I am a computational scientist with experience ranging from continuum contact methods to molecular simulation. I have interest in molecular to tissue-level biomechanics and models of microscopically rough contact. I have worked with molecular methods to (a) screen electrolytes based on their transport properties for batteries and related electrochemical  systems,  (b) estimate fracture toughness of minerals in reacting environments for fracking and sequestration. Currently, I am using machine learning and uncertainty techniques to model material variability. I designed neural networks to embed exact symmetries and physical constraints and to extract microstructures features needed to make accurate predictions of mechanical response.

(ps the "PhD" is just to distinguish this page from those of more famous golf course designers etc with the same name)

Citations ResearchGate Linkedin Berkeley ORCiD

Talks

• Universal constitutive models, sparsification and uncertainty quantification, 8th U.S. National congress on computational mechanics, 20-24 July 2025, Chicago, IL USA

Classes

Publications

1. Patel, Ravi G., Reese E. Jones, D. Thomas Seidl, Brian N. Granzow, and Jan N. Fuhg. A General, Automated Method for Building Structural Tensors of Arbitrary Order for Anisotropic Function Representations. (2025) arXiv.

2. Foster, ME, Norm Bartelt, Reese E Jones, Interplay of Water Film Dewetting and Hydrogen Evolution on Pt(111): Insights from a Machine Generated Interatomic Potential (2025)

3. Jones, Reese E., Adrian Buganza Tepole, and Jan N. Fuhg. Differentiable neural network representation of multi-well, locally-convex potentials. (2025) arXiv

4. Way, Lauren, Catalin Spataru, Reese Jones, Dallas Trinkle, Andrew Rowberg, Joel Varley, Robert Wexler et al. Defect diffusion graph neural networks for materials discovery in high-temperature, clean energy applications. Chemistry of Materials (2024) chemrxiv

5. Guan, Pinwen, Catalin Spataru, Vitalie Stavila, Reese Jones, Peter Sharma, and Matthew Witman. Thermodynamic modeling of complex solid solutions in the Lu-HN system via graph neural network accelerated Monte Carlo simulations. (2024) chemrxiv

6. Safta, Cosmin, Reese E. Jones, Ravi G. Patel, Raelynn Wonnacot, Dan S. Bolintineanu, Craig M. Hamel, and Sharlotte LB Kramer. Uncertainty quantification of neural network models of evolving processes via Langevin sampling. (2025) arXiv .

7. Witman, Matthew D., Lauren Way, Catalin D. Spataru, Reese Jones, Sean R. Bishop, Anthony H. McDaniel, Andrew Rowberg et al. Structure-Property Defect Models for Materials Discovery in Clean Energy Applications. In 247th ECS Meeting (May 18-22, 2025). ECS, 2025.

8. Yan, Ryan, D. Thomas Seidl, Reese E. Jones, and Panayiotis Papadopoulos. A Direct-adjoint Approach for Material Point Model Calibration with Application to Plasticity.  arXiv preprint arXiv:2501.04584 (2025).

9. Jones, Reese E., and Jan N. Fuhg. An attention-based neural ordinary differential equation framework for modeling inelastic processes. (2025) arXiv.

10. Jadoon, Asghar A., D. Thomas Seidl, Reese E. Jones, and Jan N. Fuhg. Input specific neural networks. (2025) arXiv.

11. Padmanabha, Govinda Anantha, Cosmin Safta, Nikolaos Bouklas, and Reese E. Jones. Condensed Stein Variational Gradient Descent for Uncertainty Quantification of Neural Networks. Journal of Machine Learning for Modeling and Computation (2024) arXiv

12. Jadoon, Asghar A., Karl A. Kalina, Manuel K. Rausch, Reese Jones, and Jan N. Fuhg. Inverse design of anisotropic microstructures using physics-augmented neural networks. Journal of the Mechanics and Physics of Solids (2024) arXiv

13. Jadaan, Dafer K., Jessica Rimsza, Reese Jones, and Richard A. Regueiro. Poromechanical cohesive interface element with combined Mode I-II cohesive zone elastoplasticity for simulating fracture in fluid-saturated porous media. Computers & Structures  (2024)

14. Padmanabha, Govinda Anantha, Jan Niklas Fuhg, Cosmin Safta, Reese E. Jones, and Nikolaos Bouklas. Improving the performance of Stein variational inference through extreme sparsification of physically-constrained neural network models. Computer Methods in Applied Mechanics and Engineering (2024) arXiv.

