Metal-Binding Affinity and Selectivity of Nonstandard Natural Amino Acid Residues from DFT/CDM Calculations,

is now available on the The Journal of Physical Chemistry B website.

http://pubs.acs.org/articlesonrequest/AOR-GciNX8QYwZUjRIapnu9E

108.   Finding Structural Motifs Across Protein Families.                                                                                               

                                     Chih Yuan Wu, Yao Chi Chen & Carmay Lim*, (2010), submitted (01/10).

107. The Scorpion Motif – A Conserved Structural Motif in the Catalytic Domains of PARP and ADPRT

          Families for Binding  NAD+.                                                                                                                                                                                        Yu-Ming Lee & Carmay Lim*, J. Med. Chem. (2010) submitted (01/27).

106.  Arrangement of 3D Structural Motifs in Ribosomal RNA.                                                                                       

                                      Karen Sargsyan & Carmay Lim*, Nucleic Acids Res. (2010) accepted (01/27).

105.  Factors Governing the Na⁺ vs. K⁺ Selectivity in Sodium Ion Channels.                                         

                                      Todor Dudev & Carmay Lim*, J. Am. Chem. Soc. (2010) in press (01/8).                                  (http://pubs.acs.org/articlesonrequest/AOR-UIuisQMwNv78vnDDZ2pw)

104. Redesign of High-Affinity Nonspecific Nuclease with Altered Sequence preference.                                     

                                      Yi-Ting Wang, Jon D. Wright, Lyudmila G. Doudeva, Hua-Ci Jhang, Carmay Lim^* and

                                      Hanna S. Yuan*, J. Am. Chem. Soc. (2009) 131:17345–17353.

103. Metal−Binding Affinity and Selectivity of Rare Natural Amino Acid Residues from DFT/CDM Calculations.

                                      Todor Dudev & Carmay Lim*, J. Phys. Chem. B (2009) 113: 11754–11764.

102.  Determinants of K⁺ vs. Na⁺ Selectivity in Potassium Channels.                                                               

                                      Todor Dudev & Carmay Lim*, J. Am. Chem. Soc. (2009) 131:8092–8101.

101.  A Combined Experimental and Theoretical Study of Long-Range Interactions Modulating Dimerization and Activity of Yeast

        Geranylgeranyl Diphosphate Synthase.                                                                    

                                      Chia-Hsiang Lo, Ying-Hsuan Chang, Jon D. Wright, Shih-Hsun Chen, Daphne Kan, Carmay Lim*,

                                      and Po-Huang Liang*,  J. Am. Chem. Soc. (2009) 131:4051-62. 

100.  Factors Governing Metal–Ligand Bond Distances and Coordination Geometries of Metal Complexes.                                 

                                       Gopi Kupparaj, Minko Dudev & Carmay Lim*, J. Phys. Chem. B (2009) 113:2952–2960.

99.  Strategies to Model the Near–Solute Solvent Molecular Density/Polarization.                     

                                           Pei-Kun Yang & Carmay Lim*, J. Comp. Chem. (2009) doi:10.1002/jcc.21089.

98.  Force Fields Including Charge Transfer and Local Polarization Effects: Application to Proteins Containing Multi/Heavy

      Metal   Ions.                                                                                                                          

                                           Dmitri V. Sakharov & Carmay Lim*, J. Comp. Chem. (2009) 30:191–202.

97.  Common Physical Basis of Macromolecule–Binding Sites in Proteins.                                                                    

                                           Yao Chi Chen & Carmay Lim*, Nucleic Acids Res. (2008) 36:7078-7087.

 96.  Predicting RNA–binding sites on proteins based on electrostatics, evolution, and geometry.                          

                                            Yao Chi Chen & Carmay Lim*, Nucleic Acids Res. (2008) 36(5):e29. 

95.  The Importance of Excluded Solvent Volume Effects in Computing Hydration Free Energies.                                   

                                             Pei-Kun Yang & Carmay Lim*, J. Phys. Chem. B (2008) 112:14863–14868.

