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Contact Information

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: 865-576-9919
Email:


View Ying Wai Li's profile on LinkedIn

Education



 2007 - 2012
Ph.D. in Physics, Center for Simulational Physics, University of Georgia, USA
Advisor: Prof. David P. Landau
Dissertation: Unraveling Universal Thermodynamic and Structural Behavior of HP Model Protein Adsorption: A Wang-Landau Study

 2005 - 2007
M.Phil. in Physics, Chinese University of Hong Kong, Hong Kong
Advisor: Prof. Hai-Qing Lin
Thesis: Numerical Studies on Quantum Phase Transitions of Anderson Models

 2002 - 2005
B.Sc. (major in Physics, minor in Mathematics), Chinese University of Hong Kong, Hong Kong
Advisor: Prof. Hai-Qing Lin
Thesis: Numerical Integration

Honors and Awards



 Robert C. Anderson Memorial Award 2013

A university-wide 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.

 Graduate Student Excellence-in-Research Awards    (Mathematics and Physical Sciences area) 2013

A university-wide 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, university-wide 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.

Anderson-Pioletti 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.


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 coarse-grained polymer or protein models within the context of statistical mechanics: classical Monte Carlo methods, including advanced algorithms such as Wang-Landau 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 "hands-on" 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



28.  Delayed Slater Determinant Update Algorithms for High Efficiency Quantum Monte Carlo
T. McDaniel, E. D'Avezedo, Y. W. Li, P. R. C. Kent and K. Wong
J. Chem. Phys., submitted.

27.  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
Physical Review E, submitted.

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, 13:1-13:4 (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. 563-576 (2016)


A. ValentimJ. C. S. Rocha, S.-H. Tsai, Y. W. LiM. 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 ProceedingsJohn Wiley & Sons, Inc., Hoboken, NJ, USA, P. 811-818 (2015)

18.  Effect of single-site mutations on HP lattice proteins             [selected as a PRE Editors' Suggestion]
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, 43-47 (2014)

Y. W. LiT. 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, 640-655 (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 Wang-Landau 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 Wang-Landau sampling
Y. W. Li, T. Wüst and D. P. Landau
J. Phys.: Conf. Ser. 402, 012046 (2012)

7.   Wang-Landau 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 non-coding 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 Wang-Landau sampling
T. Wüst, Y. W. Li and D. P. Landau
J. Stat. Phys. 144, 638-651 (2011)

4.   Stable stem enabled Shannon entropies distinguish non-coding 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), 184-189 (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, 1896-1899 (2011)

2.   Numerical integration using Wang-Landau 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", to be published by CRC / Taylor and Francis.

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, Springer-Verlag, Berlin, Heidelberg, Chapter 7, pp.169-183 (2011)

Presentations


National / International Conferences:

Invited Talks

Recent advances in accelerated Monte Carlo algorithms
           IX Brazilian Meeting on Simulational Physics, Natal, Brazil
August 2017

Scalable and efficient first-principles 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 histogram-free 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 finite-temperature study of materials
American Physical Society March Meeting, New Orleans, LA, U.S.A.
March 2017

Efficient, histogram-free Wang-Landau 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 Wang-Landau 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

Replica-exchange Wang-Landau sampling for the study of spin systems
American Physical Society March Meeting, Denver, CO, U.S.A.
March 2014

Performance analysis for replica-exchange Wang-Landau sampling

Center for Simulational Physics 27th Annual Workshop, University of Georgia, Athens, GA, U.S.A.

February 2014

Scalability and performance analysis for replica-exchange Wang-Landau sampling

SIAM Conference on Parallel Processing and Scientific Computing, Portland, OR, U.S.A.

February 2014

Generic parallel Wang-Landau 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 Wang-Landau study
American Physical Society March Meeting, Boston, MA, U.S.A.
February - March 2012

Generic transition hierarchies of lattice HP protein adsorption: A Wang-Landau 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 Wang-Landau 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 Wang-Landau sampling
American Physical Society March Meeting, Denver, CO, U.S.A.
March 2007

Numerical integration using Wang-Landau 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

Wang-Landau 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: replica-exchange Wang-Landau sampling        [Tutorial lectures II and III]
           IX Brazilian Meeting on Simulational Physics, Natal, Brazil
August 2017

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, Winston-Salem, NC, U.S.A.
November 2014

Generic structural transition hierarchies for protein adsorption: Insights from Wang-Landau 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 Wang-Landau 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 Wang-Landau 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

Training on Parallel Computing Techniques (selected)



Object-Oriented, 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

Pan-American Advanced Studies Institute (PASI), National Science Foundation, U.S.A.
Universidad Tecnica Federico Santa Maria (UTFSM), Valparaiso, Chile
January 2011

Proven Algorithmic Techniques for Many-core 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

Many-Core Processors for Science and Engineering Applications
Virtual School of Computational Science and Engineering
National Center for Supercomputing Applications (NCSA), University of Illinois, Urbana-Champaign, IL, U.S.A.
August 2009