Peer-reviewed Journals

 

30.       Zhu X-G, Long SP (2009) Photosynthesis in silico. A complete dynamic model of leaf photosynthesis – progress, insights and access, Plant Cell and Environment  (Invited review, to appear).

29.       Zhu X-G, Humphries S, Chen DR, Long SP. (2009) A guide to using WIMOVAC to scale from biochemistry to plant-environment interactions. Plant Cell and Environment  (Invited review, to appear).

28.       Miguez FE, Zhu X-G, Humphries, S, Bollero G, Long SP. Parameterization and validation of WIMOVAC for photosynthesis and biomass modeling in Miscanthus giganteus (submitted).

27.       Zhu X-G, Long SP, Ort DR (2009). Defining, realizing and extending the efficiency of crop photosynthesis.  Annual Review of Plant Biology, 61 (to appear).

26.       Zhu X-G, Wang SW, Shook E, Long SP. Revealing a hidden dimension to global food insecurity, ozone. Nature (in revision)

25.       Zhu X-G, Long SP, Ort DR (2008). What is the maximum efficiency with which photosynthesis can convert solar energy into biomass? Current Opinion in Biotechnology. 19: 153-159

24.       Chen CP, Zhu X-G, Long SP. The effect of leaf-level spatial variability in photosynthetic capacity on biochemical parameter estimates using the Farquhar et al. (1980) model: a theoretical approach. Plant Physiology 148:1139-1147.

23.       Wang Z, *Zhu X-G, Li YY, Chang X, Chen  YZ, Li YX, Liu L. Though with constraints imposed by endosymbiosis, preferential attachment is still a plausible mechanism responsible for evolution of chloroplast metabolic network. Journal of Evolutionary Biology 22:71-79.

22.       Zhu X-G, de Sturler E, Alba R (2008). A simple model of the Calvin cycle has only one physiologically feasible steady state under the same external condition. Nonlinear Analysis.

21.       Wang SW and Zhu X-G (2008) Coupling cyberinfrastructure and GIS to empower ecological and environmental research. Bioscience 58: 6-7.

20.       Chen C-C, Zhu X-G and Zhong S (2008) Selection of thermodynamic models for combinatorial control of multiple transcription factors in early differentiation of embryonic stem cells. BMC Genomics.

19.       Zhu X-G , de Sturler E, Long SP (2007) Optimized distribution of carbon metabolism enzymes can dramatically increase photosynthetic CO2 uptake rate. - Theoretical explorations using a complete model of photosynthetic carbon metabolism. Plant Physiology 145: 513-526.

18.       Wang Z, Zhu  X-G, Yang J, Chen Y,  Li Y, Liu L (2006) Comparison of modularization methods in application to different biological networks. Lecture Notes in Computer Science 4316: 185-195.

17.       Long SP, Zhu X-G, Naidu SL, Ort DR (2006) Can improvement in Photosynthesis Increase Crop Yields? Plant Cell and Environment 29: 315-330.

16.       Wang Z, Zhu X-G, Chen YZ, Yang J, Li YY, Li YX, Liu L (2006) Exploring photosynthesis evolution by comparative analysis of metabolic network between chloroplast and cyanobacteria. BMC Genomics 7: 100.

15.       Zhu X-G, Govindjee,  Baker, NR, deSturler E, Long SP (2005) Fluorescence in silico:  Simulations of chlorophyll a fluorescence induction kinetics of green plants via representation of the complete sequence of excitation energy and electron transport events around photosystem II. Planta 223: 114-133.

14.       Wittig W, Bernacchi CJ, Zhu X-G, Gielen B, Miglietta F, Angelis PD, Ceulemans R, Long SP (2005) Modeling gross primary production for Populus spp grown under free-air CO2 enrichment. Global Change Biology 11: 644-656.

13.       Zhu X-G, Portis AR, Long SP (2004). Would transformation of C3 crop plants with foreign Rubisco increase productivity? A computational analysis extrapolating from kinetic properties to canopy photosynthesis. Plant Cell and Environment 27:155-165.

12.       Rogers A., et al, Zhu X-G, DeLucia E.H., Ort DR, Long SP (2004) Leaf photosynthesis and carbohydrate dynamics of soybean grown throughout their life-cycle under Free-Air Carbon dioxide Enrichment. Plant Cell & Environment 27: 449-458.

11.       Zhu X-G, Whitmarsh J, Ort DR, Long SP (2004). Study of the effects of photoinhibition on dynamics of carbon uptake using reverse ray-tracing algorithm. Journal of Experimental Botany 55: 1167-1175.

