1. Gupta, P. Zhang, J. Sheriff, D. Bluestein, and Y. Deng, A multiscale model of recruitment aggregation of platelets by correlating with in vitro results, Cellular and Molecular Bioengineering, Submitted (11/2018)
  2. D. Liang, H. Li, and Y. Deng, Mechanism of dynamic phase transition and synchronous stability in Hindmarsh–Rose neuronal network, Int. J. Mod. Phys. B; Vol. 32 No. 28 (2018). DOI: 10.1142/S0217979218503083
  3. Zhang, Z. Ye, and Y. Deng, Parallel MCMC method for optimization, Parallel Comp., (Submitted 4/2018)
  4. Ye, K. Xiao, and Y. Deng, A unified theory of the mobile sequential recommendation problem, Proceedings of the 2018 IEEE International Conference on Data Mining, IEEE ICDM 2018 (November 17-20, 2018 in Singapore)
  5. Yazdani A., Zhang P., Sheriff J., Slepian M.J., Deng Y., Bluestein D. (2018), Multiscale Modeling of Blood Flow-Mediated Platelet Thrombosis, In: Andreoni W., Yip S. (eds) Handbook of Materials Modeling. Springer Nature 2018. DOI: https://doi.org/10.1007/978-3-319-50257-1_69-1
  6. Cun, L. Pei, and Y. Deng, Analysis of parallel matrix multiplications, Math. Comp., (Submitted 8/2018)
  7. Ye, L. Zhang, K. Xiao, W. Zhou, Y. Ge, and Y. Deng, Multiuser Mobile Sequential Recommendations: An Efficient Parallel Computing Paradigm. Proceedings of ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD’18). ACM, New York, NY, USA, Article 4, 9 pages.
  8. Deng, M. Guo, A. Ramos, X. Huang, and W. Liu, Examining the performance dependence of computer clusters on networks topologies, IEEE Trans. Parallel and Distributed Systems, (Submitted 5/2018)
  9. Sabino, M. Vasconcelos, Y. Deng, A. Ramos, Symmetry-guided design of topologies for supercomputer networks, Int. J. Mod. Phys. C; Vol. 29 (2018) pp. 1- 17. DOI: https://doi.org/10.1142/S0129183118500481
  10. Gao, P. Zhang, G. Marom, Y. Deng, and D. Bluestein, Reducing the effects of compressibility in DPD-based blood flow simulations through severe a stenotic
    microchannel, Journal of Comp. Phys.; Vol. 35 (2017) pp. 812-827. DOI:
    http://dx.doi.org/10.1016/j.jcp.2017.01.062
  11. Zhang, L. Zhang, M. Slepian, and Y. Deng, and D. Bluestein, A multi-scale model of platelets: correlating with in-vitro results, Journal of Biomechanics; Vol.
    60 (2017) pp. 26-33. DOI: 10.1016/j.jbiomech.2016.11.019
  12. Deng and L. Zhang, Perspectives on Exascale-Era Computing, China Science and Technology Review, 2016, 34 (21): 85-94; DOI: 10.3981/j.issn.1000-7857.2016.21.012; http://www.kjdb.org/CN/Y2016/V34/I21/85
  13. Ye, K. Xiao, and Y. Deng, and Y. Ge, Applying simulated annealing and parallel computing to the mobile sequential recommendation, IEEE Transaction on Knowledge and Data Engineering (TKDE); (Accepted 3/28/2018)
  14. Ye, X. Fan, and Y. Deng, Adaptive cooling schedules for simulated annealing, Computational Optimization and Applications; (Submitted 2016)
  15. Ye, K. Xiao, and Y. Deng, Investigation of Simulated Annealing Cooling Schedule for Mobile Recommendations, The ICDM Workshop on Data Mining and Human Mobility Computing, November 2015 Atlantic City, NJ. Conference Paper; DOI:10.1109/ICDMW.2015.226
  16. Zhang, C. Cao, N. Zhang, M. J. Slepian, Y. Deng, D. Bluestein, A Predicative Multiscale Model for Simulating Platelets Activation in Shear Flows, 2015 BMES Annual Meeting, October 7-10, 2015. Tampa, FL. Conference Paper
