N. Sukumar | Department of Chemistry

Profile

N.
Sukumar
Professor
Department of Chemistry
Center for Informatics
School of Natural Sciences (SoNS)
C-121G
Block-C, Shiv Nadar University
Dadri Uttar Pradesh
India
Extn: 
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Profile Summary 

My research uses computational and cheminformatic methods for the design of drug-like molecules, polymers and nanomaterials with specific chemical and biological properties, and the development of cheminformatics software and network measures for moleclar design. Current research interests include analysis of chemical space networks and application of machine learning in chemistry. I have also worked on the development of novel molecular descriptors and robust property modeling methods for the prediction and interpretation of protein-ligand binding and protein similarity classification.

Experience in quantum chemistry, QSAR, in silico drug design, software development, statistical modeling, machine learning, web design, teaching at all levels; science administration, conference organization, scientific & photographic editorial experience. Editor of a book on Electron Density and co-uthor of several book chapters and research articles in physics, chemistry, biology & philosophy journals and popular science magazines; presented research papers & invited lectures at national & international scientific & photography conferences.

Educational Qualifications 
1984
Ph.D. Chemistry
State University of New York, Stony Brook
1979
M.Sc. Chemistry
Indian Institute of Technology, Kanpur
1976
B.Sc. (Hons. Chemistry)
St. Xavier’s College, University of Calcutta
Work Experience 
01/06
12/11
Research Associate Professor
Rensselaer Polytechnic Institute
Troy, NY
11/09
01/10
Visiting Scientist
Institute of Mathematical Sciences
Chennai
01/03
01/03
Visiting Scientist
Bioinformatics group, Wadsworth Center
Albany, NY
08/93
07/97
Alexander von Humboldt Fellow
University of Bonn
Bonn, Germany
09/92
07/93
Pool Officer
Indian Institute of Technology, Madras
Chennai
03/90
03/91
Visiting Fellow
Panjab University, Chandigarh
Chandigarh
11/85
11/87
Research Associate
University of New Orleans
New Orleans
11/84
11/85
Research Associate
University of Southern California
Los Angeles
03/91
12/97
Proprietor
Theorie International
Madras
Teaching & Research Interests: 

My research uses computational and cheminformatic methods for the discovery of molecules and materials with specific chemical and biological properties, and the development of cheminformatics software. Current research interests include analysis of chemical space networks and application of machine learning in chemistry. I have worked on the development of novel molecular descriptors and robust property modeling methods for the prediction and interpretation of protein-ligand binding and protein similarity classification.

ORCID: 0000-0002-2724-9944

RESEARCH STUDENTS GUIDED

  • Ganesh Prabhu, Department of Chemistry, Shiv Nadar University, 2012-2017. Ph.D. thesis entitled “Diversity Oriented Synthesis of a Molecular Library, Analysis of Molecular Diversity through Network/Graph Measures and Correlation with Biological Activity Profile(s)” June 2017
  • Pinaki Saha, Department of Chemistry, Shiv Nadar University, 2013-2018. Ph.D. thesis entitled "Application of electron density-based analysis in the study of nanoclusters and biomolecular interactions" Jan.2018.
  • Rudra Agarwal, Department of Chemistry, Shiv Nadar University, undergraduate thesis entitled "ab initio calculation and design of novel structures, May 2018.

Currently active research programs include:
1. Drug, polymer and nanomaterials design through QSAR/QSPR modeling, deep learning and statistical learning algorithms;
2. Protein and DNA bioinformatics using structure-based methods and molecular descriptors;
3. Chemical and biological networks: We are developing novel ways of looking at chemical space, using graph and network properties for the study and design of molecular libraries.
4. Computational Nanoscience and the Materials Genome Initiative: Discerning and exploiting patterns in chemical data lies at the heart of any systematic program for materials design: mining this growing mass of experimental data using the tools of ab initio quantum chemistry, statistical learning and pattern recognition to discover complex quantitative relationships between chemical structure and the properties of clusters, nanoalloys and nanomaterials, complementing first-principles computations.