15. Fuhg, Jan N., Asghar Jadoon, Oliver Weeger, D. Thomas Seidl, and Reese E. Jones. Polyconvex neural network models of thermoelasticity. Journal of the Mechanics and Physics of Solids  (2024) arXiv

16. Patel, Ravi, Cosmin Safta, and Reese E. Jones. Equivariant graph convolutional neural networks for the representation of homogenized anisotropic microstructural mechanical response. Computer Methods in Applied Mechanics and Engineering (2024) arXiv

17. Jones, Reese E., Craig M. Hamel, Dan Bolintineanu, Kyle Johnson, Robert Buarque de Macedo, Jan Fuhg, Nikolaos Bouklas, and Sharlotte Kramer. Multiscale simulation of spatially correlated microstructure via a latent space representation.  International Journal of Solids and Structures. (2024) arXiv

18. Hauth, Jeremiah, Cosmin Safta, Xun Huan, Ravi G. Patel, and Reese E. Jones. Uncertainty Quantification of Graph Convolution Neural Network Models of Evolving Processes. Computer Methods in Applied Mechanics and Engineering (2024) arXiv

19. Rimsza, Jessica M., and Reese E. Jones. Inelastic relaxation processes in amorphous sodium silicates. Journal of the American Ceramic Society 107, no. 3 (2024): 1883-1894.

20. Bridgman, Wyatt, Uma Balakrishnan, Reese Jones, Jiefu Chen, Xuqing Wu, Cosmin Safta, Yueqin Huang, and Mohammad Khalil. Enhancing Polynomial Chaos Expansion Based Surrogate Modeling using a Novel Probabilistic Transfer Learning Strategy. International Journal of Uncertainty Quantification (2023) arXiv

21. De, Saibal, Reese E. Jones, and Hemanth Kolla. Accurate Data-Driven Surrogates of Dynamical Systems for Forward Propagation of Uncertainty. International Journal of Numerical Methods in Engineering (2023) arXiv

22. Fuhg, Jan N., Reese E. Jones, and Nikolaos Bouklas. Extreme sparsification of physics-augmented neural networks for interpretable model discovery in mechanics Computer Methods in Applied Mechanics and Engineering (2023) arXiv

23. Bridgman, Wyatt, Reese E Jones, Mohammad Khalil, Robust scalable initialization for Bayesian variational inference with multi-modal Laplace approximations Probabilistic Engineering Mechanics (2023)

24. Fuhg, Jan N., Nikolaos Bouklas, and Reese E. Jones. Stress representations for tensor basis neural networks: alternative formulations to Finger-Rivlin-Ericksen. Journal of Computing and Information Science in Engineering (2023) arXiv.

25. Foster, Michael E., Ian Kendrick, Sanjeev Mukerjee, and Reese Jones. Role of Graphene on Ni/NiO for the Hydrogen Evolution Reaction. The Journal of Physical Chemistry C 126, no. 38 (2022): 16158-16163.

26. Fuhg, Jan Niklas, Craig M. Hamel, Kyle Johnson, Reese Jones, and Nikolaos Bouklas. Modular machine learning-based elastoplasticity: Generalization in the context of limited data. Computer Methods in Applied Mechanics and Engineering 407 (2023): 115930.

27. Jones, Reese, Cosmin Safta, and Ari Frankel. Deep learning and multi-level featurization of graph representations of microstructural data.  Computational Mechanics (2023) arXiv.

28. Villarreal, Ruben, Nikolaos N. Vlassis, Nhon N. Phan, Tommie A. Catanach, Reese E. Jones, Nathaniel A. Trask, Sharlotte LB Kramer, and WaiChing Sun. Design of experiments for the calibration of history-dependent models via deep reinforcement learning and an enhanced Kalman filter. Computational Mechanics (2023) arXiv .

29. J.M. Rimsza, R.E. Jones, Fracture Mechanisms of Sodium Silicate Glasses, International Journal of Applied Glass Science 14, 1: 27-37 (2023)

30. Fuhg, Jan N., Nikolaos Bouklas, and Reese E. Jones. Learning hyperelastic anisotropy from data via a tensor basis neural network. Journal of Mechanics and Physics of Solids (2022) arXiv.