10.       Ainsworth EA, et al, Zhu X-G, Curtis PS, Long SP (2002) A meta-analysis of elevated [CO2] effects on soybean (Glycine max) physiology, growth and yield. Global Change Biology 8: 695-709.

9.         Wang Q, Zhang QD, Zhu X-G, Lu CM, Kuang TY, Li CQ (2002) PSII photochemistry and xanthophyll cycle in two super high yield rice hybrids, Liangyoupeijiu and Hua-an 3 during photoinhibition and subsequent restoration. Acta Botanica Sinica 44: 1297-1302 (Now Journal of Integrative Plant Biology). 

8.         Zhu X-G., Wang Q, Zhang QD, Lu CM, Kuang TY (2002) The response of photosynthesis to salt stress in winter wheat. Plant Nutrition and Fertilizer Science 8: 177 – 180.

7.         Zhang Q, Zhu X-G, Wang Q, Lu C, Kuang T, Zhang W, Zhang J. (2001) Photosynthetic characters of F1 hybrids in winter wheat and their parents. Acta Agronomica Sinica 27: 653-657.

6.         Zhu X-G, Zhang QD, Wang Q, Lu CM (2001) Effects of photoinhibition and its recovery on photosynthetic functions of winter wheat under salt stress. Acta Botanica Sinica 43: 1250-1254 (Now Journal of Integrative Plant Biology).

5.         Zhang QD, Zhu X-G, Wang Q, Lu CM, Kuang TY, Zhang WX, Zhang JH (2001) The comparative study of the photosynthetic performance of F1 and the parental generations of winter wheat.  Acta Agronomica Sinica 27: 653 – 657.

4.         Zhang QD, Jiang GM, Zhu X-G, Wang Q, Lu CM, Bai KZ, Kuang TY, Wei QK, Li ZS (2001) Comparative study of the photosynthetic performance of 12 genotypes of winter wheat. Acta Phytoecologica Sinica 25: 532 – 536.

3.         Zhu X-G, Zhang QD, Kuang TY (1999) Effects of NaCl stress on light utilization and dissipation by PSII. Acta Biophysica Sinica 15: 787-791.

2.         Zhu X-G, Zhang QD (1999) The effects of NaCl on photosynthesis performance (review). Chinese Bulletin of Botany 4: 332-338.

1.         Zhang QD, Zhu X-G, Lu CM, Feng LJ, Kuang TY, Zhang JH (1998) Effects of doubled CO2 concentration on light absorption and excitation energy distribution between PSII and PSI in chloroplasts of winter wheat under salt stress.  Acta Biophysica Sinica 14: 537-542.

Book Chapters

5.         Zhu X-G. Systems Biology of Photosynthesis. In The Science of Photochemistry and Photobiology (Editor Kendric Smith).

4.         Zhu X-G, Long SP. Can increase in Rubisco specificity increase carbon gain by whole canopy? A modeling analysis. In Modeling of photosynthesis, Agu Laisk, Lada Nedbal and Govindjee (eds). In Advances in photosynthesis and Respiration (Series editor: Govindjee). (Invited chapter in review).

3.         Leakey ADB, Ort DR, Ainsworth EA, Bernacchi CJ,  Zhu X-G, Long SP (2006) Photosynthesis in a CO2 rich atmosphere. In PHOTOSYNTHESIS:  A Comprehensive Treatise: Physiology, Biochemistry, Biophysics and Molecular Biology. Julian J. Eaton-Rye and Baishnab C. Tripathy (eds). Vol 1, Springer Dordrecht.

2.         Ort DR, Ainsworth EA, Aldea M, Allen DJ, Bernacchi CJ, Berenbaum MR, Bollero GA, Cornic G, Davey PA, Dermody O, Dohleman FG, Hamilton JG, Heaton EA, Leakey ADB, Mahoney J, Mies TA, Morgan PB, Nelson RL, O'Neil B, Rogers A, Zangerl AR, Zhu X-G, DeLucia EH, Long SP (2006) SoyFACE: the effects and interactions of elevated [CO2] and [O3] on soybean. In Managed ecosystems and CO2: Case studies, processes and perspectives. Nösberger J, Long SP, Norby RJ, Stitt M, Hendrey GR, Blum H (eds). Ecological Studies Series Vol 187, Springer Verlag, pp. 71-86.