  17. Michalewicz, L. Orlowski, and Y. Deng, Creating interconnect topologies by algorithmic edge removal: MOD and SMOD graphs, International Journal of Supercomputing Frontiers and Innovations, Vol. 2 No. 4 (2015) pp. 16-47. DOI: 10.14529/jsfi150302
  18. Zhang, N. Zhang, Y. Deng, and D. Bluestein, Scalability Test of Multiscale Fluid- Platelet Model for Three Top Supercomputers, Computer Physics Communications Vol. 204 (2016) pp. 132-140. DOI:10.1016/j.cpc.2016.03.019
  19. Zhang, K. Xiao, Q. Liu, Y. Tao, and Y. Deng, Modeling Social Attention for Stock Analysis: An Influence Propagation Perspective, The 15th IEEE International Conference on Data Mining, ICDM 2015, Atlantic City, NJ 2015 (Accepted 8/2015. Regular paper. Acceptance rate: 8.4%)
  20. Zhang, P., Sheriff, J., Soares, J.S., Gao, C., Pothapragada, S., Zhang, N., Deng, Y., Bluestein, D. Multiscale Modeling of Flow Induced Thrombogenicity Using Dissipative Particle Dynamics and Coarse Grained Molecular Dynamics. Proceedings of the ASME 2013 Summer Bioengineering Conference, Sunriver, Oregon, June 26-29, 2013. DOI: 10.1115/SBC2013-14187
  21. Bluestein, D., Soares, J.S., Zhang, P., Gao, C., Pothapragada, S., Zhang, N., Slepian, M.J., Deng, Y. Multiscale Modeling of Flow Induced Thrombogenicity with Dissipative Particle Dynamics (DPD) and Molecular Dynamics (MD). Proceedings of the ASME/FDA 2013 1st Annual Frontiers in Medical Devices: Applications of Computer Modeling and Simulation FMD 2013, Washington, D.C., September 11-13, 2013. DOI: 10.1115/FMD2013-16176
  22. Bluestein, D., Soares, J.S., Zhang, P., Gao, C., Pothapragada, S., Zhang, N., Slepian, M.J., Deng, Y. Multiscale Modeling of Flow Induced Thrombogenicity Using Dissipative Particle Dynamics and Molecular Dynamics. Proceedings of the ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology, Boston, Massachusetts, USA, February 4–6, 2013. DOI: 1115/NEMB2013-93094
  23. Pothapragada, J. Sheriff, M. L., D. Bluestein, and Y. Deng, A Quantitative Model for Shear Flow-Induced Platelet Morphological Changes and Corroboration with In Vitro Experiments, Journal of Mathematical Biology (Submitted 12/2014)
  24. Sedighi, Y. Deng, and P. Zhang, Fairness of task scheduling in high performance computing environments, Scalable Comp: Practice and Experience, Vol. 15 Num. 3 (2014) 273-288
  25. Zhang, C. Gao, N. Zhang, M. J. Slepian, Y. Deng, and D. Bluestein, Multiscale Particle-Based Modeling of Flowing Platelets in Blood Plasma Using Dissipative Particle Dynamics and Coarse Grained Molecular Dynamics, Cellular and Molecular Bioengineering, Vol. 7 No. 4 (2014) 552-574 DOI: 10.1007/s12195-014- 0356-5
  26. Zhang, N. Zhang, Y. Deng, and D. Bluestein, A Multiple Time Stepping Algorithm for Multiscale Modeling of Platelets Flowing in Blood Plasma, Journal of Computational Physics; Vol. 284 (2015) pp. 668-686; DOI: 10.1016/j.jcp.2015.01.004
  27. Zhang and Y. Deng, R. Feng, X. Luo and J. Wu, Evaluation of various networks configured by adding bypass or torus links, IEEE Trans. Parallel and Distributed Systems, Vol. 26, No. 4 (2015) pp. 984-995; DOI: 10.1109/TPDS.2014.2315201
