R&D Computational Scientist
Scientific Computing Group
National Center for Computational Sciences
Oak Ridge National Laboratory
Oak Ridge, TN 37831, USA
Office: Rm E303, Building 5600 Phone: 8655769919
Email:


Education
Research Interests
My research interests cover a broad range of areas in condensed matter physics, numerical methods and computer science. Emphasis is placed on the understanding of general physical behavior of coarsegrained polymer or protein models within the context of statistical mechanics: classical Monte Carlo methods, including advanced algorithms such as WangLandau sampling and multicanonical sampling, for performing computer simulations and ground state searches; canonical and microcanonical analyses for the study of thermodynamics and structural transition processes.
Other research interests and "handson" experience include: (physics:) protein simulations at the atomic level, physical properties of classical or quantum spin models, quantum entanglement, quantum information, numerical weather forecast; (computation:) molecular dynamics, algorithm design and optimization, numerical calculation techniques, high performance computing and machine learning.
Publications
30. Confinement effect on structural phases and transitions of an HP lattice protein B. Pattanasiri, Y. W. Li, T. Wüst and D. P. Landau Physical Review E, submitted.
29. A practical guide to replicaexchange WangLandau simulations T. Vogel, Y. W. Li and D. P. Landau J. Phys.: Conf. Ser., submitted.
28. Influence of substrate pattern on the adsorption of HP lattice proteins M. S. Wilson, G. Shi, T. Wüst, Y. W. Li and D. P. Landau Mol. Simulat., submitted.
T. McDaniel, E. D'Avezedo, Y. W. Li, P. R. C. Kent and K. Wong J. Chem. Phys. 147, 174107 (2017)
Y. W. Li and M. Eisenbach in Proceedings of the Platform for Advanced Scientific Computing Conference (PASC '17). Association for Computing Machinery (ACM), New York, NY, USA, Article 10, 7 pages (2017)
S. Yuk, K. Pitike, S. Nakhmanson, M. Eisenbach, Y. W. Li and V. Cooper Scientific Reports 7, 43482 (2017)
T. McDaniel, E. D'Avezedo, Y. W. Li, P. Kent, M. Wong and K. Wong Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale, Association for Computing Machinery (ACM), New York, NY, USA, 13:113:4 (2016)
M. G. Lopez, C. Bergstrom, Y. W. Li, W. Elwasif and O. Hernandez in "High Performance Computing", M. Taufer, B. Mohr, J. Kunkel (Eds.), ISC High Performance 2016. Lecture Notes in Computer Science, vol 9945, Springer, pp. 563576 (2016)
A. Valentim, J. C. S. Rocha, S.H. Tsai, Y. W. Li, M. Eisenbach, C. E. Fiore and D. P. Landau
J. Phys.: Conf. Ser. 640, 012006 (2015)
B. Pattanasiri, Y. W. Li, T. Wüst and D. P. Landau
J. Phys.: Conf. Ser. 640, 012015 (2015)
G. Shi, T. Wüst, Y. W. Li and D. P. Landau
J. Phys.: Conf. Ser. 640, 012017 (2015)
D. Perera, Y. W. Li, M. Eisenbach, T. Vogel and D. P. Landau
TMS2015 Supplemental Proceedings, John Wiley & Sons, Inc., Hoboken, NJ, USA, P. 811818 (2015)
G. Shi, T. Vogel, T. Wüst, Y. W. Li and D. P. Landau
Phys. Rev. E. 90, 033307 (2014)
T. Vogel, Y. W. Li, T. Wüst and D. P. Landau
Phys. Rev. E. 90, 023302 (2014)
Y. Zhao, S. W. Cheung, Y. W. Li and M. Eisenbach
Physics Procedia 57C, 4347 (2014)