1.         Long SP, Zhu X-G, Naidu SL, Rains CA, Ort DR (2005) Limits to efficiencies of primary production - constraints and opportunities. In Yields of farmed species: constraints and opportunities in the 21st century. Sylvester-Bradley R, Wiseman J (eds). Norttingham University Press.

 

Invited Talks

12.       Options to engineer higher photosynthetic energy conversion efficiency in bioenergy crops. 18th Western Photosynthesis Conference, January 8-11, 2009, Asilomar Conference Grounds, Pacific Grove, California.

11.       What computational and systems biology can offer to plant biology research? Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, April 18th , 2008, Shanghai.

10.       Guiding biotechnological improvements of photosynthesis using an integrated dynamic model of photosynthesis. Brookhaven National Laboratory, Jan 25, 2008, Upton, New York.

9.         e-Photosynthesis: a new dynamic mechanistic model for integrative photosynthesis research. Plant Biology Departmental Colloquium, UIUC, 19th October 2007, Urbana, IL.

8.         Optimizing nitrogen allocation in Miscanthus giganteus for higher biomass production. C4 CAM: from molecular diversity to ecological convergence. 17-20th July 2007, University of Cambridge, UK.

7.         Multiscale systems biology research of photosynthesis ranging from genome to productivity. Institute of Soil Sciences, Chinese Academy of Sciences. 21st June 2006, Nanjing, China.

6.         System Biology Research in Photosynthesis.  Guiding improvement in photosynthesis and crop productivity in the 21st century. Shanghai Center for Bioinformatics Technologies, 6th April 2006, Shanghai, China.

5.         Integrative computational biology research in photosynthesis: current status and challenges. Chinese Academy of Sciences and Marx Plank Institute Partner Institute of Computational Biology, 5th April 2006, Shanghai, China.

4.         e-Photosynthesis: A system biology platform for guiding improvement in photosynthesis and crop productivity. Bioinformatics seminar series of Department of Computer Science, 24th February 2006, UIUC, Urbana, IL.

3.         Identification of enzymes to modify for improved crop yield potential using systems biology approach. Young Excellence in Bioengineering Seminar series. 26th January 2006, UIUC, Urbana, IL.

2.         Computational plant biology in the post-genomic era. Computational biology group, 6th September 2005, UIUC, Urbana, IL.

1.         Biological cellular metabolism modeling in the post-genomic era. The Bioinformatics Seminar Series, 4th March 2005, UIUC, Urbana, IL.

Conference Abstract (Oral presentation, presenter indicated by * )

18.       Using a systems approach to guide improvements of photosynthetic efficiency for biomass production.  *Zhu X-G and Long SP The Pan American Congress on Plants and BioEnergy June 22-25, Merida, Mexico.

17.       *Shook E, Wang S, Zhu X-G, Liu Y. Synthesizing spatial-temporal data to enable geospatial analysis of biomass-based bioenergy. Annual Meeting of Association of American Geographers-West Lakes Division, November 8-10th 2007, Urbana, IL.

16.       *Zhu X-G, Long S. P. A unifying model of photosynthesis and stomatal responses to environmental factors – control of stomatal conductance by ATP and ABA. 14th International Congress of Photosynthesis. 22-27th July 2007, Glasgow, UK.

15.       *Long S, Dohleman F, Zhu X-G. Achieving environmentally and economically viable biofuel feedstock crops. Why improvement of photosynthetic efficiency is critical and attainable. 14th International Congress of Photosynthesis. 22-27th July 2007, Glasgow, UK.

14.       *Chen C-C, Zhu X-G, Zhong S. Selection of thermodynamic models for combinatorial control of multiple transcription factors in early differentiation of embryonic stem cells. The 2007 World Congress in Computer Science, Computer Engineering, & Applied Computing.  25-27th June 2007, Las Vegas, Nevada.  

13.       *Zhu X-G, deSturler E, Long SP. Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate.  A numerical simulation using an evolutionary algorithm. ComBIO, 24-28th September 2006,Queensland, Australia.

12.       *Chen CP, Zhu X-G, Long SP.  The effect of leaf-level heterogeneity on photosynthesis, as described in current global C-cycle models.  Graduate Ecology and Evolutionary Biology Symposium Feb 2006, Champaign, Illinois.

11.       *Zhu X-G, Portis AR, Ort DR, Long SP. Changes in enzyme activities in the C2 pathway do not lead to a substantial increased photosynthesis rate. An in silico anlaysis.  Proceedings of the 35th Biological systems simulation conference, 19-21st April 2005, Phoenix, Arizona.