Awards(Selected): 
19931997

Alexander von Humboldt Foundation Fellow

2005

Betty Barker Award, Schenectady Photographic Society, Schenectady, NY

2016

Associate of the Photographic Society of America

Scholarly Activity

Conference/Symposium

2018

N. Sukumar, Pinaki Saha, Amol B. Rahane, Rudra Agarwal and Vijay Kumar, What does electron density analysis tell us about bonding in transition metal-doped boron and carbon clusters? Sagamore XIX Conference on Quantum Crystallography, Halifax, Canada, July 11, 2018

2017

Pinaki Saha, Amol B. Rahane, Vijay Kumar and N. Sukumar, M@B14: A journey of a doped boron cluster from nanodrum to nanotube, Symposium on “Emerging Materials” Shiv Nadar University, 12 August 2017

2017

Ganesh Prabhu, Vivek Ananth R.P., Jayaraman Valadi, Michael P.Krein, N. Sukumar, Descriptor Selection for QSAR Modelling using Network Measures, Int. Conf, Drug Design, April 7-9th, 2017

2017

Pinaki Saha, Amol B. Rahane, Vijay Kumar, and N. Sukumar, Double ring tubular structures of boron clusters stabilized by metal atom doping: M@B14 (M = Cr, Fe, and Ni), 253rd Nat. Meet. Amer. Chem. Soc., San Francisco, CA, April 2-6, 2017

2015

Ganesh Prabhu, Subhabrata Sen, Sudeepto Bhattacharya, Michael P.Krein, N. Sukumar, Quantifying the diversity of chemical libraries through network modeling, 250th Nat. Meet. Amer. Chem. Soc., Boston, MA, August 16–20, 2015

2015

N. Sukumar, Pinaki Saha, Vijay Kumar, Amol B. Rahane, Analysis of the electron density features of boron clusters and effects of doping, SAGAMORE XVIII Conference on Charge, Spin and Momentum Densities, Santa Margherita di Pula, Sardinia, Italy, June 7-12, 2015

2015

N. Sukumar, P. Saha, V. Kumar, A. Rahane, K. Wu, C. M. Breneman, Informatics modeling used to leverage first-principles computation for accelerated materials discovery, Korean Physical Society, April 22, 2015

2015

N. Sukumar, K. Wu, P. Saha, C. M. Breneman, G. Pilania, C. C. Wang, G. Sotzing, R. Ramprasad, B. L. Chittari and V. Kumar, Materials informatics modeling for the design of advanced materials, 9th International Conference on Computational Physics (ICCP9), Singapore, January 7 – 11, 2015

2014

N. Sukumar, Michael Krein, Ganesh Prabhu, Sudeepto Bhattacharya, Subhabrata Sen, and V. K. Jayaraman, “Chemical Library Design using Graphical and Network measures” - International Humboldt Kolleg on Bench to bedside translational research: Potential benefits of interdisciplinary collaboration, Manipal, India, Nov.15-17, 2013

2013

N. Sukumar, Michael Krein, Ganesh Prabhu, Sudeepto Bhattacharya, Subhabrata Sen, and V. K. Jayaraman, “Chemical Library Design using Graphical and Network measures” - International Humboldt Kolleg on Bench to bedside translational research: Potential benefits of interdisciplinary collaboration, Manipal, India, Nov.15-17, 2013

2013

Swapnil Shukla, Kalpesh Shelke, Shameek Ghosh, Bimlesh Lochab, N. Sukumar, V. K. Jayaraman, “Modeling the Curing Characteristics of Monomers” First National Conference on Mapping the “Materials Genome”, Shiv Nadar University, India, March 8-10, 2013

Journal Publications (accepted or published)