Y. W. Li, T. Vogel, T. Wüst and D. P. Landau
J. Phys.: Conf. Ser. 510, 012012 (2014)
T. Vogel, Y. W. Li, T. Wüst and D. P. Landau
J. Phys.: Conf. Ser. 487, 012001 (2014)
Y. W. Li, T. Wüst and D. P. Landau
Mol. Simulat. 40, 640655 (2014)
B. Pattanasiri, Y. W. Li, D. P. Landau, T. Wüst and W. Triampo
J. Phys.: Conf. Ser. 454, 012071 (2013)
T. Vogel, Y. W. Li, T. Wüst and D. P. Landau
Phys. Rev. Lett. 110, 210603 (2013)
10. Generic folding and transition hierarchies for surface adsorption of HP lattice model proteins
Y. W. Li, T. Wüst and D. P. Landau
Phys. Rev. E 87, 012706 (2013)
9. Conformational transitions of a confined lattice protein: A WangLandau study
B. Pattanasiri, Y. W. Li, D. P. Landau, T. Wüst and W. Triampo
J. Phys.: Conf. Ser. 402, 012048 (2012)
8. Surface adsorption of lattice HP proteins: thermodynamics and structural transitions using WangLandau sampling
Y. W. Li, T. Wüst and D. P. Landau
J. Phys.: Conf. Ser. 402, 012046 (2012)
7. WangLandau simulations of adsorbed and confined lattice proteins
B. Pattanasiri, Y. W. Li, D. P. Landau and T. Wüst
Int. J. Mod. Phys. C 23, 1240008 (2012)
6. Stable stem enabled Shannon entropies distinguish noncoding RNAs from random backgrounds
Y. Wang, A. Manzour, P. Shareghi, T. I. Shaw, Y. W. Li, R. L. Malmberg and L. Cai
BMC Bioinformatics 13 (Suppl 5), S1 (2012)
5. Unraveling the beautiful complexity of simple lattice model polymers and proteins using WangLandau sampling
T. Wüst, Y. W. Li and D. P. Landau
J. Stat. Phys. 144, 638651 (2011)
4. Stable stem enabled Shannon entropies distinguish noncoding RNAs from random backgrounds
Y. Wang, A. Manzour, P. Shareghi, T. I. Shaw, Y. W. Li, R. L. Malmberg and L. Cai
The Proceedings of 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 184189 (2011)
3. Monte Carlo simulations of the HP model (the "Ising model" of protein folding)
Y. W. Li, T. Wüst and D. P. Landau
Comput. Phys. Commun. 182, 18961899 (2011)
2. Numerical integration using WangLandau sampling
Y. W. Li, T. Wüst, D. P. Landau and H. Q. Lin
Comput. Phys. Commun. 177, 524 (2007)
1. Fidelity, dynamic structure factor, and susceptibility in critical phenomena
W. L. You, Y. W. Li and S. J. Gu
Phys. Rev. E 76, 022101 (2007)
Book Chapters
Development of QMCPACK for Exascale Scientific Computing A. Benali, D. M. Ceperley, E. D’Azevedo, M. Dewing,
P. R. C. Kent, J. Kim, J. T. Krogel, Y.
W. Li, Y. Luo, T. McDaniel, M. A. Morales, A. Mathuria, L. Shulenburger and N. M. Tubman
in "Exascale Scientific Applications: Programming Approaches for Scalability, Performance, and Prortability", CRC / Taylor and Francis, Chapter 21, pp. 461480 (2017)
Biologically inspired surface physics: The HP protein model
Y. W. Li, T. Wüst and D. P. Landau
in "Nanophenomena at Surfaces: Fundamentals of Exotic Condensed Matter Properties", M. Michailov (Ed.), Springer Series in Surface Sciences, vol. 47, SpringerVerlag, Berlin, Heidelberg, Chapter 7, pp.169183 (2011)
Presentations
National / International Conferences:
Invited Talks
Scalable and efficient multicanonical algorithms for firstprinciples based Monte Carlo simulations IPAM Workshop on Optimization and Optimal Control
for Complex Energy and Property Landscapes, University of California Los Angeles, Los Angeles, CA, U.S.A.