  28. Pothapragada, P. Zhang, J. Sheriff, M. L., M. J. Slepian, Y. Deng, and D. Bluestein, A Phenomenological Particle-Based Platelet Model for Simulating Filopodia Formation during Early Activation, International Journal for Numerical Methods in Biomedical Engineering, Vol. 31, No. 3 pp 1-16 (2015); DOI: 10.1002/cnm.2702
  29. Zhang, L. Zhao, J. Xu, Y. Deng, W. Zhu, and S. Wu, PPSeq: A scalable parallel processing suite for sequence alignment, Bioinformatics, (Submitted on 9/2014)
  30. Zhang, L. Liu, and Y. Deng, A data-driven paradigm for mapping problems, Parallel Comp, Vol. 48 (2015) pp 108-124; DOI: 10.1016/j.parco.2015.05.002
  31. Zhang, P. Zhang, W. Kang, D. Bluestein, and Y. Deng, Parameterizing the Morse potential for coarse-grained modeling of blood plasma, Journal of Comp. Phys., Vol. 257 Part A (2014) pp. 726-736; DOI: 10.1016/j.jcp.2013.09.040
  32. Feng, P. Zhang and Y. Deng, Deadlock-free Routing Algorithms for 6D Mesh/iBT Interconnection Networks, SNPD 2013. 14th IEEE/ACIS International Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (2013); DOI: 10.1109/SNPD.2013.43
  33. Deng, C. Marques, R. Powell and P. Zhang, Analysis of power and Linpack efficiencies of the world’s Top 500 supercomputers, Parallel Comp. Vol. 39, Issues 6-7 (2013) pp. 271-279; DOI: 10.1016/j.parco.2013.04.007
  34. Feng, P. Zhang, J. Davenport, and Y. Deng, Network design considerations for Exascale supercomputers, International Conference on Parallel and Distributed Computing and Systems (Peer-reviewed and Accepted 9/6/2012)
  35. Deng, A. Ramos, and J. Hornos, Group theory insights for design of supercomputer network topologies, Int. J. Mod. Phys. B Vol. 26 No. 31 (2012) 1250169 (7 pp)
  36. Feng, P. Zhang and Y. Deng, Simulated Performance Evaluation of a 6D Mesh/iBT Interconnect, SNPD 2012. 13th ACIS International Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (2012) pp.253-259
  37. Zhang and Y. Deng, An Analysis of the Topological Properties of the Interlaced Bypass Torus (iBT) Networks, Applied Mathematics Letters, Vol. 25 Issue 12 (2012) 2147-2155
  38. Deng and P. Zhang, Perspectives on Exascale Computing, New Computing Architectures and Applications, Vol.1. pp 8-22 (9/2010)
  39. Zhang, Y. Gao, J. Fierson, and Y. Deng, An Eigenanalysis-based Task Mapping on Parallel Computers with Cellular Networks (PDF), Math. Comp. Vol. 83, no 289 (2014) pp. 1721-1756. DOI: http://dx.doi.org/10.1090/S0025-5718-2013-02770-6
  40. Zhang and Y. Deng, Design and Analysis of Pipelined Broadcast for the All-Port Interlaced Bypass Torus Networks, IEEE Trans. Parallel and Distributed Systems Vol. 23 Issue 12 (2012) pp. 2245-2253
  41. Zhang, R. Powell, and Y. Deng, Interlacing Bypass Rings to Torus Networks for Generating more Efficient Networks, IEEE Trans. Parallel and Distributed Systems Vol. 22 Issue 2 (2011) pp. 287-295
  42. Feng, M. Xenos, G. Girdhar, J. Davenport, Y. Deng, D. Bluestein, Viscous Flow Simulation in a Stenosis Model Using Discrete Particle Dynamics: A Comparison Between DPD and CFD, Biomechanics and Modeling in Mechanobiology Vol. 11 Issues 1-2 (2012) pp. 119-129
  43. Yamaguchi, T. Ishikawa, Y. Imai, N. Matsuki, M. Xenos, Y. Deng, D. Bluestein, Particle Based Methods for Multiscale Modeling of Blood Flow in the Circulation and in Devices– Challenges and Future Directions, Annals of Biomedical Eng. 2009; 38(3): 1225–1235
  44. Chen and Y. Deng, A Detailed analysis of communication load balance on BlueGene supercomputer, Comp. Phys. Comm., 180 (2009), pp 1251-1258
