Publications

a. Papers in refereed journals (On Molecular Systems Biology AND System Ecology )

1. Wang C, Thakuri B, Roy AK, Mondal N, Qi Y, Chakraborty A* (2023) Changes in the associations between malaria incidence and climatic factors across malaria endemic countries in Africa and Asia-Pacific region. Journal of Environmental Management 331: 117264 (doi: 10.1016/j.jenvman.2023.117264). (*Corresponding author)

2. Wang C, Feng L, Thakuri B, Chakraborty A* (2022) Ecological risk assessment of organochlorine pesticide mixture in South China Sea and East China Sea under the effects of seasonal changes and phase-partitioning. Marine Pollution Bulletin 185: 114329. (*Corresponding author)

3. Wang C, Thakuri B, Roy AK, Mondal N, Chakraborty A* (2022) Phase partitioning effects on seasonal compositions and distributions of terrigenous Polycyclic Aromatic Hydrocarbons along the South China Sea and East China Sea. Science of The Total Environment 828: 154430 (*Corresponding author)

4. Kumawat N, Tucs A, Bera S, Chuev GN, Valiev M, Fedotova MV, Kruchinin SE, Tsuda K, Sljoka A, Chakraborty A*(2022) Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex. Molecules 27: 799 (doi: 10.3390/molecules27030799) (*Corresponding author)

5. Das JK, Thakuri B, Kuman KM, Roy S, Sljoka A, Sun GQ, Chakraborty A* (2021) Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine the Infectivity of SARS-CoV‑2 Emerging Variants. ACS Omega 6: 31305-31320. (doi: 10.1021/acsomega.1c05155) (*Corresponding author)

6. Bhuyan S, Das D, Chakraborty A, Mandal S, Dhanabal K, Roy B.G. (2021) A Carbohydrate-based Synthetic Approach to Diverse Structurally and Stereochemically Complex Chiral Polyheterocycles. Chem Asian J 16: 4108-4121 (doi: 10.1002/asia.202101123)

7. Bera S , Rashid M, Medvinsky AB, Sun GQ, Li BL, Acquisti C, Slijoka A, Chakraborty A*(2020) Allosteric regulation of Glutamate dehydrogenase deamination activity. Scientific Reports 10: 16523

(*Corresponding author and primary supervisor of first author PhD student)

8. Li T, Ce Wang CE, Xu Z, Chakraborty A* (2020) A coupled method of on-line solid phase extraction with the UHPLC-MS-MS for detection of sulfonamides antibiotics residues in aquaculture. Chemospehere 254:126765 https://doi.org/10.1016/j.chemosphere.2020.126765 (*corresponding author)

9. Rashid M, Bera S, Banerjee M, Medvinsky A, Sun GQ, Li B-L, Slijoka A, Chakraborty A*(2019) Feedforward regulation of plant nitrate transporter NRT1.1 biphasic adaptive activity. Biophysical Journal (cell press) 118: 898-908. https://doi.org/10.1016/j.bpj.2019.10.018

(*Corresponding author and primary supervisor of first author PhD student)

10. Rashid M, Bera S , Medvinsky A, Sun GQ, Li B-L, Chakraborty A* (2018) Adaptive Regulation of Nitrate Transceptor NRT1.1 in Fluctuating Soil Nitrate Conditions. iScience (Cell Press) 2: 41-50.

(*Corresponding author and Primary supervisor of first author PhD student)

11. Lamba S, Bera S, Medvinsky A, Sun GQ, Acquiati C, Li B-L, Chakraborty A* (2017) Organization of microbial nitrogen pathways with switch-like adjustment to fluctuating soil redox conditions. Royal Society Open Science 4: 160768 (https://dx.doi.org/10.1098/rsos.160768).