94.  Reformulation of Maxwell’s Equations to Incorporate Near–Solute Solvent Structure.                                                      

                                             Pei-Kun Yang & Carmay Lim*, J. Phys. Chem. B (2008), 112: 10791–10794. 

93.  Physical Basis of Structural and Catalytic Zn-binding Sites in Proteins.                                                      

                                             Yu-Ming Lee & Carmay Lim*, J. Mol. Biol. (2008) 379:545–553.

92.  Mononuclear versus Binuclear Metal–Binding Sites: Metal Binding Affinity and Selectivity from PDB Survey and

      DFT/CDM Calculations.         

                                              Tsung-YingYang, Todor Dudev & Carmay Lim^*, J. Am. Chem. Soc. (2008) 130:3844–3852.

91.  Metal Binding Affinity and Selectivity in Metalloproteins: Insights from Computational Studies                            

                                              Todor Dudev & Carmay Lim*, Annual Reviews in Biophysics. (2008) 37:97–116

90.  Mechanisms of DNA–Binding Loss upon Single–Point Mutation in p53.                                                                

                                              Jon D. Wright & Carmay Lim*, J. Biosciences (2007) 32, 827–839. 

89.  All–Electron Calculations of the Nucleation Structures in Metal–Induced Zinc–Finger Folding: Role of the Peptide Backbone.

                                              Todor Dudev & Carmay Lim*, J. Am. Chem. Soc. (2007) 129:12497–12504.

88.  Discovering Structural Motifs Using a Structural Alphabet: Application to Mg–Binding Sites.                    

                                              Minko Dudev & Carmay Lim*, BMC Bioformatics (2007) 8:106–118.

87.  Predicting DNA–Binding Amino Acid Residues from Electrostatic Stabilization upon Mutation to Asp/Glu and

      Evolutionary Conservation.                                                                                                                     

                                              Yao Chi Chen, Chih Yuan Wu & Carmay Lim*, Proteins: Structure, Function &

                                              Bioinformatics (2007) 67: 671−680.

86.  Polarization–Consistent vs Correlation–Consistent Basis Sets in Predicting Molecular and Spectroscopic Properties.             

                                               Teobald Kupka & Carmay Lim*, J. Phys. Chem. A (2007) 111(10): 1927–1932.

85.  Effect of Carboxylate–Binding Mode on Metal Binding/Selectivity and Function in Proteins.                                                        

                                               Todor Dudev & Carmay Lim*, Acc. Chem. Res. (2007) 40: 85−93.

84.  Factors Governing the Metal Coordination Number in Group IA and IIA Metal Hydrates From DFT Calculations.  

                                               Ingvar Tunell & Carmay Lim*, Inorg. Chem. (2006) 45:4811−4819. 

83.  Factors Governing the Metal Coordination Number in Metal Complexes From Cambridge Structure Database Analyses.      

                                               Minko Dudev, Jonathan Wang, Todor Dudev & Carmay Lim*, J. Phys. Chem. B (2006)

                                               110: 1889–1895.

82.  Competition Between Protein Ligands and Cytoplasmic Inorganic Anions for the Metal Cation.                        

                                               Todor Dudev & Carmay Lim*, J. Am. Chem. Soc. (2006) 128, 10541–10548. 

81.  A DFT/CDM Study of Metal–Carboxylate Interactions in Metalloproteins: Factors Governing the Maximum Number of

     Metal–Bound Carboxylates.  

                                               Todor Dudev & Carmay Lim*, J. Am. Chem. Soc. (2006) 128: 1553–1561.

80.  Quantifying Polypeptide Conformational Spaces.                                                                                                                  

                                               David Sullivan* & Carmay Lim*, J. Phys. Chem. B (2006) 110, 16707–16717.

79.  Toward Absolute Density of States Calculation for Proteins.                                                                             

                                               David Sullivan* & Carmay Lim*, J. Phys. Chem. B (2006) 110, 12125–12128.

78.  Computational Studies of the Coordination Stereochemistry, Bonding & Metal Selectivity of Mercury.       

                                               Hui-Chung Tai & Carmay Lim*. J. Phys. Chem. A, Truhlar issue (2006) 110: 452–462.