  45. Deng, A. Korobka, Z. Lou, and P. Zhang, Perspectives on Petascale Processing, KISTI Supercomputer, Vol. 31 (2008), pp. 36-59
  46. Chen and Y. Deng, Task mapping on supercomputers with cellular networks, Comp. Phys. Comm. 179 (2008), pp. 479-485
  47. Chen and Y. Deng, Simulations of a specific inhibitor of the disheveled PDZ domain, J. Mol. Modeling, Vol. 15 (2009), pp. 91-96
  48. Wang, H. Zhang, Y. Deng, and L. Ming, Efficient Parallel Radiosity for Terascale Applications, 2008 International Conference on Computer Science and Software Engineering, Wuhan, China, Dec 12-14 Vol. 2 (2008), pp. 1074-1077
  49. Oh and Y. Deng, A efficient parallel implementation of the smooth particle mesh Ewald method for molecular dynamics simulations, Comp. Phys. Comm. 177 (2007), pp. 426-431
  50. Fang, G. Martyna, and Y. Deng, A fine grained parallel smooth particle mesh Ewald algorithm for biophysical simulation studies: applications to the 6D torus supercomputer, Comp. Phys. Comm. 177 (2007), pp. 362-377
  51. Chen, X. Chen, and Y. Deng, Simulating Botulinum Neurotoxin with Constant pH Molecular Dynamics in Generalized Born Implicit Solvent, Comp. Phys. Comm. 177 (2007), pp. 210-213
  52. Fang and Y. Deng, and G. Martyna, Parallel FFT on QCDOC supercomputer, Comp. Phys. Comm. 176 (2007) 531-538
  53. Han, Y. Deng, J. Glimm, G. Martyna, Error and timing analysis of multiple Time Stepping for MD, Comp. Phys. Comm. 176 (2007), pp. 271-291
  54. Chen and Y. Deng, Botulinum structures at various temperatures and pH values, J. Mol. Modeling, 13 (5) (2007) 559-572
  55. Rissland and Y. Deng, Supercomputers and their effects on molecular dynamics, IEEE Potentials, April/May Issue, 9-12 (2005). Chinese Translation appeared in China Computer World Vol. 34 (May 2005)
  56. Xiang, A. Korobka, Y. Deng, Nankai Stars: an example of designing, constructing, evaluating, and applying a 5-Tflops Beowulf supercomputer (2004).
  57. Deng, J. Glimm, J. Davenport, X. Cai, and E. Santos, Performance Models on QCDOC for Molecular Dynamics with Coulomb Potentials, Int. J. High Performance Computing Applications. Vol. 18, Num. 2 (2004) 183-198
  58. Deng, J. Glimm, and J. Davenport, Global Communication Schemes on QCDOC, IEEE Transactions on Parallel and Distributed Computing.
  59. Li and Y. Deng: Biography of Prof Chen Ning Yang (in Chinese, Word format), Biographies of Contemporary Chinese Scientists, Vol. 3 (1994). English translation (in PDF) appears in “C. N. Yang: A Great Physicist of the 20th Century”, Chapter 19, edited by C. S. Liu and S.-T. Yau
  60. Yasar and Y. Deng, D. Saltz, and R. Tuzun: Guest Editors for New Trend in High Performance Computing, Special Issue of Parallel Computing. Vol. 27 Issues 1-2 (2001)
  61. Stojic and J. Glimm and Y. Deng and J. Haus, Transverse magnetic modes in two- dimensional triangular photonic crystals Phys. Rev. E, Vol. 64 (2001), pp. 1-7
  62. Deng and A. Korobka, Performance of a supercomputer Built with Commodity Components, Parallel Computing, Vol. 27 Issues 1-2 (2001), pp. 91-108
  63. Deng, J. Glimm, Y. Wang, A. Korobka, M. Eisenberg, and A. P. Grollman, Prediction of Protein Binding to DNA in the Presence of Water-Mediated Hydrogen Bonds, Journal of Molecular Modelling. Vol. 5 (1999) 125-133.