(*Corresponding author and Primary supervisor of first author PhD student)

12. Bera S , Lamba S, Rashid M, Sharma A, Medvinsky A, Acquiati C, Li B-L, Chakraborty A* (2016) Robust regulation of hepatic pericentral amination by glutamate dehydrogenase kinetics. Royal Society Integrative Biology 8: 1126-1132. (*Corresponding author and primary supervisor of first author PhD student)

13. Chakraborty A*, Sun GQ, Mustavich L, Huang SH, Li BL (2013) Biochemical interactions between HIV-1 integrase and reverse transcriptase. FEBS Letters 587: 425-429. (*eleven US patents cite this article).

(*Corresponding author)

On Ecology/Systems Ecology

14. Adamovich B, Medvinsky AB, Nikitina LV, Radchikova NP, Mikheyeva TM, Kavalevskaya RZ, Veras YK, Chakraborty A, Rusakov AV, Nurieva NI, Zhukova TV (2019) Relations between variations in the lake bacterioplankton abundance and the lake trophic state: evidence from the 20-year monitoring. Ecological Indicators 97: 120-129.

15. Medvinsky AB, Adamovich BV, Aliev RR, Chakraborty A, Lukyanova EV, Mikheyeya TM, Nikitina LV, Nurieva N, Rusakov A, Zhukova T (2017) Temperature as a factor affecting fluctuations and predictability of the abundance of lake. Ecological Complexity 32: 90-98.

16. Medvinsky A, Adamovich BV, Chakraborty A, Lukyanova EV, Mikheyeva TM, Nurieva NI, Radchikova NP, Rusakov AV, Zhukova TV (2015) Chaos far away from the edge of chaos: A recurrence quantification analysis of plankton time series. Ecological Complexity 23:61-67.

17. Shi PJ, Ishikawa T, Sandhu HS, Hui C, Chakraborty A*, Xian SJ, Katsunori T, Li BL (2014) On the 3/4 – exponent von Bertalanffy equation for ontogenetic growth. Ecological Modelling 276: 23-28. (*corresponding author)

18. Sun GQ, Chakraborty A, Liu QX, Jin Z, Anderson KE, Li BL (2014) Influence of time delay and nonlinear diffusion on herbivore outbreak. Communications in nonlinear science and numerical simulations 19: 1507-1518.

19. Shi PJ, Men XY, Sandhu HS, Chakraborty A*, Li BL, Yang F, Sun Y, Ge F (2013) The "general" ontogenetic growth model is inapplicable to crop growth. Ecological Modelling 266: 1-9. (*corresponding author)

20. Chakraborty A, Shi PJ, Liu QX, Yang QP, Li BL (2013) A commensal consumer-induced mediation effects on resource-consumer interactions. Proc. Natl.Acad. Sci. India, Sect.B Biol.Sci. 83:385-404.

21. Sun G, Jin Z, Song LP, Chakraborty A, Li BL (2011) Phase transition in spatial epidemics using cellular automata with noise.Ecological Research 26: 333-340.

22. Chakraborty A, Li BL (2011) Contribution of biodiversity to ecosystem functioning: a non-equilibrium thermodynamic perspective.Journal of Arid Land 3: 71-74.

23. Chakraborty A, Li BL (2010) Departure from naturalized to invasive stage: A disturbance-induced mechanism and associated interacting factors. Journal of Plant Ecology 3: 231-242. (* selected in editor choice category)

24. Chakraborty A, Li BL (2010) The role of fluctuating resource supply in a habitat maintained by the competition-colonization trade-off. Annals of the New York Academy of Sciences 1195: 27-39.

25. Sun GQ, Jin Z, Chakraborty A, Li BL (2010) Influence of infection rate and migration on extinction of disease in spatial epidemics. Journal of Theoretical Biology 264: 95-103.

(*cited in Science paper (DOI: 10.1126/science.abc5096) on COVID-19)

26. Chakraborty A, Sun GQ, Li BL (2010) Spatial organization of multiple plant species in arid ecosystems: linking patterns and processes. Journal of Arid Land 2: 9-13.