77.  Empirical Force Fields For Biologically Active Divalent Metal Cations in Water.                                                       

                                                C. Satheesan Babu* & Carmay Lim*, J. Phys. Chem. A, Truhlar issue (2006) 110: 691–699.

76.  Zn Protein Simulations Including Charge Transfer and Local Polarization Effects.                                                              

                                                Dmitri V. Sakharov & Carmay Lim*, J. Am. Chem. Soc. (2005) 127: 4921–4929.

75.  Differential Effects of the Zn–His– [Asp/Glu,Bkb] Triad on Zn–Core Stability and Reactivity.                                              

                                                Yen-lin Lin, Yu-ming Lee & Carmay Lim*, J. Am. Chem. Soc. (2005) 127: 11336–11347. 

74.  Factors Governing the Substitution of La³⁺ for Ca²⁺ and Mg²⁺ in Metalloproteins: A DFT/CDM Study.                                     

                                                Todor Dudev, Li-Ying Chang & Carmay Lim*, J. Am. Chem. Soc. (2005) 127: 4091–4103.

73.  Configurational Entropy of Proteins: Covariance Matrix vs. Cumulative Distribution Calculations.                

                                                David Sullivan & Carmay Lim*, J. Chin. Chem. Soc. (2004) 51: 1209–1219.

72.  Oxyanion Selectivity in Sulfate and Molybdate Transport Proteins: An Ab Initio/CDM Study.                 

                                                 Todor Dudev & Carmay Lim*, J. Am. Chem. Soc. (2004) 126: 10296–10305.

71.  Monodentate vs. Bidentate Carboxylate Binding in Magnesium and Calcium Proteins: What Are the Basic Principles?               

                                                 Todor Dudev & Carmay Lim*, J. Phys. Chem. B (2004) 108: 4546–4557.

70.  Factors Governing the Protonation State of Zn-bound Histidine in Proteins                                     

                                                 Yen-lin Lin & Carmay Lim*, J. Am. Chem. Soc. (2004) 126: 2602–2612.

69.  A Combined Experimental and Theoretical Study of Divalent Metal Ion Selectivity and Function in Proteins. Application to E.

      coli Ribonuclease H1.          

                             C. Satheesan Babu, Todor Dudev, Ruby Casareno, Jimmy A. Cowan & Carmay Lim*,

                                                  J. Am. Chem. Soc. (2003) 125: 9318–9328.

68.  1st–2nd Shell Interactions in Metal Binding Sites in Proteins: A PDB Survey+DFT/CDM Calculations.       

                                                 Todor Dudev, Yen-lin Lin, Minko Dudev & Carmay Lim*, J. Am. Chem. Soc. (2003) 125:

                                                 3168–3180.

67.  Metal Binding and Selectivity in Zinc Proteins.                                                                                                

                                                 Todor Dudev* & Carmay Lim*, J. Chin. Chem. Soc. (2003) 50: 1093–1102.

66.  Principles Governing Mg, Ca, and Zn Binding and Selectivity in Proteins.                                                                  

                                                 Todor Dudev* & Carmay Lim*, Chemical Reviews (2003) 103: 773–787.

65.  Inducing Antigenic Cross–Reactivity against B cells in Mice by Immunizing with Human Iga to Mice.          

                                                 Jim J.C. Sheu, Tammy Cheng, Carmay Lim & Tse Wen Chang*, J. Immunology (2003)

                                                170: 1158–1166.

64.  Nonconvergence of the Solute Potential in an Infinite Solvent & Its Implications in Continuum Models.       

                                                 Pei-Kun Yang & Carmay Lim*, J. Phys. Chem. B (2002) 106: 12093–12096.

63.  Representing an Infinite Solvent System with a Rectangular Finite System Using Image Charges.                 

                                               Pei-Kun Yang, Shu-Huey Liaw & Carmay Lim*, J. Phys. Chem. B (2002) 106: 2973–2982.

62.  On the Charge and Molecule Based Summations of Solvent Electrostatic Potentials and the Validity of Electrostatic

      Linear Response in Water.     