Recent advances in accelerated Monte Carlo algorithms IX Brazilian Meeting on Simulational Physics, Natal, Brazil
Scalable and efficient firstprinciples based Monte Carlo simulations on
high performance computers [Keynote Talk in Computational Statistical Mechanics Session]XXIX IUPAP Conference on Computational Physics (CCP2017), Paris, France July 2017
First principles based statistical mechanics on high performance computers
Center for Simulational Physics 28th Annual Workshop, University of Georgia, Athens, GA, U.S.A.
February 2015
Oral Presentations
A histogramfree multicanonical Monte Carlo algorithm for the basis expansion of density of states
Platform for Advanced Scientific Computing (PASC17), Lugano, Switzerland June 2017
OWL: A scalable Monte Carlo simulation suite for finitetemperature study of materials American Physical Society March Meeting, New Orleans, LA, U.S.A. March 2017
Efficient, histogramfree WangLandau sampling for the construction of analytical density of states Center for Simulational Physics 30th Annual Workshop, University of Georgia, Athens, GA, U.S.A. February 2017
"Binless WangLandau sampling"  a multicanonical algorithm with histograms Center for Simulational Physics 29th Annual Workshop, University of Georgia, Athens, GA, U.S.A. February 2016
Density
functional theory based statistical mechanics for finite temperature magnetism
Workshop on Stochastic Methods in Electronic Structure Theory, Telluride Science Research Center, Telluride, CO, U.S.A. June 2015
Replicaexchange WangLandau sampling for the study of spin systems
American Physical Society March Meeting, Denver, CO, U.S.A.
March 2014
Performance analysis for replicaexchange WangLandau sampling
Center for Simulational Physics 27th Annual Workshop, University of Georgia, Athens, GA, U.S.A.
February 2014
Scalability and performance analysis for replicaexchange WangLandau sampling
SIAM Conference on Parallel Processing and Scientific Computing, Portland, OR, U.S.A.
February 2014
Generic parallel WangLandau sampling for complex systems
American Physical Society March Meeting, Baltimore, MD, U.S.A.
March 2013
Generic transition hierarchies of lattice HP protein adsorption: A WangLandau study
American Physical Society March Meeting, Boston, MA, U.S.A.
February  March 2012
Generic transition hierarchies of lattice HP protein adsorption: A WangLandau study
Center for Simulational Physics 25th Annual Workshop, University of Georgia, Athens, GA, U.S.A.
February 2012
Surface adsorption of lattice HP proteins: studies on thermodynamics and structural transitions using WangLandau sampling
Conference on Computational Physics (CCP 2011), Gatlinburg, TN, U.S.A.
October  November 2011
Thermodynamics and structural properties of surface adsorption of lattice proteins
American Physical Society March Meeting, Dallas, TX, U.S.A.
March 2011
Thermodynamics of lattice proteins interacting with an adsorbing surface
XXIV IUPAP International Conference on Statistical Physics (Statphys24), Cairns, QLD, Australia
July 2010
Numerical integration using WangLandau sampling
American Physical Society March Meeting, Denver, CO, U.S.A.
March 2007
Numerical integration using WangLandau sampling
Center for Simulational Physics 20th Annual Workshop, University of Georgia, Athens, GA, U.S.A.
February 2007
Poster Presentations
Enhancing scalability of Monte Carlo methods on high performance computers for materials science research  Current developments and future challenges
2015 Smoky Mountains Computational Sciences and Engineering Conference, Gatlinburg, TN, U.S.A.
September 2015
Density functional theory based statistical mechanics for finite temperature magnetism
Workshop on Stochastic Methods in Electronic Structure Theory, Telluride Science Research Center, Telluride, CO, U.S.A.
June 2015
Monte Carlo simulations of HP protein adsorption within confined space between two attractive surfaces
Center for Simulational Physics 24th Annual Workshop, University of Georgia, Athens, GA, U.S.A.
February 2011
WangLandau sampling of protein adsorption using HP model
Center for Simulational Physics 24th Annual Workshop, University of Georgia, Athens, GA, U.S.A.