27. Wu H, Chakraborty A*, Li BL, Kenerley CM (2009) Formulating variable carrying capacity by exploring a resource dynamics-based feedback mechanism underlying the population growth models. Ecological Complexity 6: 403-412. (*corresponding author)

28. Chakraborty A, Li BL (2009) Plant-to-Plant direct competition for belowground resource in an overlapping depletion zone. Journal of Arid Land 1: 9-15.

29. Chakraborty A, Li BL (2009) Post-fire ecological succession: A theoretical modeling framework. Acta Ecologica Sinica 29: 7-12.

30. Medvinsky AB, Rusakov AV, Chakraborty A, Li BL, Marchenko AI, Sokolov MS (2009) Mathematical modeling the spatial distribution of the pollen produced by genetically modified crops. Biophysics 54: 941-945.

31. Chakraborty A, Bhattacharaya DK (2007) A process-based model on methane emission with its oxidation process from rice fields and corresponding control indices. Environmental Modeling and Assessment 12: 185-199.

32. Chakraborty A, Bhattacharaya DK (2006) A process-based mathematical model on methane production with emission indices for control. Bulletin of Mathematical Biology 68: 1293-1314.

33. Chakraborty A, Bhattacharya DK, Li BL (2006) Spatiotemporal dynamics of methane emission from rice fields at global scale. Ecological Complexity 3: 231-240.

b. Papers in conference proceedings

Kundu N, Chakraborty A, Pal M (2002). Advantages of estimation of Kharif crop using RadarSat ScanSar data.https://airsar.jpl.nasa.gov/documents/worshop2002/papers/L2.pdf.

c. Digital data Repository

#Lamba S, Bera S, Rashid M, Medvinsky AB, Sun G, Acquisti C, Chakraborty A*, Li B (2017) Data from: Organization of biogeochemical nitrogen pathways with switch-like adjustment in fluctuating soil redox conditions. Dryad Digital Repository. https://dx.doi.org/10.5061/dryad.n04g0 (*Corresponding author)

d. Papers presented in conferences but not published

Invited Lecture

1. Department of Mathematics, Nar Bahadur Bhandari Government College Tadong, National Mathematics Day, commemorating the birth anniversary of renowned Mathematician Srinivasa Ramanujan on 22nd December 2021. Title of the talk: Mathematics and its applications in biology and medicine.

2. Department of Mathematics, Kalyani Mahavidyalaya, W.B., International Webinar on "Mathematics in Data Analysis and Internet Security during COVID-19 pandemic", Sept 09-10, 2020. Title of the talk: Mathematical and computational examinations of successful entry of SARS-CoV-2 into human host cells.

(youtube link: https://www.youtube.com/watch?v=Gl8StgRuz-A&feature=emb_err_woyt )

3. Department of Mathematics, Sripat Singh College, Murshidabad, W.B., National Seminar on Environmental perturbation: root causes and remedies, February 02, 2020. Title of the talk:" N-cycle and its anthropogenic perturbation: causes and consequences".

4. Invited visit at The Three Gorges Environment Institute, Chinese Academy of Sciences, Chongqing on June 15, 2019.

5. Department of Mathematics, Shanxi University, China, June 17, 2019. Title of the lecture "Organization of nitrogen biogeochemical pathways underground".

6. School of Energy and Environment, Southeast University, China, 4 lectures from June 10-14, 2019. Title of the lecture "Limiting Resource-Diversity-Functioning of the Systems (R-D-FS) framework and ecological regulation".

7. Institute of Mathematical Sciences (IMSc), Chennai, September 25, 2019. Title of the talk: Biocomplexity: Limiting resource-diversity-the functioning of systems (R-D-FS) framework.

8. 5-days workshop on "Celestial Mechanics and Dynamical Astronomy (CMDA)" 07-11 January 2019.Central University of Rajasthan. Title of the talk: On stability theory.

9. Birla Institute of Technology and Science, Pilani, International conference on life science research and its interface with engineering and allied sciences (LSRIEAS-2019), Nov 1-3, 2018. Title of the talk: "Allosteric regulation of glutamate dehydrogenase molecule-a key molecule in Hyperinsulinism and Hyperammonemia syndrome (HI/HA)".