                                               C. Satheesan Babu, Pei-Kun Yang & Carmay Lim*, J. Biol.  Phys. (2002) 28: 95–113.

61.  Factors Governing Intrinsic Chemical Reactivity Differences between Clavulanic & Penicillanic Acids.     

                                               Yen-lin Lin, Nai-yuan Chang & Carmay Lim*, J. Am. Chem. Soc. (2002) 124: 12042–12053.

60.  Long–Range Effects of Mutating R248 to Q/W in the p53 Core Domain.                                             

                                                Sergey Yu Noskov, Jon D. Wright & Carmay Lim*, J. Phys. Chem. B (2002) 106: 13047–13057.

59.  Factors Governing Loss & Rescue of DNA Binding upon Single & Double Mutations in the p53–CD.                                 

                                                Jon D. Wright, Sergey Yu Noskov & Carmay Lim*, Nucleic Acids Res. (2002) 30: 1563–1574.

58.  Factors Governing the Protonation State of Cysteines in Proteins. An Ab Initio/CDM Study.                           

                                               Todor Dudev & Carmay Lim*, J. Am. Chem. Soc. (2002) 124: 6759–6766.

57.  Free Energy Decomposition of Protein–Protein Interactions.                                                            

                                               Sergey Yu Noskov & Carmay Lim*, Biophys. J. (2001) 81: 737–750.

56.  Constructing a Human Membrane & Secreted Protein–Enriched cDNA Library using a Minimal Set of PCR Primers.

                                               Fan Yi, Chih Yuan Wu, Cheng Wei Chen, Tse Wen Chang^* & Carmay Lim*,

                                               Nucleic Acids Res. (2001) 29: e114.

55.  A Fast Method For Predicting Amino Acid Mutations That Lead to Unfolding.                                        

                                               Jon D. Wright & Carmay Lim*, Prot. Engineering (2001) 14: 479–486.

54.  Incorporating Nonlinear Solvent Response in Continuum Dielectric Models Using A Two–Sphere Description of the

      Born Radius.                  

                                                C. Satheesan Babu & Carmay Lim*, J. Phys. Chem. A (2001) 105: 5030–5036.

53.  Solvation Free Energies of Polar Molecular Solutes: Application of the Two–Sphere Born Radius in Continuum Models

      of Solvation.    

                                                C. Satheesan Babu & Carmay Lim*, J. Chem. Phys. (2001) 114: 889–899.

52.  Modeling Zn²⁺-Cysteinate Complexes in Proteins.                                                                   

                                                 Todor Dudev & Carmay Lim*, J. Phys. Chem. B (2001) 105: 10709–10714.

51.  Metal Selectivity in Metalloproteins: Zn²⁺ vs. Mg²⁺.                                                                                 

                                                Todor Dudev & Carmay Lim*, J. Phys. Chem. B (2001) 105: 4446–4452.

50.  Conformational Analysis of Long Spacers in PROSITE Patterns.                                                          

                                                Kuen-Yi Lin, Jon Wright & Carmay Lim*, J. Mol. Biol. (2000) 299: 537–548.

49.  Design, Synthesis, and SAR of Novel Carbapenem Antibiotics with High Stability to Xanthomonas

      maltophilia Oxyiminocephalosporinase Type II.

                                                Gholam H. Hakimelahi*, Ali A. Moosavi-Mohavedi, Shwu-Chen Tsay, Fu-Yuan Tsai,

                                                Jon Wright, Todor Dudev,

                                                Shahram Hakimelahi & Carmay Lim*, J. Med. Chem. (2000) 43: 3632–3640. 

48.  Tetrahedral vs. Octahedral Zinc Complexes with Ligands of Biological Interest: A DFT/CDM Study.                            

                                                 Todor Dudev & Carmay Lim*, J. Am. Chem. Soc. (2000) 122: 11146–11153.

47.  Metal Binding in Proteins: The Effect of the Dielectric Medium.                                                                                     

                                                Todor Dudev & Carmay Lim*, J. Phys. Chem. B (2000) 104: 3692–3694.