31. Trageser, Jeremy E., Chven A. Mitchell, Reese E. Jones, Edward N. Matteo, Jessica M. Rimsza, and Laura J. Pyrak-Nolte. The effect of differential mineral shrinkage on crack formation and network geometry.  Scientific Reports 12, no. 1 (2022): 22264.

32. C.E. Torrence, J.E. Trageser, R.E. Jones, J.M. Rimsza, Sensitivity of the strength and toughness of concrete to the properties of the interfacial transition zone, Construction and Building Materials, 336:126875 (2022)

33. Bridgman, Wyatt, Xiaoxuan Zhang, Greg Teichert, Mohammad Khalil, Krishna Garikipati, and Reese Jones. A heteroencoder architecture for prediction of failure locations in porous metals using variational inference. Computer Methods in Applied Mechanics (2022) arXiv

34. Jones, R. E., A. L. Frankel, and K. L. Johnson. A neural ordinary differential equation framework for modeling inelastic stress response via internal state variables.  Journal of Machine Learning for Modeling and Computing  (2021) arXiv

35. R. Skelton and R. E. Jones, A Computational Study of Structure and Transport in Pyrrolidinium-Li-TFSI Silica Ionogels. Journal of Physical Chemistry B, (2021) [pdf]

36. Ari Frankel, Cosmin Safta, Coleman Alleman, Reese Jones, Mesh-based graph convolutional neural networks for modeling materials with microstructure, Journal of Machine Learning for Modeling and Computing, (2021) [arXiv]

37. Jessica M. Rimsza,, Scott J. Grutzik, Reese E. Jones, Inelastic Relaxation in Silica via Reactive Molecular Dynamics, Journal of the American Ceramic Society, (2021)

38. C.D. Spataru, M.D. Witman, and R.E. Jones, Tuning the critical Li intercalation concentrations for MoX2 bilayer phase transitions, Physical Review Materials, (2021)

39. Jones, Reese E., Michael T. Redle, Hemanth Kolla, and Julia A. Plews. A minimally invasive, efficient method for propagation of full‐field uncertainty in solid dynamics. International Journal for Numerical Methods in Engineering 122, no. 23 (2021)

40. Gregory H. Teichert, Mohammad Khalil, Coleman Alleman, Krishna Garikipati, Reese E. Jones, Sensitivity of void mediated failure to geometric design features of porous metals, International Journal of Solids and Structures, (2021) [arXiv] 

41. R. Skelton and R. E. Jones, Strain-rate and temperature effects on the mechanical properties of simulated silica ionogels, Journal of Physical Chemistry B, (2021) 

42. D. Littlewood, R. Jones, N. Morales, J. Plews, U. Hetmaniuk and J. Lifflander, Hierarchical Parallelism for Transient Solid Mechanics Simulations, in: WCCM-ECCOMAS2020.

43.  Jones, Reese, Jessica Rimsza, Jeremy Tragesar, Joshua Hogancamp, Simulation of hardened cement degradation and estimation of uncertainty in predicted failure times with peridynamics Construction and Building Materials 286:122927 (2021).

44. Cailliez, Fabien, Pascal Pernot, Francesco Rizzi, Reese Jones, Omar Knio, Georgios Arampatzis, and Petros Koumoutsakos. Bayesian calibration of force fields for molecular simulations. Uncertainty Quantification in Multiscale Materials Modeling, pp. 169-227(2020).

45. Khalil, M., G. H. Teichert, C. Alleman, N. M. Heckman, R. E. Jones, K. Garikipati, and B. L. Boyce. Modeling strength and failure variability due to porosity in additively manufactured metals. Computer Methods in Applied Mechanics and Engineering, 373:113471 (2021) [arXiv].

46. Frankel, Ari, Reese Jones, and Laura Swiler. Tensor Basis Gaussian Process Models of Hyperelastic Materials. Journal of Machine Learning for Modeling and Computing 1, no. 01 (2020) [arXiv].

47. Heckman, Nathan M., Thomas A. Ivanoff, Ashley M. Roach, Bradley H. Jared, Daniel J. Tung, Harlan J. Brown-Shaklee, Todd Huber et al. Automated high-throughput tensile testing reveals stochastic process parameter sensitivity. Materials Science and Engineering: A 772 (2020): 138632.

48. Frankel, Ari, Kousuke Tachida, and Reese Jones. Prediction of the evolution of the stress field of polycrystals undergoing elastic-plastic deformation with a hybrid neural network model. Machine Learning: Science and Technology 1, no. 3 (2020) [arXiv].