10. Department of Mathematics, NIT Patna, National conference on mathematical biology July 7-8, 2018. Title of the talk "The deterministic models in biology: from molecules to ecosystems".

11. Department of Mathematics, Kalyani Mahavidyalaya, City Centre Complex, W.B., UGC sponsored national seminar on "Recent developments in Mathematics and its applications in other branches of science", Dec.15,2016. Title of the talk: "21st century mathematics: trends and emergence".

12. Department of Mathematics, Sripat Singh College, W.B., UGC sponsored national seminar on "Emerging advances in Mathematics and its applications in natural sciences", Dec.17,2016. Title of the talk: "Chaos far away from the edge of chaos".

13. Central University of Rajasthan, Department of Mathematics, 5-days workshop on "Mathematical modeling and simulation" March 14-18, 2016. Title of the talk " Graph-based approaches in Dynamical Systems".

14. Manipal University, Jaipur, India on Dec. 18, 2015. Title of the talk:" Regulation of bio available nitrogen forms through microbial biochemical pathways".

15. Malaviya National Institute of Technology (MNIT), Jaipur, India on Jan. 20, 2015. Title of the talk: "Mathematical Modeling, MATLAB Programming and their Applications in Engineering and Sciences".

16. The Department of Physics, Central University of Rajasthan, Dynamics Day Rajasthan: Interdisciplinary Symposium on Complex Systems' on Nov. 29, 2014. Title of the talk: Biocompexity across the levels of biological organizations.

17. Indian Statistical Institute (ISI), Kolkata on August 27, 2013. The title of the talk: linking biodiversity to ecosystem functions.

18. Indian Institute of Technology (IIT), Rajasthan on May 7, 2012. The title of the talk: The role of limiting resource from ecosystems to genes: Complex System approaches.

19. Department of Applied Mathematics, IT-BHU on October 19,2011. Title of the talk: From ecosystem to genes: resource-based approaches and modeling.

20. Department of Mathematics, University of Burdwan, W.B. on Jan.10, 2006. Title of the talk: Spatio-temporal analysis and its applications.

21. Department of Mathematics, The IIS University, April 9, 2014. Title of the talk: "Mathematical modeling and various techniques.

Presentations

International

1. Int. Conference on Optimization, Computing and Business Analysis for Sustainable Development organized by the Dept. of Mathematics, Central University of Rajasthan, January 30-31, 2015. Title of the talk: "On the ¾-exponent von Bertanlantfy equation for ontogenetic growth".

2. International Conference on Advances in Dynamical Systems organized by Dept. of Mathematics, Central University of Rajasthan on 10-13 March. 2014. Title of the talk: "Feedback and feedforward regulation of dynamical systems".

3. International Workshops on Climate Change Impacts and Societal Adaptation organized by Central University of Rajasthan and Swedish Meteorological and Hydrological Institute (Sweden) on 7-8 Nov. 2013. Title of the talk: "Regulation of ecosystem productivity through alteration of microbial nitrogen pathways".

4. Winter Seminar Series-2011, Jan.19, 2011, Department of Botany and Plant Sciences, University of California, Riverside. Title of the talk: Modeling species interactions in variable environments: linking patterns and processes of plant species invasions.

5. Biocomplexity seminar, Sept, 2009. Center for Conservation Biology, University of California, Riverside. Title of the talk: Landscape modeling efforts for N-biocomplexity program.

6. 93rd ESA Annual Meeting, Aug. 3-8, 2008. The Midwest Airlines Center, Milwaukee, Wisconsin. Title of the talk: The role of fluctuating resource supply in a habitat maintained by the competition-colonization trade-off.

7. ESA/SER Joint meeting, Aug.5-10, 2007, San Jose McEnery Convention Center, California. Title of the talk: Plant competitive interactions in an overlapping depletion zone.

8. 7th Conference of the International Academy Of Physical Sciences (CONIAPS-VII), Dec. 21 – 23, 2004, University of Allahabad, Allahabad. Title of the talk: A process based mathematical model on methane emission and corresponding emission indices for its control.