46.  Incremental Binding Free Energies In Mg²⁺ Complexes: A DFT Study.                                                                     

                                                Todor Dudev & Carmay Lim*, J. Phys. Chem. A (1999) 103: 8093–8100. 

45.  Competitive Binding in Mg Coordination Chemistry: Water vs Ligands of Biological Interest.                             

                                                Todor Dudev, Jimmy Cowan & Carmay Lim*, J. Am. Chem. Soc. (1999) 121: 7665–7673.

44.  Theory of Ionic Hydration: New Insights from Simulation and Experiment.                                    

                                                C. Satheesan Babu & Carmay Lim*, J. Phys. Chem. B (1999) 103: 7958–7968.

43.  A New Interpretation of the Effective Born Radius from Simulation and Experiment.                              

                                                C. Satheesan Babu & Carmay Lim*, Chem. Phys. Lett. (1999) 310: 225–228.

42.  Ring Strain vs. Solvent Effects in Phosphate Base Hydrolysis.                                 

                                                Carmay Lim, Phosphorus, Sulfur & Silicon (1999) 144–146: 769–773.

41.   Exploring the Dynamic Information Content of a Protein NMR Structure: Comparison of a Molecular Dynamics Simulation with

       the NMR and X–Ray Structures of E. Coli RNase HI.                                                                                                                   

                                                Marios Philippopoulos & Carmay Lim*, Proteins: Structure, Function & Genetics (1999)

                                                36: 87–110.

40.  Prediction of an Anti–IgE Binding Site on IgE.                                                                                   

                                                 Jon Wright & Carmay Lim*, Protein Engineering (1998) 11: 421–427.

39.  Ring Strain Energies from Ab Initio Calculations.                                                                                    

                                                Todor Dudev & Carmay Lim*, J. Am. Chem. Soc. (1998) 120, 4450–4458.

38.  Factors Governing the Enhanced Reactivity of Five–Membered Cyclic Phosphate Esters.                    

                                                Nai-Yuan Chang & Carmay Lim*, J. Am. Chem. Soc. (1998) 120, 2156–2167. 

37.  Protein Dynamics: Molecular Dynamics Simulation, NMR Spectroscopy and X–ray Crystallography.                

                                                 Marios Philippopoulos & Carmay Lim*, Advances in Computational Life Sciences (1998)

                                                 Vol. 2: Humans to Proteins. M. Michalewicz (Ed.), CSIRO Mathematical & Information Sciences 

36.  An ab Initio Study of Nucleophilic Attack of Trimethyl Phosphate.                               

                                                 Nai-Yuan Chang & Carmay Lim*, J. Phys. Chem. A (1997) 101, 8706–8713. 

35.  Accuracy and Precision of NMR Relaxation Experiments and MD Simulations for Characterizing Protein Dynamics.       

                                                Marios Philippopoulos, Arthur Mandel, Arthur G. Palmer III* & Carmay Lim*,

                                                Proteins: Structure, Function, and Genetics (1997) 28, 481–493.

34.  Structural Characterization of the Phosphotyrosine Binding Region of a High Affinity SH2 Domain–Phosphopeptide Complex by

      MD Simulation and Chemical Shift Calculations.                                                                                                        

                                                 Ming-Hsiang Feng, Marios Philippopoulos, Alexander D. MacKerell Jr. & Carmay Lim*,

                                                 J. Am. Chem. Soc. (1996) 118, 11265–11277.

33.  Positive Charge at Position 549 is Essential for Phosphatidylinositol 4,5–Bisphosphate but not Phosphatidylinositol–

      Hydrolyzing Activities of Human Phospholipase Cδ1.                                                                                      

                                                 Li-Ping Wang, Carmay Lim, Y.-S. Kuan, Chih-lin Chen, Hwei-Fang Chen & King Klim*,

                                                J. Biol. Chem. (1996) 271, 24505–24516.

32.  The Binding Mode of an E–64 Analog to the Active site of Cathepsin B.                  

                                                 Ming Hsiang Feng, Shek Ling Chan, YueFang Xiang, Carol P. Huber & Carmay Lim*,

                                                 Protein Engineering (1996) 9, 977–986.