49. JM Rimsza, R Jones, and L Criscenti. Mechanisms of Silica Fracture in Aqueous Electrolyte Solutions. Frontiers in Materials 6 (2019): 79.

50. FS Gittleson, DK Ward, RE Jones, RA Zarkesh, T Sheth, ME Foster. Correlating structure and transport behavior in Li+ and O_2 containing pyrrolidinium ionic liquids.Physical Chemistry Chemical Physics 21, no. 31 (2019): 17176-17189.

51. F Rizzi, M Khalil, RE Jones, JA Templeton, JT Ostien, BL Boyce. Bayesian modeling of inconsistent plastic response due to material variability. Computer Methods in Applied Mechanics and Engineering 353 (2019): 183-200 [arXiv].

52. RE Jones, WC Tucker, MJL Mills, S Mukerjee, Insight into hydrogen production through molecular simulation of an electrode-ionomer electrolyte system Journal of Chemical Physics 151, 034702 (2019)

53. AL Frankel, RE Jones, C. Alleman, JA Templeton, Predicting the mechanical response of oligocrystals with deep learning Computational Materials Science 169, 109099 (2019) [arXiv].

54. RE Jones, JA Templeton, CM Sanders, JT Ostien,  Machine learning models of plastic flow based on representation theory Computer Modeling in Engineering and Sciences, v117:n3 (2018) 309-342 [pdf]

55. RE Jones, WC Tucker,  JM Rimsza,  LJ Criscenti, Atomic-scale interaction of a crack and an infiltrating fluid. Chemical Physics Letters, 1:100005 (2018) [pdf]

56. JM Rimsza, RE Jones, LJ Criscenti, Chemical effects on subcritical fracture in silica from molecular dynamics simulations. Journal of Geophysical Research - Solid Earth, (2018)

57. Rimsza, Jessica M., Reese E. Jones, and Louise J. Criscenti. Interaction of NaOH solutions with silica surfaces. Journal of colloid and interface science 516 (2018): 128-137.

58. Rimsza, Jessica M., Reese E. Jones, and Louise J. Criscenti. Crack propagation in silica from reactive classical molecular dynamics simulations. Journal of the American Ceramic Society 101, no. 4 (2018): 1488-1499.

59. Jones, R., J. M. Rimsza, and L. J. Criscenti. An atomic-scale evaluation of the fracture toughness of silica glass. Journal of physics: condensed matter, 30, no. 24 (2018): 245901. [pdf]

60. Jones, Reese E., and Donald K. Ward. Influence of defects on the thermal conductivity of compressed LiF. Physical Review B, 97 no. 5 (2018): 054103.

61. Chu, K., J. Gruber, X. W. Zhou, R. E. Jones, S. R. Lee, and G. J. Tucker. Molecular dynamics studies of InGaN growth on nonpolar (1120) GaN surfaces. Physical Review Materials 2, no. 1 (2018): 013402.

62. Zhou, Xiaowang W., Reese E. Jones, and Kevin Chu. Polymorphic improvement of Stillinger-Weber potential for InGaN. Journal of Applied Physics 122, no. 23 (2017): 235703.

63. Jones, R. E., D. K. Ward, F. S. Gittleson, and M. E. Foster. Assessing electrolyte transport properties with molecular dynamics. Journal of The Electrochemical Society 164, no. 6 (2017): A1258-A1267.

64. Zhou, X. W., and R. E. Jones. A Stillinger-Weber Potential for InGaN. Journal of Materials Science Research 6, no. 4 (2017): 88.

65. Rimsza, J. M., R. E. Jones, and L. J. Criscenti. Surface structure and stability of partially hydroxylated silica surfaces. Langmuir 33, no. 15 (2017): 3882-3891.

66. He, Yuping, Catalin D. Spataru, Francois Léonard, Reese E. Jones, Michael E. Foster, Mark D. Allendorf, and A. Alec Talin. Two-dimensional metal–organic frameworks with high thermoelectric efficiency through metal ion selection. Physical Chemistry Chemical Physics 19, no. 29 (2017): 19461-19467.

67. Gruber, J., X. W. Zhou, R. E. Jones, S. R. Lee, and G. J. Tucker. Molecular dynamics studies of defect formation during heteroepitaxial growth of InGaN alloys on (0001) GaN surfaces. Journal of Applied Physics 121, no. 19 (2017): 195301.