10.       *Long SP, Zhu X-G, Ainsworth AE, Bernacchi C, Portis AR, Raines CA (2005) Rubisco and global atmospheric change. First International Symposium on Chloroplast Bioengineering. 2-5th May 2005, Urbana, IL

9.         *Zhu X-G, Portis AR, Ort DR, deSturler E, Sobh N, Whitmarsh JC, Long SP. Physiological role of photorespiratory enzymes in carbon metabolism. A system biology approach. Understanding complex system symposium, Computational Complexity and Bioinformatics, 16-19th May 2005, Urbana, IL.

8.         *Zhu X-G, Portis AR, Ort DR, Long SP. Can manipulation of the C2 pathway enzyme activities increase photosynthetic rate? An in silico anlaysis. American Society of Plant Biologist, Midwest sectional meeting. 18-19th March 2005, St. Louis, MO.

7.         *Wittig, VE, Bernacchi C, Zhu X-G, Ceulemans R, de Angelis P, Gielen B, Miglietta F, Morgan PB, Long SP. Modeling gross primary production for Populus ssp gropwn under free-air CO2 enrichment. The 89th Annual Ecological Society of America Meetings, 2004, Portland, OR.

6.         *Zhu X-G, Ort DR, Long SP.  A novel model of photosynthesis electron transfer - Prediction of the internal environment of chloroplast. The30th Midwest Photosynthesis Meeting, 29-31st October 2004, Marshall, Indiana.

5.         *Zhu X-G, Govindjee, Long SP. Fluorescence in silico:  Simulations of chlorophyll a fluorescence induction kinetics of green plants. The 29th Midwest Photosynthesis Meeting, 2- 4th November 2003, Marshall, Indiana.

4.         *Zhu X-G, Hollis K, Sobh N, Long SP, Whitmarsh J. Modeling Photosynthesis: Towards an e-Photosynthesis Workbench. Understanding complex system symposium - Complexity in Physical, and Biological Structures, Medicine & Ecology. 13-15th May 2002, Urbana, Illinois.

3.         *Zhu X-G, Whitmarsh J, Long SP. Towards a dynamic model of photosynthesis that integrate the light reactions, Calvin cycle and photorespiration. The 28th Midwest Photosynthesis Meeting, 27-29th October 2002, Marshall, Indiana.

2.         *Long SP, Ainsworth EA, Bernacchi CJ, Heaton EA, Morgan PB, Naidu SL, Ort DR, Zhu X-G. The central role of plant biology, from molecular to ecophysiological research, in understanding and adapting to global atmospheric change. Annual Meeting of the American Society of Plant Biologist. 3-7th August 2002, Denver, Colorado.

1.         *Long SP, Ainsworth EA, Bernacchi CJ, Davey PA, Naidu SL, Zhu X-G. Photosynthetic dimensions of global change. Proceedings of the 12th international congress on photosynthesis. 18-23rd August 2001, Brisbane, Australia.

Conference Abstract (Poster presentation)

21.       Rosenthal DM, Bernacchi CJ,  Zhu XG, Ort DR. How will soybeans respond to elevated temperatures when grown at future CO2 concentrations under fully open air field conditions (FACE). Plant Biology 2008, June 26-July 1st 2008, Merida, Mexico.

20.       Chen CP, Zhu X-G, Long SP. Estimating spatial distributions of Vc,max and Jmax via a novel application of chlorophyll fluorescence imaging. Plant Biology 2008, June 26-July 1st 2008, Merida, Mexico.

19.       Sun JD, Feng ZZ, Leakey A, Zhu X-G, Ort DR. CO2 enrichment and leaf aging downregulate both maximum rate of Rubisco carboxylation and mesophyll conductance in SoyFACE. Plant Biology 2008, June 26-July 1st 2008, Merida, Mexico.

18.       Zhu X-G. A systems model of photosynthesis. Bring Plant and Computing Scientists together to Solve Grand Challenges. Cold Spring Harbor Laboratory, April 7-9, 2008, New York.

17.       Miguez FE, Zhu X-G, Long SP, Bollero GA. Mathematical modeling of Miscanthus giganteus. ASA-CSSA-SSSA 2007 International Meeting, 4-8th November 2007, New Orleans, Louisiana.

16.       Zhu X-G, Long SP. What is the signal linking photosynthesis to stomatal conductance? - A theoretical exploration. Plant Biology 2007, 7-11th July 2007, Chicago, IL.