31.  A Commentary on the Relationship Between Continuum Dielectric Theory, and Thermodynamics.       

                                                Shek Ling Chan, Wen Ching Hu & Carmay Lim*, Proceedings of HPC–Asia (1995).

30.  Dynamic Model of Lignin Growing in Restricted Spaces.                                                                     

                                                Marc Roussel & Carmay Lim*, Macromolecules (1995) 28, 370–376.

29.  Discrete, Dynamic Polymer Modeling: A Pseudo–Diatomic Model of Lignin.                              

                                                Marc Roussel & Carmay Lim*, J. Comp. Chem. (1995) 16, 1181–1191.

28.  Identifying the Mechanism of Protein Loop Closure: A Molecular Dynamics Simulation of the Bacillus Stearothermophilus LDH

      Loop in Solution.         

                                                 Marios Philippopoulos, YueFang Xiang & Carmay Lim*, Protein Engineering (1995) 8, 565–573.

27.  Molecular Dynamics Simulation of E. Coli Ribonuclease HI in Solution: Correlation with NMR and X–ray Data and Insights

      into Biological Function.    

                                                 Marios Philippopoulos & Carmay Lim*, J. Mol. Biol. (1995) 254, 771–792.

26.  Solution Free Energies from a Combined Quantum Mechanical & Continuum Dielectric Approach.     

                                                 Carmay Lim*, Shek Ling Chan & Philip Tole, in ACS Symposium Series No. 568: Structure

                                                 and Reactivity in Aqueous Solution. C.J. Cramer & G.D. Truhlar (editors), American

                                                 Chemical Society (1994).

25.  Computational Approaches to the Blood Substitute Problem.                                                               

                                                  Shek Ling Chan & Carmay Lim*, Chemistry (1994) 52, 261–268.

24.  Conformational Distribution of a Tetrapeptide in Solution Using a Combined Random Search and Continuum

      Dielectric Approach.      

                                                  Shek Ling Chan & Carmay Lim*, J. Phys. Chem. (1994) 98, 12805–12814. 

23.   Reducing the Error due to the Uncertainty in the Born Radius in Continuum Dielectric Calculations.                                      

                                                  Shek Ling Chan & Carmay Lim*, J. Phys. Chem. (1994) 98, 692–695.

22.  Internal Motions in the Molecular Tumbling Regime: Effect on NMR Dipolar Cross–relaxation and Interproton

      Distance Determination.      

                                                  Marios Philippopoulos & Carmay Lim*, J. Phys. Chem. (1994) 98, 8264–8273.

21.  The Double Catalytic Triad, Cys25–His159–Asp158 and Cys25–His159–Asn175, in Papain Catalysis: Role of Asp158

      and Asn175.      

                                                  Jing Wang, YueFang Xiang & Carmay Lim*, Protein Engineering (1994) 7, 75–82.

20.  The Significance of Electrostatic Effects in Phospho–Ester Hydrolysis.                              

                                                  Philip Tole & Carmay Lim*, J. Am. Chem. Soc. (1994) 116, 3922–3931.

19.  Simulation Analysis of the Binding Interactions in the RNase A/3’–UMP Enzyme–Product Complex as a Function of pH.     

                                                  John Straub, Carmay Lim & Martin Karplus*, J. Am. Chem. Soc. (1994) 116, 2591–2599.

18.  Do Stereoelectronic Effects Control the Structure and Reactivity of TBP Phosphoesters?                     

                                                  Philip Tole & Carmay Lim*, in ACS Symposium Series No. 539: The Anomeric Effect and

                                                  Associated Stereoelectronic Effects.  G.R. Thatcher (ed.), Am. Chem. Soc. (1993).

17.  New Insights into the Base–Catalyzed Hydrolysis of Methyl Ethylene Phosphate.                       

                                                  Philip Tole & Carmay Lim*, J. Phys. Chem. (1993) 97, 6212–6219.

16.  Concerted Hydroxyl Ion Attack and Pseudorotation in a Quantum Mechanical Study of Methyl Ethylene Phosphate Hydrolysis.       