68. Gittleson, Forrest S., Reese E. Jones, Donald K. Ward, and Michael E. Foster. Oxygen solubility and transport in Li–air battery electrolytes: establishing criteria and strategies for electrolyte design. Energy & Environmental Science 10, no. 5 (2017): 1167-1179.

69. Jones, R. E., F. S. Gittleson, J. A. Templeton, and D. K. Ward. A Simple Model for Interpreting the Reaction–Diffusion Characteristics of Li-Air Batteries. Journal of The Electrochemical Society 164, no. 1: A6422-A6430, (2017).

70. Zhou, X. W., Reese E. Jones, and Jacob Gruber. Molecular dynamics simulations of substitutional diffusion. Computational Materials Science 128: 331-336, 2017.

71. AA Talin, RE Jones, PE Hopkins, Metal-organic frameworks for thermoelectric energy-conversion applications, MRS Bulletin, 41 (11), 877-882, (2016).

72. RE Jones, JA Zimmerman, G Po, Comparison of Dislocation Density Tensor Fields Derived from Discrete Dislocation Dynamics and Crystal Plasticity Simulations of Torsion, Journal of Materials Science Research, 5,4, 2016 [pdf]

73. RE Jones, DK Ward, Estimates of crystalline LiF thermal conductivity at high temperature and pressure by a Green-Kubo method, Physical Review B, 94, 014309, (2016)

74. RE Jones, CR Weinberger, SP Coleman, GJ Tucker, Introduction to Atomistic Simulation Methods, in Multiscale Materials Modeling for Nanomechanics, Volume 245 of the series Springer Series in Materials Science pp 1-52, (2016) [pdf]

75. RE Jones, JA Templeton, JA Zimmerman, Principles of Coarse-Graining and Coupling Using the Atom-to-Continuum Method, in Multiscale Materials Modeling for Nanomechanics, Volume 245 of the series Springer Series in Materials Science pp 223-259, (2016) [pdf]

76. J Ling, RE Jones, JA Templeton. Machine learning strategies for systems with invariance properties. Journal of Computational Physics 318 (2016): 22-35.

77. MC Shaughnessy, RE Jones, Efficient use of an adapting database of ab initio calculations to generate accurate Newtonian dynamics, Journal of Chemical Theory and Computation, (2015) [pdf]

78. M Salloum, K Sargsyan, R Jones, HN Najm, B Debusschere, Quantifying Sampling Noise and Parametric Uncertainty in Atomistic-to-Continuum Simulations Using Surrogate Models, Multiscale Modeling and Simulation, 13 (3), 953-976, (2015)

79. KJ Erickson, F Léonard, V Stavila, ME Foster, CD Spataru, RE Jones,Brian M Foley, Patrick E Hopkins, Mark D Allendorf, A Alec Talin, Thin Film Thermoelectric Metal–Organic Framework with High Seebeck Coefficient and Low Thermal Conductivity, Advanced Materials, (2015)

80. VA Kuzkin, AM Krivtsov, RE Jones, JA Zimmerman, Material frame representation of equivalent stress tensor for discrete solids, Physical Mesomechanics 18 (1), 13-23, (2015)

81. XW Zhou, ME Foster, R Jones, P Yang, H Fan, FP Doty, A Modified Stillinger-Weber Potential for TlBr, and Its Polymorphic Extension, Journal of Materials Science Research, 4 (3), p15, (2015)

82. BF Donovan, CJ Szwejkowski, JC Duda, R Cheaito, JT Gaskins,C-Y Peter Yang, Costel Constantin, Reese E Jones, Patrick E Hopkins, Thermal boundary conductance across metal-gallium nitride interfaces from 80 to 450 K, Applied Physics Letters 105 (20), 203502, (2014)

83. D Ward, R Jones, J Templeton, K Reyes, M Kane, Improved Parameterization of an Ethylene Carbonate Molecular Dynamics Model in Li-Air Batteries for Accurate Density and Transition Temperatures, ECS Transactions 61 (27), 181-191, (2014)

84. K. K. Mandadapu, R. E. Jones, J. A. Zimmerman, On the microscopic definitions of the dislocation density tensor. Mathematics and Mechanics of Solids, (2014,  [pdf]

85.  R. E. Jones, D. K. Ward, J. A. Templeton, Spatial resolution of the electrical conductance of ionic fluids using a Green-Kubo method, J. Chem. Phys., 141, 184110, 2014 [pdf]