  64. Chen, Y. Deng, and X. Nie, Y. Tu Clustering Kinetics of Granular Media in Three Dimensions, Physical Letters, Vol. 269 (2000), pp. 218-223
  65. Chu and Y. Deng, Quick Minimization of Total Energy of Large Lennard-Jones Clusters, Grand Challenges in Computer Simulation, Proceedings of ASTC Conference. Ed. Adrian Tentner, San Diego, CA (1999), pp. 37-42
  66. Deng, R. Peierls, and C. Rivera, An adaptive load balancing method for parallel molecular dynamics simulations (in pdf or ps), Journal of Computational Physics. Vol. 161 (2000), pp. 250-263
  67. Chu, Y. Deng, and J. Reinitz, Parallel Simulated Annealing Algorithms by Mixing States, Journal of Computational Physics. Vol. 148 (1999), pp. 646-662
  68. Deng and C. Rivera, Simple energy minimization for huge Lennard-Jones clustersby dramatic parameter reduction, Applied Math Letters Vol. 12, (1999) pp. 119-125
  69. Deng and C. Rivera, Approximate energy minimization for Large Lennard-Jonesclusters, Journal Global Optimization. 16 (2000) pp. 325-341
  70. Deng and R. Peierls, An Asynchronous Decomposition Approach to Parallel Global Optimization, Applied Math Letters. Vol. 11 (1998), pp. 55-59
  71. Asvestas, Y. Deng, J. Glimm, and F.Tangerman, Electromagnetic Scattering from large cavities, Communications of Applied Analysis Vol. 2, Num. 1 (1998), pp. 37- 48
  72. Qian and Y. Deng, A Lattice BGK Model for Viscoelastic Media, Physical Review Letters. Vol.79 No.14 (1997), pp. 2742-2746
  73. Alan McCoy and Y. Deng, Parallel embedded-atom method simulations with delayed electron density approximations, Computer Physics Communications, 100 (1997), pp. 41-46
  74. Alan McCoy and Y. Deng, Parallel Particle Simulations of Thin-Film Deposition, Int. J. High Performance Computing Applications, Vol. 13, No. 1 (1999), pp. 16- 32
  75. Deng, M. Mu, and C-C Chou, Numerical Methods for Simulating Ginsburg- Landau Vortices, in Proceedings of High Performance Computing 1996, Ed. Adrian Tentner, San Diego, CA (1996) pp. 96-100
  76. Deng and R. A. McCoy, Computing Sticking Coefficients for Cu-Cu by Localized Molecular Dynamics on Parallel Processors, in Proceedings of High Performance Computing 1996, Ed. Adrian Tentner, San Diego, CA (1996) 18-24.
  77. Mu, Y. Deng, and C-C Chou, Ginsburg-Landau Vortices for Type-II Superconductors: A Numerical Study, SIAM J. Sci. Comp. V. 19, No 4, (1998) pp. 1333-1339
  78. C-C. Chou and Y. Deng, Numerical Solutions of a Nonlinear Evolution System with Small Dissipation on Parallel Processors, J. Sci. Comp. Vol. 13 No. 4 (1998) pp. 405-417
  79. Wang and Y. Deng, Multi-item stochastic inventory models with constraints and their parallel computation, in Computational Economic Systems: Models. Methods and Econometrics, Advances in Computational Economics, Vol. 5 (1996) pp. 103- 122
  80. C-C Chou and Y. Deng, Decomposing 40 Billion Integers by Four Tetrahedral Numbers, Math. Comp. V. 66 N 218 (1997) pp. 893-901
  81. Deng, J. Glimm, Q. Yu, and M. Eisenberg, Global Minimization for Problems with Multiple Local Minima, Appl. Math. Lett. Vol 6 (1993) pp. 89-90
  82. C-C Chou, Y. Deng, G. Li, and Y. Wang, Parallelizing Strassen’s method for matrix multiplication on distributed- memory MIMD architectures, in International Journal of Computers and Mathematics with Applications, 30 (2) (1995) pp. 49-69
  83. Deng, A. McCoy, R. Marr, R. Peierls, and O. Yasar, Molecular dynamics on distributed-memory MIMD computers with load balancing, Appl. Math Letters, V. 8 (3) (1995) pp. 37-41
  84. Deng, R. A. McCoy, R. B. Marr, R. F. Peierls and O. Yasar, Molecular dynamics for 400 million particles with short-ranged interactions, Proceedings of High Performance Computing 1995, San Diego, CA (1995) pp. 95-100
  85. Deng, R. A. McCoy, R. B. Marr, and R. F. Peierls, An Unconventional Method for Load Balancing, 7th SIAM Conference on Parallel Processing, San Francisco, CA (1995) pp. 645-651
  86. Campbell, Y. Deng, J. Glimm, M. Eisenberg, and A. Grollman, Analysis and prediction of hydrogen bonding of protein-dna complexes on parallel processors, J. Comp. Chem, Vol 17 (15) (1996) pp. 1712-1725.