                                                  Carmay Lim* & Philip Tole, J. Phys. Chem. (1992) 96, 5217–5218.

15. Endocyclic and Exocyclic Cleavage of Phosphorane Monoanion: A Detailed Mechanism of the RNase A

     Transphosphorylation Step.    

                                                   Carmay Lim* & Philip Tole, J. Am. Chem. Soc. (1992) 114, 7245–7252.

14.  Absolute pKa Calculations with Continuum Dielectric Methods.                                                        

                                                   Carmay Lim, Don Bashford & Martin Karplus*, J. Phys. Chem. (1991) 95, 5610–5620.

13.  Dianionic Pentacoordinate Species in the Base–Catalyzed Hydrolysis of Ethylene and Dimethyl Phosphate.

                                                    Annick Dejaegere, Carmay Lim & Martin Karplus*, J. Am. Chem. Soc. (1991) 113, 4353–4355.

12.  Nonexistence of Dianionic Pentacovalent Intermediates in an ab Initio Study of the Base–Catalyzed Hydrolysis of

      Ethylene Phosphate.     

                                                    Carmay Lim & Martin Karplus*, J. Am. Chem. Soc. (1990) 112, 5872–5873.

11.  Simulation Analysis of Structures on the Reaction Pathway of RNase A.                                      

                                                    Karen Haydock, Carmay Lim, Axel Brünger & Martin Karplus*, J. Am. Chem. Soc. (1990)

                                                   112, 3826–3831.

10.  Molecular and Harmonic Dynamics Simulations of Proteins.                                                

                                                    Carmay Lim, Dzung Nguyen, John Straub, Bruce Tidor & Martin Karplus, John von

                                                    Neumann National  Supercomputer Center, Annual Research Report (1988).

9.      Trajectory Studies of Hyperthermal Xenon Scattering from GaAs (110).                              

                                                    Carmay Lim, John C. Tully, Aviv Amirav, Paula Trevor & Mark J. Cardillo, J. Chem.

                                                     Phys. (1987) 87, 1808–1816.

8.      Atom–surface Scattering Dynamics at Hyperthermal Energies.                                                

                                                    Aviv Amirav, Mark J. Cardillo, Paula Trevor, Carmay Lim & John C. Tully, J. Chem.

                                                   Phys. (1987) 87, 1796–1807.

7.      Molecular Dynamics of Nonequilibrium Infrequent Events: Laser–induced Desorption from Surfaces.          

                                                    Carmay Lim & John C. Tully, J. Chem. Phys. (1986) 85, 7423–7433.

6.      The Effect of Vibrational–Rotational Disequilibrium on the Rate Constant for an Atom–Transfer Reaction.     

                                                     Carmay Lim & Donald G. Truhlar*, J. Phys. Chem. (1986) 90, 2616–2634.

5.      New Techniques for the Study of Nonequilibrium Effects in Non–First–Order Systems.                             

                                                     Carmay Lim & Donald G. Truhlar, Chem. Phys. Lett. (1985) 114, 253–257.

4.      Internal–state Nonequilibrium Effects for a Fast, Second–Order Reaction.                                          

                                                     Carmay Lim & Donald G. Truhlar*, J. Phys. Chem. (1985) 89, 5–7.

3.      Study of Mixture Effects in the Nonequilibrium Kinetics of Homonuclear Diatomic Dissociation and Recombination.      

                                                     Carmay Lim & Donald G. Truhlar*, J. Phys. Chem. (1984) 88, 778–792.

2.      Nonequilibrium Effects in Chemical Kinetics: Straight–Line Paths for Homonuclear Diatomic Dissociation–

      Recombination Process.      

                                                     Carmay Lim & Donald G. Truhlar*, J. Phys. Chem. (1983) 81, 2683–2699.

1.      The Existence of Straight–Line Paths, Invariant Vectors, and Invariant Tensors Characterizing Nonequilibrium State

      Distributions during Chemical  Reactions.     

                                                     Carmay Lim & Donald G. Truhlar, J. Chem. Phys. (1983) 79, 3296–3306.