86. X Zhou, RE Jones, PE Hopkins, TE Beechem, Thermal boundary conductance between Al films and GaN nanowires investigated with molecular dynamics, Physical Chemistry Chemical Physics 16 (20), 9403-9410, 2014

87. PE Hopkins, JC Duda, B Kaehr, XW Zhou, CYP Yang, RE Jones, Ultrafast and steady-state laser heating effects on electron relaxation and phonon coupling mechanisms in thin gold films, Applied Physics Letters 103 (21), 211910, 2013

88.  JC Duda, CYP Yang, BM Foley, R Cheaito, DL Medlin, RE Jones, PE Hopkins, Influence of interfacial properties on thermal transport at gold: silicon contacts, Applied Physics Letters 102 (8), 081902, 2013

89. XW Zhou, RE Jones, CJ Kimmer, JC Duda, PE Hopkins, Relationship of thermal boundary conductance to structure from an analytical model plus molecular dynamics simulations, Physical Review B 87 (9), 094303, 2013

90. X. W. Zhou, R. E. Jones, J. C. Duda, P. E. Hopkins, Molecular dynamics studies of material property effects on thermal boundary conductance, Physical Chemistry Chemical Physics, 15:11078-11087, 2013 [pdf]

91.  R. E. Jones, J. C. Duda, X. W. Zhou, C. J. Kimmer, P. E. Hopkins, Investigation of size and electronic effects on Kapitza conductance with non-equilibrium molecular dynamics, Applied Physics Letters, 102:183119, (2013), [pdf]

92. F. Rizzi, R. E. Jones, B. J. Debusschere, O. M. Knio. Uncertainty quantification in MD simulations of concentration driven ionic flow through a silica nanopore. Part I: sensitivity to physical parameters of the pore. J. Chem. Phys., 138:194104, 2013 [pdf]

93. F. Rizzi, R. E. Jones, B. J. Debusschere, O. M. Knio. Uncertainty quantification in MD simulations of concentration driven ionic flow through a silica nanopore. Part II: uncertain potential parameters. J. Chem. Phys., 138:194105, 2013 [pdf]

94.  J. A. Zimmerman, and R. E. Jones. The application of an atomistic J-integral to a ductile crack. J. Phys.-Cond.Mat., 25(15):155402, (2013) [pdf]

95. JC Duda, CJ Kimmer, WA Soffa, XW Zhou, RE Jones, PE Hopkins, Influence of crystallographic orientation and anisotropy on Kapitza conductance via classical molecular dynamics simulations, Journal of Applied Physics 112 (9), 093515, (2013)

96. A. A. Selezenev, A. Yu Aleinikov, N. S. Ganchuk, S. N. Ganchuk, R. E. Jones, and J. A. Zimmerman. Molecular dynamics calculation of the thermal conductivity coefficient of single-layer and multilayer graphene sheets. Physics of the Solid State 55, no. 4 (2013): 889-894.

97. R. E. Jones, and K. K. Mandadapu. Adaptive Green-Kubo estimates of transport coefficients from molecular dynamics based on robust error analysis.J. Chem. Phys. , 154102, (2012). [pdf]

98.  M. Salloum, K. Sargsyan, R. Jones, B. Debusschere, H. N. Najm, and H. Adalsteinsson. A Stochastic Multiscale Coupling Scheme to Account for Sampling Noise in Atomistic-to-Continuum Simulations. Multiscale Model. Simul. 550–584, (2012). [pdf]

99.  XW Zhou, RE Jones, Effects of nano-void density, size and spatial population on thermal conductivity: a case study of GaN crystal, Journal of Physics: Condensed Matter 24 (32), 325804, (2012)

100.  A. A. Selezenev, A. Yu. Aleynikov, P. V. Ermakov, N. S. Ganchuk, S. N. Ganchuk, and R. E. Jones. Molecular-dynamic calculation of Ge single crystal thermal conductivity coefficient. Sov. Phys. Sol. State, (2012).

101. J. T. Lloyd, J. A. Zimmerman, R. E. Jones, X. W. Zhou, and D. L. McDowell. Finite element analysis of an atomistically derived cohesive model for brittle fracture. Mod. Sim. Matl. Sci. Eng., 19(6):065007, (2011).

