@article{shi_chinn_sharma-shivappa_2014, title={Interactions between fungal growth, substrate utilization, and enzyme production during solid substrate cultivation of Phanerochaete chrysosporium on cotton stalks}, volume={37}, ISSN={1615-7591 1615-7605}, url={http://dx.doi.org/10.1007/s00449-014-1224-3}, DOI={10.1007/s00449-014-1224-3}, abstractNote={Fungal pretreatment, using lignin-degrading microorganisms to improve lignocellulosic feedstocks with minimal energy input, is a potential alternative to physiochemical pretreatment methods. Identifying the kinetics for fungal pretreatment during solid substrate cultivation is needed to help establish the processing conditions for effective scale up of this technology. In this study, a set of mathematical models were proposed for describing the interactions between holocellulose consumption, lignin degradation, cellulase, ligninolytic enzyme, and the growth of Phanerochaete chrysosporium during a 14 day fungal pretreatment process. Model parameters were estimated and validated by the System Biology Toolbox in MatLab. Developed models provided sufficiently accurate predictions for fungal growth (R (2) = 0.97), holocellulose consumption (R (2) = 0.97), lignin degradation (R (2) = 0.93) and ligninolytic enzyme production (R (2) = 0.92), and fair prediction for cellulase production (R (2) = 0.61). The models provide valuable information for understanding the interactive mechanisms in biological systems as well as for fungal pretreatment process scale up and improvement.}, number={12}, journal={Bioprocess and Biosystems Engineering}, publisher={Springer Science and Business Media LLC}, author={Shi, Jian and Chinn, Mari S. and Sharma-Shivappa, Ratna R.}, year={2014}, month={Jun}, pages={2463–2473} }
 @article{shi_sharma-shivappa_chinn_2012, title={Interactions between fungal growth, substrate utilization and enzyme production during shallow stationary cultivation of Phanerochaete chrysosporium on cotton stalks}, volume={51}, ISSN={["1879-0909"]}, DOI={10.1016/j.enzmictec.2012.03.006}, abstractNote={Microbial pretreatment of lignocellulosic feedstocks is an environment friendly alternative to physio-chemical pretreatment methods. A better understanding of the interactive fungal mechanisms in biological systems is essential for enhancing performance and facilitating scale-up and commercialization of this pretreatment technique. In this study, mathematical models were developed for describing cellulose and hemicellulose consumption, lignin degradation, cellulase and ligninolytic enzyme production and oxygen uptake associated with the growth of Phanerochaete chrysosporium during a 14-day shallow stationary submerged fungal pretreatment process on cotton stalks. Model parameters were estimated and validated by Statistics Toolbox in MatLab 7.1. Models yielded sufficiently accurate predictions for cellulose and hemicellulose consumption (R²=0.9772 and 0.9837), lignin degradation (R²=0.9879 and 0.8682) and ligninolytic enzyme production (R²=0. 8135 and 0.9693) under both 1-day and 3-day oxygen flushing conditions, respectively. The predictabilities for fungal growth (R²=0.6397 and 0.5750) and cellulase production (R²=0.0307 and 0.3046) for 1-day and 3-day oxygen flushing, respectively, and oxygen uptake (R²=0.5435) for 3-day oxygen flushing were limited.}, number={1}, journal={ENZYME AND MICROBIAL TECHNOLOGY}, author={Shi, Jian and Sharma-Shivappa, Ratna R. and Chinn, Mari S.}, year={2012}, month={Jun}, pages={1–8} }
 @article{lee_shi_venditti_jameel_2009, title={Autohydrolysis pretreatment of Coastal Bermuda grass for increased enzyme hydrolysis}, volume={100}, ISSN={["1873-2976"]}, DOI={10.1016/j.biortech.2008.12.068}, abstractNote={Coastal Bermuda grass (GBG) was pretreated using an autohydrolysis process with different temperatures and times, and the pretreated materials were enzymatically hydrolyzed using a mixture of cellulase, xylanase and β-glucosidase with different enzyme loadings to evaluate sugar yields. Compared with untreated CBG, autohydrolysis pretreatments at all elevated temperatures and residence times tested enhanced enzymatic digestibility of both cellulose and hemicellulose. Increasing the temperature and residence time also helps to solubilize hemicelluloses, with 83.3% of the hemicelluloses solubilized at 170 °C for 60 min treatment. However, higher temperatures and longer times resulted in an overall lower sugar recovery when considering monosaccharides in the prehydrolyzate combined with the enzyme hydrolyzate. Autohydrolysis at 150 °C for 60 min provided the highest overall sugar yield for the entire process. A total of 43.3 g of sugars, 70% of the theoretical sugar yield, can be generated from 100 g CBG, 15.0 g of monosaccharide in the prehydrolyzate and 28.3 g in the enzyme hydrolyzate. The conversion efficiency could be further improved by optimizing enzyme dosages and xylanases:cellulases ratio and pretreatment conditions to minimize sugar degradation.}, number={24}, journal={BIORESOURCE TECHNOLOGY}, author={Lee, Jung Myoung and Shi, Jian and Venditti, Richard A. and Jameel, Hasan}, year={2009}, month={Dec}, pages={6434–6441} }
