Xiao Zhu

Profile Photo

Senior Research Scientist

YONG 932
(765) 49-60232
zhu472@purdue.edu

Dr. Xiao Zhu is a Senior Research Scientist at Research Computing with responsibility for advanced support, scientific applications, and faculty partnerships. He holds a joint position in the Department of Chemistry. Dr. Zhu has been collaborating with Purdue research groups and the XSEDE community on various projects. His current research focuses on algorithm development, implementation and performance optimization involved in molecular dynamics calculations on modern HPC architectures. He also has extensive experiences in high-performance computing applications, profiling and benchmark, optimization and parallel computing.

Before moving to Purdue in 2014, Dr. Zhu was a staff member at the Texas Advanced Computing Center. He obtained his Ph.D. in Chemistry from University of Wisconsin-Madison in 2010. From 2011 to 2012, he was a postdoctoral fellow at Northwestern University.

Education

  • B.E, Polymer Materials and Engineering, University of Science and Technology of China (2003)
  • Ph.D, Computational Chemistry, University of Wisconsin-Madison (2010)
  • MBA, Purdue University (2017)

Grants and Awards

  • Category I: Anvil - A National Composable Advanced Computational Resource for the Future of Science and Engineering (NSF, Co-PI, 10/2020 - )
  • CICI: CE: Enhancing Cybersecurity for Broadening Data-Driven Research and Partnerships (NSF, Co-PI, $841,506, 9/2017 - 9/2020)

Engagement

  • Program Committee, Student Cluster Competition at the International Conference for High Performance Computing, Networking, Storage and Analysis (2016, 2017, 2018)
  • Program Committee, Reproducibility Challenge at the International Conference for High Performance Computing, Networking, Storage and Analysis (2019, 2020)
  • Technical Program Committee, Practice and Experience in Advanced Research Computing Conference (2018, 2019, 2020)
  • Technical Paper Chair of Practice and Experience in Advanced Research Computing Conference (2018)
  • XSEDE Campus Champion, 2014 -
  • Associate Editor, Journal of Molecular Modeling, 2020 -

