@article{gupta_hall_voegler_1999, title={Computer simulation of the competition between protein folding and aggregation}, volume={158}, ISSN={["1879-0224"]}, DOI={10.1016/s0378-3812(99)00119-3}, abstractNote={In an attempt to gain insights that might eventually lead to the development of new ways to avoid or minimize losses due to protein aggregation, we have performed dynamic Monte Carlo simulations on very simple lattice models of systems containing both isolated and multiple protein chains. Protein folding pathways, intermediate populations, refolding yields and aggregation were monitored as a function of both denaturant and protein concentrations. We find that there exists optimum levels of denaturant and protein concentration at which the refolding yield is highest, in agreement with some experimental observations.}, number={1999 June}, journal={FLUID PHASE EQUILIBRIA}, author={Gupta, P and Hall, CK and Voegler, A}, year={1999}, month={Jun}, pages={87–93} }
 @article{gupta_hall_voegler_1998, title={Effect of denaturant and protein concentrations upon protein refolding and aggregation: A simple lattice model}, volume={7}, ISSN={["0961-8368"]}, DOI={10.1002/pro.5560071218}, abstractNote={Abstract}, number={12}, journal={PROTEIN SCIENCE}, author={Gupta, P and Hall, CK and Voegler, AC}, year={1998}, month={Dec}, pages={2642–2652} }
 @article{gupta_hall_1997, title={Effect of solvent conditions upon refolding pathways and intermediates for a simple lattice protein}, volume={42}, ISSN={["0006-3525"]}, DOI={10.1002/(SICI)1097-0282(19971005)42:4<399::AID-BIP3>3.0.CO;2-L}, abstractNote={Folding pathways and intermediates for a two‐dimensional lattice protein have been investigated via computer simulation at various denaturant concentrations. The protein is represented as a chain of 8 hydrophobic (H) and 12 polar (P) beads on a square lattice sequenced in such a way that the native state is a compact hydrophobic core surrounded by a shell of polar beads. Two nonbonded H beads are said to attract each other with a potential of mean force of strength ϵ. Increasing |ϵ/kT| mimics decreasing the denaturant concentration in the solution. Dynamic Monte Carlo simulations have been performed in order to investigate the folding transition and the folding pathways. Sharp folding—unfolding transitions are observed and the folding process proceeds along well‐defined pathways that are populated by partially folded intermediates. The folding pathways as well as the populations of the intermediates are strongly dependent upon the denaturant concentration. Generally, intermediates containing long open stretches of H beads are more populated at high denaturant concentration, whereas compact intermediates containing a substantial number of hydrophobic contacts are more populated at low denaturant concentrations. The folding process is also observed to be cooperative in nature in that the chain does not start folding until a key fold in the middle section of the chain is formed correctly. © 1997 John Wiley & Sons, Inc. Biopoly 42: 399–409, 1997}, number={4}, journal={BIOPOLYMERS}, author={Gupta, P and Hall, CK}, year={1997}, month={Oct}, pages={399–409} }