  87. Asvestas, B. Bielefeld, Y. Deng, J. Glimm, and F.Tangerman, Boundary integral methods applied to electromagnetic scattering problems on parallel processors, Proc. Amer. Math. Soc. Vol 122 (1994) pp. 719-726.
  88. Deng and C. N. Yang, Waring’s Problem for Pyramidal Numbers, Science in China (Series A), 37 (3), (March 1994) pp. 377-383
  89. Hu Wang, Y. Deng, J. L. Stephenson, and R. Tewarson, An efficient algorithm for solving n-nephron models of the Renal Inner Medilla, International Journal of Computers and Mathematics with Applications, 28 (5) (1994) pp. 1-12
  90. Deng, J. Glimm, and D. Sharp, Mixing and Chaotic Microstructure, Los Alamos Science November Vol. 21 (1993) pp.124-132
  91. Chen, Y. Deng, J. Glimm, G. Li, D. Sharp, and Q. Zhang, A renormalization group scaling analysis for compressible two-phase flow, J. Phys. Fluids A 5 (11) (1993) pp. 2929-2937
  92. Campbell, Y. Deng, J. Glimm, and Q. Yu, Analysis and prediction of protein binding on dna: pattern recognition of hydrogen bonds, in High Performance Computing and its Applications in the Physical Sciences (1993) pp. 248-256
  93. Romy Hoque and Y. Deng, Frontiers for the Teraflop in the 21st Century in CSI Communications. Vol. 17 Num. 1 (1993) pp. 5-12
  94. Deng and C. N. Yang, Eigenvalues and eigenfunctions of the Huckel Hamiltonian carbon-60, Physical Letters A, Vol. 170 (1992) pp. 116-126.
  95. Deng, J. Glimm, and D. H. Sharp, Perspectives on Parallel Computing, Daedalus Vol 12 (1992) pp. 31-52
  96. Chen, Y. Deng, J. Glimm, and G. Li, Parallel Interface Methods for Multi-phase Flow Problems on iPSC/860, in Intel Supercomputer Systems Conference Proceedings: Technology Focus Conference (1992) pp. 377-391
  97. Deng and J. Glimm, Fluid Dynamics Using Interface Methods on Parallel Processors in Parallel CFD. Implementations and Results Using Parallel Computers Ed. Horst Simon, MIT Press (1992) 257-270.
  98. Brown, N. Christ, Y. Deng, T. Woch, and M. Gao, Nature of the deconfining phase transition in SU(3) gauge theory Phys. Rev. Lett. 61 (1988) 2058-2062
  99. Deng, Simulating lattice gauge theory on special-purpose supercomputers, Ph.D. Thesis Columbia University (1989). Generous reference to my thesis.
  100. Deng, Energy density and pressure in SU(3) Lattice Gauge Theory at Finite Temperature ed. A. S. Kronfeld and P. B. Mackenzie, Nuclear Physics B (Proc. Suppl.) 9 (1989) pp. 334-339
  101. Deng, The performance of the microcanonical updating algorithm, ed. K. Haller et al. in Proceedings of the Storrs Meeting on Particles and Fields, (1989) pp. 238-241, World Scientific, Singapore