Selected Publications

  • Stephen Lien Harrell, Betsy Hillery, and Xiao Zhu. “Introducing Novices to Scientific Parallel Computing”, J. Comput. Sci. Educ., 11(1), 88-92, 2020.
  • Preston Smith, Stephen Lien Harrell, Alex Younts, and Xiao Zhu. ”Community Clusters or the Cloud: Continuing cost assessment of on-premises and cloud HPC in Higher Education.” In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning), p. 97. ACM, 2019.
  • Abhinav Thota, Le Mai Weakley, Ben Fulton, H. E. Dennis, Laura Huber, Scott Michael, Winona Snapp-Childs, Stephen Lien Harrell, Alexander Younts, Daniel T. Dietz, Christopher Phillips, and Xiao Zhu ”Research Computing Desktops: Demystifying research computing for non-Linux users.” In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning), p. 54. ACM, 2019.
  • Shivam Trivedi, Lauren Featherstun, Nathan DeMien, Callum Gunlach, Sagar Narayan, Jacob Sharp, Brian Werts, Lipu Wu, Carolyn Ellis, Lev Gorenstein, Erik Gough, Alex Younts, and Xiao Zhu. ”PULSAR: Deploying Network Monitoring and Intrusion Detection for the Science DMZ.” In Proceedings of the Practice and Experience in Advanced Research Computing on Rise of the Machines (learning), p. 53. ACM, 2019.
  • Jaya Krishna Koneru, Xiao Zhu, and Jagannath Mondal. “A Quantitative Assessment of the Conformational Heterogeneity in Amylose across Force Fields”, J. Chem. Theory Comput., 15(11), 6203-6212, 2019.
  • Jonathan C. Overton, Xiao Zhu, and Nathan S. Mosier. “Molecular Dynamics Simulations and Experimental Verification to Determine Mechanism of Cosolvents on Increased 5-Hydroxymethylfurfural Yield from Glucose”, ACS Sustain. Chem. Eng., 7(15), 12997-13003, 2019.
  • Lilin Cheng, Xiao Zhu, Bruce Hamaker, Hui Zhang, and Osvaldo Campanella. “Complexation process of amylose under different concentrations of linoleic acid using a molecular dynamics simulation method.” Carbohydr. Polym., 216, 157-166, 2019.
  • Stephen Lien Harrell, Marisa Brazil, Alex Younts, Daniel T. Dietz, Preston M. Smith, Erik Gough, Xiao Zhu, and Gladys K. Andino. ”Mentoring Undergraduates into Cyber-Facilitator Roles.” In Proceedings of the Practice and Experience on Advanced Research Computing, p. 70. ACM, 2018
  • Jennifer R. Baker, Jayne Gilbert, Stefan Paula, Xiao Zhu, Jennette A. Sakoff and Adam McCluskey. “Dichlorophenylacrylonitriles as AhR Ligands displaying selective breast cancer cytotoxicity in vitro.” ChemMedChem, 13(14), 1447-1458, 2018.
  • Lilin Cheng, Tao Feng, Boyu Zhang, Xiao Zhu, Bruce Hamaker, Hui Zhang, and Osvaldo Campanella. “A molecular dynamics simulation study on the conformational stability of amylose-linoleic acid complex in water.” Carbohydr. Polym., 196, 56-65, 2018.
  • Meng-Ke Zhang, Yuan Lyu, Xiao Zhu, Jin-Peng Wang, Zheng-Yu Jin, and Ganesan Narsimhan. “Enhanced solubility and antimicrobial activity of alamethicin in aqueous solution by complexation with gamma-cyclodextrin.” J. Funct. Foods, 40, 700-706, 2018.
  • Ning Xiang, Yuan Lyu, Xiao Zhu, and Ganesan Narsimhan.“Investigation of the interaction of amyloid beta peptide (11-42) oligomers with a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane using molecular dynamics simulation.” Phys. Chem. Chem. Phys., 20, 6817-6829, 2018.
  • Yuan Lyu, Ning Xiang, Xiao Zhu, and Ganesan Narsimhan. “Potential of mean force for insertion of antimicrobial peptide melittin into a pore in mixed DOPC/DOPG lipid bilayer by molecular dynamics simulation.” J. Chem. Phys., 146(15), 155101, 2017.
  • Di Zhang, Karl N. Blodgett, Xiao Zhu, and Timothy S. Zwier. ”Single Conformation Spectroscopy of Suberoylanilide Hydroxamic Acid: A Molecule Bites Its Tail.” J. Phys. Chem. A, 121(5), 986-997, 2017.
  • Michael E., Baldwin, Xiao Zhu, Preston M. Smith, Stephen L. Harrell, Robert Skeel, and Amiya Maji. “Scholar: A campus hpc resource to enable computational literacy.” In Education for High-Performance Computing (EduHPC), 2016 Workshop, 25-31. IEEE, 2016
  • Feng, Tao, Xiao Zhu, and Osvaldo Campanella. “Molecular modeling tools to characterize the structure and complexation behavior of carbohydrates.” Curr. Opin. Food Sci., 9, 62-69, 2016.
  • Albino Bacolla, Xiao Zhu, Hanning Chen, Katy Howells, David N. Cooper, and Karen M. Vasquez, “Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes”, Nucleic Acids Res., 43(10), 5065-5080, 2015.
  • Na Zhang, Peng Zhang, Li Zhang, Xiao Zhu, Lei Huang, and Yuefan Deng. “Performance examinations of multiple time-stepping algorithms on stampede supercomputer.” In Proceedings of the 2015 XSEDE Conference: Scientific Advancements Enabled by Enhanced Cyberinfrastructure, 8. ACM, 2015
  • Xiao Zhu, Yang Yang, Haibo Yu, “In Silico Enzyme Modelling”, Australian Biochemist, 45(2), 12-15, 2014.
  • Ulyana S. Cubeta, Edward Ko, Xiao Zhu and Hanning Chen, “Molecular Modeling of Singlet Fission in Dye Sensitized Solar Cells”, XSEDE 13, San Diego, CA, July 2013.
  • Ke Zhang, Xiao Zhu, Fei Jia, Evelyn Auyeung and Chad A. Mirkin, “Temperature-Activated Nucleic Acid Nanostructures”, The Journal of American Chemical Society, 135(38), 14102-14105, 2013.
  • Hanning Chen and Xiao Zhu, “Electrostatic Screening Effects on a Model System for Molecular Electronics”, XSEDE 12, Chicago, IL, July 2012.
  • Guanhua Hou, Xiao Zhu, Marcus Elstner and Qiang Cui, “A Modified QM/MM Hamiltonian with the Self-Consistent Charge Density-Functional-Tight-Binding Theory for Highly Charged QM Regions”, Journal of Chemical Theory and Computation, 8(11), 4293-4304, 2012.
  • Xiao Zhu and George C. Schatz, “Molecular Dynamics Study of the Role of the Spine of Hydration in DNA A-Tracts in Determining Nucleosome Occupancy”, Journal of Physical Chemistry B, 116(46), 13672-13681, 2012.
  • Tatiana Prytkova, Xiao Zhu, Jonathan Widom and George C. Schatz, “Modeling DNA-Bending in the Nucleosome: Role of AA Periodicity”, Journal of Physical Chemistry B, 115(26), 8638-8644, 2011.