phase transition pKa’s. More recently, we extended the method to study self-assembly and dynamics of polysaccharide-based hydrogels using all-atom CpHMD. 
Polysaccharide-based hydrogel films

Tsai CC, Payne GF, and Shen J*,  Exploring pH-responsive, switchable crosslinking mechanisms for programming reconfigurable hydrogels based on aminopolysaccharides.

Chem Mater 30, 8597-8605, 2018

Wu S, Yan K, Zhao Y, Tsai CC, Shen J, Bentley WE, Chen Y, Deng H, Du Y, Payne GF* and Shi X*,

Electrical writing onto a dynamically responsive polysaccharide medium: patterning structure and function into a reconfigurable medium

Adv Funct Mater, 28: 1803139, 2018.

Yan K, Liu Y, Zhang J, Correa SO, Shang W, Tsai CC, Bentley WE, Shen J, Scarcelli G, Raub CB, Shi XW, Payne GF*,

Electrical programming of soft matter: using temporally varying electrical inputs to spatially control self assembly. 

Biomacromolecules 19: 364-373, 2018. 

Tsai, CC, Morrow BH, Chen W, Payne GF and Shen J*, 

Towards understanding environmental control of hydrogel film: how salt modulates the flexibility of chitosan chains.

Macromolecules 50: 5946-5952, 2017.

Kim E, Liu Y, Ben-Yoav H, Winkler TE, Yan K, Shi S, Shen J, Kelly DL, Ghodssi R, Bentley WE, and Payne GF*, 

Fusing sensor paradigms to acquire chemical information: an integrative role for smart biopolymeric hydrogels.

Adv Healthcare Mater 5: 2595-2616, 2016.

Morrow BH, Payne GF, and Shen J*,
Stimuli-responsive self-assembly of polysaccharide through a rugged energy landscape.
J Am Chem Soc 137: 13024-13030, 2015.

Kim E, Xing Y, Cheng Y, Wu H-C, Liu Y, Morrow BH, Ben-Yoav H, Ghodssi R, Rubloff GW, Shen J, Bentley WE, Shi X, and Payne GF*,

Chitosan to connect biology to electronics: Fabricating the bio-device interface and communicating across this interface.

Polymers 7: 1-46, 2015.

Peptide-based Nanofiber

Cote Y, Fu IW, Dobson ET, Goldberger JE, Nguyen HD, and Shen J*,

Mechanism of the pH-controlled self-assembly of nanofibers from peptide amphiphiles.

J Phys Chem C 118: 16272-16278, 2014.

Surfactants for detergents 

Morrow BH, Eike DM, Murch BP, Koenig PH, and Shen J*,
Predicting proton titration in cationic micelle and bilayer environments.
J Chem Phys 141: 084714, 2014.

Morrow BH, Koenig PH, and Shen JK*,
Self-Assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics.
Langmuir 29: 14823-14830, 2013.


Morrow BH, Koenig PH, and Shen JK*,
Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids.
J Chem Phys 137: 194902, 2012.

Morrow BH, Wang Y, Wallace JA, Koenig PH, and Shen JK*,
Simulating pH titration of a single surfactant in ionic and nonionic micelles.
J Phys Chem B 115: 14980-14990, 2011.

Wang Y, Wallace JA, Koenig PH, and Shen JK*,
Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized Born implicit-solvent model.
J Comput Chem 32: 2358, 2011.