 @article{shi_zikry_2009, title={Grain size, grain boundary sliding, and grain boundary interaction effects on nanocrystalline behavior}, volume={520}, ISSN={["1873-4936"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-67650726010&partnerID=MN8TOARS}, DOI={10.1016/j.msea.2009.05.012}, abstractNote={A dislocation–density grain boundary (GB) interaction scheme, a GB misorientation dependent dislocation–density relation, and a grain boundary sliding (GBS) model are presented to account for the behavior of nanocrystalline aggregates with grain sizes ranging from 25 nm to 200 nm. These schemes are coupled to a dislocation–density multiple slip crystalline plasticity formulation and specialized finite element algorithms to predict the response of nanocrystalline aggregates. These schemes are based on slip system compatibility, local resolved shear stresses, and immobile and mobile dislocation–density evolution. A conservation law for dislocation–densities is used to balance dislocation–density absorption, transmission and emission from the GB. The relation between yield stresses and grain sizes is consistent with the Hall–Petch relation. The results also indicate that GB sliding and grain-size effects affect crack behavior by local dislocation–density and slip evolution at critical GBs. Furthermore, the predictions indicate that GBS increases with decreasing grain sizes, and results in lower normal stresses in critical locations. Hence, GBS may offset strength increases associated with decreases in grain size.}, number={1-2}, journal={MATERIALS SCIENCE AND ENGINEERING A-STRUCTURAL MATERIALS PROPERTIES MICROSTRUCTURE AND PROCESSING}, author={Shi, J. and Zikry, M. A.}, year={2009}, month={Sep}, pages={121–133} }
 @article{shi_zikry_2009, title={Grain-boundary interactions and orientation effects on crack behavior in polycrystalline aggregates}, volume={46}, ISSN={["1879-2146"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-69249219074&partnerID=MN8TOARS}, DOI={10.1016/j.ijsolstr.2009.07.019}, abstractNote={A dislocation-density grain–boundary interaction scheme has been developed to account for the interrelated dislocation-density interactions of emission, absorption and transmission in GB regions. The GB scheme is based on slip-system compatibility, local resolved shear stresses, and immobile and mobile dislocation-density accumulation at critical GB locations. To accurately represent dislocation-density evolution, a conservation law for dislocation-densities is used to balance dislocation-density absorption, transmission and emission from the GB. The behavior of f.c.c. polycrystalline copper, with different random low and high angle GBs, are investigated for different crack lengths. For aggregates with random low angle GBs, dislocation-density transmission dominates at the GBs, which can indicate that the low angle GB will not significantly change crack growth directions. For aggregates with random high angle GBs, extensive dislocation-density absorption and pile-ups occur. The high stresses associated with this behavior, along the GBs, can result in intergranular crack growth due to potential crack nucleation sites in the GB.}, number={21}, journal={INTERNATIONAL JOURNAL OF SOLIDS AND STRUCTURES}, author={Shi, J. and Zikry, M. A.}, year={2009}, month={Oct}, pages={3914–3925} }
 @article{shi_sharma-shivappa_chinn_2009, title={Microbial pretreatment of cotton stalks by submerged cultivation of Phanerochaete chrysosporium}, volume={100}, ISSN={["1873-2976"]}, DOI={10.1016/j.biortech.2008.10.060}, abstractNote={This study used the fungus, Phanerochaete chrysosporium, to pretreat cotton stalks with two methods, shallow stationary and agitated cultivation, at three supplemental salt concentrations. Pretreatment efficiencies were compared by evaluating lignin degradation, solid recovery and carbohydrate availability over a 14-day period. Shallow stationary cultivation with no salts gave 20.7% lignin degradation along with 76.3% solid recovery and 29.0% carbohydrate availability. The highest lignin degradation of 33.9% at a corresponding solid recovery and carbohydrate availability of 67.8% and 18.4%, respectively, was obtained through agitated cultivation with Modified NREL salts. Cultivation beyond 10 days did not significantly increase lignin degradation during 14 days of pretreatment. Manganese addition during shallow stationary and agitated cultivation resulted in higher solid recoveries of over 80% but lower lignin degradation. Although agitated cultivation resulted in better delignification, results indicate that pretreatment under submerged shallow stationary conditions provides a better balance between lignin degradation and carbohydrate availability.}, number={19}, journal={BIORESOURCE TECHNOLOGY}, author={Shi, Jian and Sharma-Shivappa, Ratna R. and Chinn, Mari S.}, year={2009}, month={Oct}, pages={4388–4395} }