102.  R. E. Jones, J. A. Templeton, and T. W. Rebold. Simulated real-time detection of a small molecule on a carbon nanotube cantilever.   J. Comp. Theo. NanoSci., 8:1364–1384, (2011). [pdf]

103. J. A. Templeton, R. E. Jones, J. W. Lee, J. A. Zimmerman, and B. M. Wong. A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling. J. Chem. Theo. Comp., 7(6):1736–1749, (2011). [pdf]

104.  E. H. Feng and R. E. Jones. Carbon nanotube cantilevers for next generation sensors. Phys. Rev. B, (83) 195412, (2011). [pdf]

105.  X. W. Zhou and R. E. Jones. Effects of cutoff functions of Tersoff potentials on molecular dynamics simulations of thermal transport. Mod. Sim. Matl. Sci. Eng., 19:025004, (2011).

106. R. E. Jones, J. A. Zimmerman, J. Oswald, and T. Belytschko. An atomistic J- integral at finite temperature based on Hardy estimates of continuum fields. J. Phys. Cond. Mat., 23:015002, (2010). [pdf]

107. J. A. Templeton, R. E. Jones, and G. J. Wagner. Application of a field-based method to spatially varying thermal transport problems in molecular dynamics. Mod. Sim. Mat. Sci. Eng., 18:085007, (2010). 

108.  R. E. Jones and J. A. Zimmerman. The construction and application of an atomistic J-integral via Hardy estimates of continuum fields. J. Mech. Phys. Solids, 58:1318–1337, (2010). [pdf]

109. E. H. Feng and R. E. Jones. Equilibrium thermal vibrations of carbon nanotubes. Phys. Rev. B, 81(12),. (2010). [pdf]

110. R. E. Jones, J. A. Templeton, G. J. Wagner, D. Olmsted, and Nomand A. Modine. Electron transport enhanced molecular dynamics for metals and semi-metals. Int. J. Num. Meth. Engin., 83(8-9):940–967, (2010). [pdf]

111.  K. K. Mandadapu, R. E. Jones, and P. Papadopoulos. A homogeneous nonequilibrium molecular dynamics method for calculating the heat transport coefficient of mixtures and alloys. J. Chem. Phys., 133(3):034122, (2010). [pdf]

112. X. W. Zhou, R. E. Jones, and S. Aubry. Molecular dynamics prediction of thermal conductivity of GaN films and wires at realistic length scales. Phys. Rev. B, 81(15):155321, (2010). [pdf]

113. R. E. Jones and C. J. Kimmer. Efficient non-reflecting boundary condition constructed via optimization of damped layers. Phys. Rev. B, 81(9):094301, (2010). [pdf]

114. J. A. Zimmerman, R. E. Jones, and J. A. Templeton. A material frame approach for evaluating continuum variables in atomistic simulations. J. Comp. Phys., 229:2364–2389, 2010. [pdf]

115. X. W. Zhou, R. E. Jones, and S. Aubry. Analytical law for size effects on thermal conductivity of nanostructures. Phys. Rev. B, 81(7):073304, (2010). [pdf]

116. T. Westover, R. Jones, J. Y. Huang, G. Wang, E. Lai, and A. Alec Talin. Photoluminescence, thermal transport, and breakdown in Joule-heated GaN nanowires. Nano Lett., 9(1):257–263, 2009. [pdf]

117. K. K. Mandadapu, R. E. Jones, and P. Papadopoulos. Generalization of the homogeneous nonequilibrium molecular dynamics method for calculating thermal conductivity to multibody potentials. Phys. Rev. E, 80(4, Part 2), 2009. [pdf]

118.  X. W. Zhou, N. R. Moody, R. E. Jones, J. A. Zimmerman, and E. D. Reedy. Molecular-dynamics-based cohesive zone law for brittle interfacial fracture under mixed loading conditions: Effects of elastic constant mismatch. Acta Mat., 57(16):4671–4686, 2009.

119. K. K. Mandadapu, R. E. Jones, and P. Papadopoulos. A homogeneous nonequilibrium molecular dynamics method for calculating thermal conductivity with a three-body potential. J. Chem. Phys., 130(20), (2009). [pdf]

120. X. W. Zhou, S. Aubry, R. E. Jones, A. Greenstein, and P. K. Schelling. Towards more accurate molecular dynamics calculation of thermal conductivity: Case study of GaN bulk crystals. Phys. Rev. B, 79(11), (2009).