February 2011
Seminars:
A mini course: replicaexchange WangLandau sampling [Tutorial lectures II and III] IX Brazilian Meeting on Simulational Physics, Natal, Brazil Computer simulations on high performance supercomputers Department colloquium, Department of Physics, Stetson University, DeLand, FL, U.S.A. October 2016
Recent developments in Monte Carlo simulations toward high performance parallel computing
Department colloquium, Department of Physics, Wake Forest University, WinstonSalem, NC, U.S.A.
November 2014
Generic structural transition hierarchies for protein adsorption: Insights from WangLandau simulation of the HP lattice proteins
Materials Theory Group meeting, Oak Ridge National Laboratory, Oak Ridge, TN, U.S.A.
September 2012
An experience sharing on effective research and time management for graduate students
Center for Simulational Physics seminar, University of Georgia, Athens, GA, U.S.A.
July 2012
Speeding up WangLandau simulation of lattice model proteins using GPUs (in "CUDA Research Fast Forward")
NVIDIA booth, International Conference for High Performance Computing, Networking, Storage and Analysis (SC11), Seattle, WA, U.S.A.
November 2011 [ slides; video (my presentation starts at 00:44)]
Thermodynamics and structural transformations of lattice HP proteins adsorption: A WangLandau study
Center for Simulational Physics seminar, University of Georgia, Athens, GA, U.S.A.
September 2011
Thermodynamics and structural properties of surface adsorption of lattice proteins
Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, U.S.A.
April 2011
A short tour of Python
Center for Simulational Physics seminar, University of Georgia, Athens, GA, U.S.A.
April 2010
First steps to GPU programming
Center for Simulational Physics seminar, University of Georgia, Athens, GA, U.S.A.
September 2009
Quantum entanglement in symmetric Anderson impurity model
Center for Simulational Physics seminar, University of Georgia, Athens, GA, U.S.A.
July 2008
Honors and Awards
A universitywide annual award given to two recent Ph.D.s for outstanding research at the University or immediately after graduating. It is presented by the Office of Vice President for Research and the University of Georgia Research Foundation, Inc. at the University of Georgia.
A universitywide annual award that recognizes the quality and significance of graduate student scholarship. It is given to a recent Ph.D. in each of the five areas by the Graduate School at the University of Georgia.
William Cummings Memorial Award  2012 
An annual award presented to a graduate student who best exemplifies excellence as a student and as a teacher of undergraduates by the Cummings family and Department of Physics and Astronomy at the University of Georgia.
Graduate School Dissertation Completion Award  2011  2012 
A competitive, universitywide annual fellowship presented to a final year Ph.D. student with excellent research and academic records by the Graduate School at the University of Georgia. AndersonPioletti Award  2009 
An annual award presented to an outstanding early graduate student who showed exceptional academic promise and good citizenship in the department. It is presented by the Anderson family and Department of Physics and Astronomy at the University of Georgia. Outstanding Teaching Assistant Award  2007 
Recognition of outstanding teaching assistants in the Department of Physics at the Chinese University of Hong Kong.
Training on Parallel Computing Techniques (selected)
ObjectOriented, Parallel and Functional Programming in Modern Fortran
Oak Ridge National Laboratory, Oak Ridge, TN, U.S.A.
February 2013
Scientific Computing in the Americas: the challenge of massive parallelism
PanAmerican Advanced Studies Institute (PASI), National Science Foundation, U.S.A.
Universidad Tecnica Federico Santa Maria (UTFSM), Valparaiso, Chile
January 2011
Proven Algorithmic Techniques for Manycore Processors
Virtual School of Computational Science and Engineering
Institute for Data and High Performance Computing, Georgia Institute of Technology, Atlanta, GA, U.S.A.
August 2010
ManyCore Processors for Science and Engineering Applications
Virtual School of Computational Science and Engineering
National Center for Supercomputing Applications (NCSA), University of Illinois, UrbanaChampaign, IL, U.S.A.
August 2009