9. The First International Symposium on Nonlinear Analysis and Applications (ISNAA-2003), Jan 2-4, 2003, Science city, Kolkata. Title of the talk: Pattern formation of soil emitting methane.

National

1. National conference on "Emerging Trends in Mathematics and its applications in engineering" organized by the Department of Mathematics, Mewar University, Rajasthan, 8-9 January, 2016. Title of the talk: "Regulation of ecosystem productivity".

2. National Conference on "Time Series, Analytics And Recent Advances In Statistical Modelling" organized by the Dept. of Statistics, Central University of Rajasthan, 24-25 August 2015.Title of the talk: "Chaos far away from the edge of chaos: A recurrence quantification analysis of plankton time series".

3. National Conference on Recent advances in statistics and their applications in finance, actuarial sciences and other areas (RASAFAS) organized by Central University of Rajasthan on 14-15 Feb. 2014. Title of the talk: "On the 3/4 exponent von Bertalanffy equation for ontogenetic growth".

4. National conference on Omics for Biotechnology (NCOB – 2012), Central University of Rajasthan, Feb. 22-23, 2012. Title of the paper: Integrating Metagenomics and Modeling Approaches.

5. National Seminar on recent developments in Pure Mathematics (NSRDPM-2005), March 29- 30, 2005, Department of Pure Mathematics, University Of Calcutta, Kolkata – 19. Title of the talk: Spatiotemporal Variation of Soil emitting Methane.

6. National symposium on Mathematical Methods and Applications, Dec. 21, 2002, Indian Institute of Technology, Madras. Tile of the talk: A spatio-temporal mathematical model on methane emission.

7. Conference on Current trends in Mathematics, Nov. 9-10, 2002, Dept. of Mathematics, University of Allahabad, India. Title of the talk: Spatiotemporal Model on Methane emission.

e. Books/Chapters in books

Reference Books published by International Publisher

1. Mathematical modeling and analysis of methane production and oxidation by Amit Chakraborty (ISBN: 978-3-659-83070-9), LAP LAMBERT academic publishing, Saarbrucken, Germany, 2016.

2. Modeling plant community ecological interactions in variable environment by Amit Chakraborty (ISBN: 978-3-659-90100-3), LAP LAMBERT academic publishing, Saarbrucken, Germany, 2016.

Subject Books State / Central Govt. Publications

1. Action Plan For Banni Grassland Development Using Remotely Sensed Data And GIS Techniques. Space Applications Centre, Indian Space Research Organization (ISRO), Dept. of Space, Govt. of India. Document number: SAC/RESA/FLPG/FED/SN/07/2000.

2. A Combined Markov And Cellular Automata (MCA) Approach to Study Interplant Community Competition And Dynamics. Space Applications Centre, Indian Space Research Organization (ISRO), Dept. of Space, Govt. of India. Document number: SAC/RESA/FLPG/FED/SN/08/2000.

Book Chapter

Lamba S, Bera S, Rashid M, Chakraborty A. 2016.Species interactions in variable environment: competition, facilitation, and functional niches. In: Sharma D, and Sharma KC ed. Climate change and environment. New India Publishing Agency, New Delhi, pp. 87-110.

Book Review

Sun GQ, Li XZ, Wang Y, Chakraborty A*, Wang Z, Wu YP (2016) Impacts of Climate change on biological dynamics. Discrete Dynamics in nature and Society (Editorial Article). https://dx.doi.org/10.1155/2016/9046107 (* guest editor)

Chakraborty A, Li BL (2007). Individual based modeling and ecology by V. Grimm, S.F. Railsback, Princeton University Press, NJ. Ecological Complexity 4, 71.

Chakraborty A, Li BL (2010). Spatiotemporal patterns in ecology and epidemiology: Theory, models, and simulation by H. Malchow, SV Petrovskii and E Venturino. Series: Chapman & Hall/CRC Mathematical & Computational Biology, UK. Ecological Complexity 7, 506-507.

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