121. B. L. Boyce, J. M. Grazier, R. E. Jones, and T. D. Nguyen. Full-field deformation of bovine cornea under constrained inflation conditions. Biomaterials, 29 (28):3896–3904, (2008). 

122. G. J. Wagner, R. E. Jones, J. A. Templeton, and M. L. Parks. An atomistic-to-continuum coupling method for heat transfer in solids. Comp. Meth. Appl. Mech. Eng., 197(41-42):3351–3365, (2008).

123. T. D. Nguyen, R. E. Jones, and B. L. Boyce. A nonlinear anisotropic viscoelastic model for the tensile behavior of the corneal stroma. J. Biomech. Eng., 130 (4), (2008). 

124. T. D. Nguyen, R. E. Jones, and B. L. Boyce. Modeling the anisotropic finite-deformation viscoelastic behavior of soft fiber-reinforced composites. Intl. J. Sol. Struct., 44(25-26):8366–8389, (2007). 

125.  B. L. Boyce, R. E. Jones, T. D. Nguyen, and J. M. Grazier. Stress-controlled viscoelastic tensile response of bovine cornea. J. Biomechanics, 40(11):2367– 2376, (2007). 

126. C. J. Kimmer and R. E. Jones. Continuum constitutive models from analytical free energies. J. Phys.-Cond. Mat., 19(32), (2007). [pdf]

127. R. E. Jones. A Greenwood-Williamson model of small-scale friction. J. Appl. Mech., 74(1):31–40, 2007. 

128.  J. M. Solberg, R. E. Jones, and P. Papadopoulos. A family of simple two-pass dual formulations for the finite element solution of contact problems. Comp. Meth. Appl. Mech. Eng., 196(4-6):782–802, (2007).

129. R. E. Jones and P. Papadopoulos. A geometric interpretation of frictional contact mechanics. Z. Ang. Math. Phys., 57(6):1025–1041, (2006). [pdf]

130. R. E. Jones and P. Papadopoulos. Simulating anisotropic frictional response using smoothly interpolated traction fields. Comp. Meth. Appl. Mech. Eng., 195(7-8), (2006). [pdf]

131. R. E. Jones and D. A. Zeigler. A method for determining the asperity distribution of contacting rough surfaces. J. Trib., 127(1), (2005). [pdf]

132. Reedy Jr, E. D., M. J. Starr, R. E. Jones, E. E. Flater, and R. W. Carpick. Contact modeling of SAM-coated polysilicon asperities. In Proceedings of the 28th Annual Meeting of the Adhesion Society. Mobile, AL, pp. 13-16. 2005.

133.  J. A. Zimmerman, E. B. Webb, J. J. Hoyt, R. E. Jones, P. A. Klein, and D. J. Bammann. Calculation of stress in atomistic simulation. Mod. Sim. Mat. Sci. Eng., 12(4), (2004). [pdf]

134. Chiesa, Michael L., Reese E. Jones, Kenneth J. Perano, and Tamara G. Kolda. Parallel optimization of forging processes for optimal material properties. In AIP Conference Proceedings, vol. 712, no. 1, pp. 2080-2084. American Institute of Physics, 2004.

135. R. E. Jones. Models for contact loading and unloading of a rough surface. Intl. J. Eng. Sci., 42(17-18):1931–1947, (2004). [pdf]

136.  R. E. Jones and P. Papadopoulos. A novel three-dimensional contact finite element based on smooth pressure interpolations. Intl. J. Num. Meth. Eng., 51(7):791 – 811, (2001). [pdf]

137.  R. E. Jones and P. Papadopoulos.    On the application of a work postulate to frictional contact.  Arch. Mech., 53:275–279, (2001). [pdf]

138.  R. E. Jones and P. Papadopoulos. A yield-limited Lagrange multiplier formulation for frictional contact, Intl. J. Num. Meth. Eng., 48(8):1127 – 49, (2000). [pdf]

139.  P. Papadopoulos, R. E. Jones, and J. M. Solberg. A novel finite-element formulation for frictionless contact problems. Intl. J. Num. Meth. Eng., 38(15): 2603–2617, (1995). [pdf]

140.  P. Papadopoulos and R.E. Jones. On a class of finite elements for frictionless contact problems. In TJR Hughes, E Onate, and OC Zienkiewicz, editors, Recent Developments In Finite Element Analysis, pages 246–254, (1994). [pdf]

and a few of my favorite things ....