15.       Hugie JA, Zhu X-G, Long SP, Riechers DE.  Elucidating the physiological mechanism for mesotrione-atrazine synergism in triazine-sensitive and triazine-resistant redroot pigweed (amaranthus retroflexus). Plant Biology 2007, 7-11th July 2007, Chicago, IL.

14.       Zhu X-G, Long SP. Guard cell movements controlled through combined effects of ABA and ATP -- A unifying models of photosynthesis and stomata responses to environmental factors. The Biology of Transpiration, from Guard Cell to Globe. 10-14th October 2006, SnowBird, Utah.

13.       Zhu X-G, deSturler E, Long SP. Optimizing the distribution of resources between enzymes of carbon metabolism can dramatically increase photosynthetic rate.  A numerical simulation using an evolutionary algorithm. Plant Biology 2006, 4-10th August 2006, Boston, Massachusetts.

12.       Wang Z, Zhu  X-G, Yang J, Chen Y, Li Y, Liu L. Comparison of modularization methods in application to different biological networks. 32th International Conference on Very Large Data Bases, 12-15th September, 2006, Seoul, Korea.

11.       LaVan DA , Aluru N , et al. , Scott HL, Zhu X-G. In Vivo power generation for neural prosthetics. NIH Neural Interfaces Workshop, 7-9 September 2005, Bethesda, Maryland.

10.       Zhu X-G, Portis AR, Ort DR, Long SP. Can manipulation of the C2 pathway enzyme activities increase photosynthetic rate? An in silico analysis. Annual Meeting of American Society of Plant Biologist 16-20th July 2005, Seattle, Washington.

9.         Castro J, Zhu X-G, Naidu S, Long SP. Rising CO2 and tropospheric O3 directly alter phenology.  Modeling Ecosystem Responses to Global Change: Techniques and Recent Advances, 9-12th Jan 2005, Fort Myers, Florida.

8.         Wittig W, Bernacchi CJ, Zhu X–G, Gielen B, Miglietta F, Angelis PD, Ceulemans R, Long SP. Gross primary production is stimulated for three Populus species grown under free air CO2 enrichment from planting through canopy closure. Modeling Ecosystem Responses to Global Change: Techniques and Recent Advances, 9-12th Jan 2005, Fort Myers, Florida.

7.         Zhu X-G, Crofts, AR, Govindjee, Ort DR, Portis AR, Whitmarsh J, Long SP (2005) e-Photosynthesis: a dynamic model of photosynthesis.  Modeling Ecosystem Responses to Global Change: Techniques and Recent Advances, 9-12th January 2005, Fort Myers, Florida. 

6.         Zhu X-G, Portis AR, Long SP (2005) Has evolution of Rubisco kept up with the increase in atmospheric CO2 concentration? Modeling Ecosystem Responses to Global Change: Techniques and Recent Advances, 9-12th January 2005, Fort Myers, Florida.

5.         Wittig, VE, Bernacchi C, Zhu X-G, Ceulemans R, de Angelis P, Gielen B, Miglietta F, Morgan PB, Long SP. Gross primary production is stimulated for Populus species grown under free-air CO2 enrichment. US Department of Energy, Global Change Education Program (GCEP), 2004, Oak Ridge, TN.

4.         Zhu X-G, Crofts AR, Govindjee, Ort DR, Portis AR, Whitmarsh J, Long SP. Virtual Leaf: Integrating the light reactions, Calvin-Benson cycle and photorespiration in a dynamic model of leaf photosynthesis. Environmental Horizons: Celebrating exploration of the environment, 14th April 2004, Urbana, Illinois.

3.         Zhu X-G, Crofts, AR, Govindjee, Ort DR, Portis AR, Whitmarsh J, Long SP. e-Photosynthesis: a dynamic model of photosynthesis. Annual Meeting of American Society of Plant Biologist 2003, 25-30th July 2003, Honolulu, Hawaii.

2.         Zhu X-G, Portis AR, Long SP. Decrease, not increase, in specificity for carbon dioxide may increase plant production. A crop canopy Perspective. Integrated Photosynthesis Research Annual Conference and Grand Reunion, 3-4th March 2001, Monticello, Illinois.

1.         Zhu X-G, Humphries SW, Long SP. WinSoy – a model and package for mechanistic prediction of the effects of climate and atmosphere changes on soybean. Integrated Photosynthesis Research Annual Conference and Grand Reunion, 3-4th March 2001, Monticello, Illinois.