2017

Suman Kumar Mandal, Pinaki Saha, Parthapratim Munshi, N. Sukumar, Exploring Potent Ligand for Proteins: Insights from Knowledge-based Scoring Functions and Molecular Interaction Energies, Struct. Chem. 28(5), 1537-1552 (2017). DOI: 10.1007/s11224-017-1007-y

2017

Abdur Rahim, Pinaki Saha, Kunal Kumar, N. Sukumar, Bani Kanta Sarma, Reciprocal carbonyl–carbonyl interactions in small molecules and proteins, Nature Comm. 8, 78 (2017). DOI: 10.1038/s41467-017-00081-x

2017

Pinaki Saha, Amol B. Rahane, Vijay Kumar, and N. Sukumar, Electronic Origin of the Stability of Transition Metal Doped B14 Drum Shaped Boron Clusters and Their Assembly in to a Nanotube. J. Phys. Chem. C, 121(20), 10728–10742 (2017). DOI: 10.1021/acs.jpcc.6b10838

2016

Ke Wu, N. Sukumar, Nicholas A. Lanzillo, Chenchen Wang, Ramamurthy “Rampi” Ramprasad, Rui Ma, Aaron F. Baldwin, Greg Sotzing, Curt Breneman, Prediction of polymer properties using Infinite Chain Descriptors (ICD) and Machine Learning: Towards optimized dielectric polymeric materials, J. Polymer Sci. B: Polymer Phys. 54, 2082–2091 (2016). DOI: 10.1002/polb.24117

2016

Ganesh Prabhu, Sudeepto Bhattacharya, Michael P.Krein, N. Sukumar, Investigation of similarity and diversity threshold networks generated from diversity-oriented and focused chemical libraries, J. Math. Chem. 54(10), 1916-1941 (2016). DOI: 10.1007/s10910-016-0657-0

2016

Pinaki Saha, Amol B. Rahane, Vijay Kumar, N. Sukumar, Analysis of the electron density features of small boron ring clusters and the effects of doping, Physica Scripta 91, 053005 (2016). DOI: 10.1088/0031-8949/91/5/053005

2014

N. Sukumar, M. P. Krein, G. Prabhu, S. Bhattacharya, S. Sen, Network Measures for Chemical Library Design, Drug Development Research 75, 402–411 (2014)

2013

G. Pilania, C. Wang, K. Wu, N. Sukumar, C. M. Breneman, G. A. Sotzing, R. Ramprasad, "New Group IV Chemical Motifs for Improved Dielectric Permittivity of Polyethylene" J. Chem. Inf. Model. 53(4):879–886 (2013) DOI: 10.1021/ci400033h

Books & Book Chapters

2014

N. Sukumar, Ganesh Prabhu and Pinaki Saha, Applications of Genetic Algorithms in QSAR/QSPR modeling, Applications of Metaheuristics in Process Engineering, Eds: Jayaraman Valadi, Patrick Siarry (Springer, 2014) pp.315-324.

2012

N. Sukumar, Ed. “A Matter of Density: Exploring the Electron Density Concept in Chemical, Biological, and Materials Sciences” (John Wiley, Hoboken, NJ, 2012). ISBN: 978-0-470-76900-3

2012

N. Sukumar, Sourav Das, Michael Krein, Curt M. Breneman, Qiong Luo, Rahul Godawat, Shekhar Garde, Inna Vitol and Kristin P. Bennett, “Molecular Descriptors for Biological Systems” in “Computational Approaches in Cheminformatics and Bioinformatics” Rajarshi Guha and Andreas Bender, Eds. (John Wiley, Hoboken, NJ, 2012), pp.107-144.

2012

N. Sukumar, Michael P. Krein and Mark J. Embrechts, "Predictive Cheminformatics in Drug Discovery: Statistical Modeling for Analysis of Micro-Array and Gene Expression Data" in "Biocomputing and Drug Discovery" Richard S. Larson, Ed. (Humana Press, London, 2012).