Publications (115 peer reviewed articles):

115. N. Arul Murugan*, A. Nordberg, H. Ågren*, Cryptic Sites in Tau Fibrils Explain the Preferential Binding of the AV-1451 PET Tracer toward Alzheimer’s Tauopathy, ACS Chem. Neurosci., 00, 000(2021) (DOI: 10.1021/acschemneuro.0c00340)

114. S. Ganguly, N. Arul Murugan, D. Ghosh, N. Narayanaswamy, T. Govindaraju, and G. Basu, DNA Minor Groove-Induced cis–trans Isomerization of a Near-Infrared Fluorescent Probe, Biochem., 00, 000(2021) (DOI: 10.1021/acs.biochem.1c00281)

113. S. Samanta, V. Rangasami, N. Arul Murugan, O. Varghese, O.Oommen, An unexpected role of an extra phenolic hydroxyl on the chemical reactivity and bioactivity of catechol or gallol modified hyaluronic acid hydrogels, Polymer Chemistry, 12, 2987-2991(2021)

112. Charuvaka Muvva, N. Arul Murugan*, V. Subramanian, Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid beta and Tau proteins using Force-field, Semi-empirical and Density Functional Theory Calculations, Int. J. Mol. Sci., 22, 3244(2021)

111. S. Samanta, K. Rajasekhar, M. Ramesh, N. Arul Murugan, S. Alam, D. Shah, J.P. Clement, T. Govindaraju*, Naphthalene monoimide derivative ameliorates amyloid burden and cognitive decline in a transgenic mouse model of Alzheimer’s disease, Advanced Therapeutics , 4(4), 2000225(2021) (DOI: https://doi.org/10.1002/adtp.202000225)
110. N. Arul Murugan,* Sanjiv Kumar, J. Jeyakanthan, V. Srivastava*, Searching for target-specific and multi-targeting organics for Covid-19 in the Drugbank database with a double scoring approach, Sci. Rep. , 10, 19125(2020)(Highlighted in KTH News and in 20 different news channels worldwide. https://nature.altmetric.com/details/93796744/news)

109. N. Arul Murugan,* Charuvaka Muvva, J.P. Chitra, J. Jeyakanthan, V. Subramanian, Performance of Force-field and Machine Learning Based Scoring Functions in Ranking MAOB Protein-inhibitor Complexes in Relevance to Developing Parkinson’s Therapeutics, Int. J. Mol. Sci., 21(20), 7648(2020)

108. N. Arul Murugan* and Robert Zaleśny*, Multiscale Modeling of Two-Photon Probes for Parkinson’s Diagnostics Based on Monoamine Oxidase B Biomarker, J. Chem. Inf. Model. 60(8), 3854(2020) DOI : 10.1021/acs.jcim.0c00423

107. P.K. Panda, N. Arul Murugan, P. Patel, S.K. Verma, W. Luo, H.-G. Rubahn, Y. K. Mishra, M. Suar, R. Ahuja, Structure-based drug designing and immunoinformatics approach for SARS-CoV-2, Science Advances, 6(28), eabb8097(2020) (DOI: 10.1126/sciadv.abb8097) (Highlighted in Nature India on 28th June, 2020).

106. Y. V. Suseela, P. Satha, N. Arul Murugan, T. Govindaraju, Recognition of G-quadruplex topology through hybrid binding with implications in cancer theranostics, Theranostics, 10, 10394(2020). (doi:10.7150/thno.48675)

105. D. Kang, Y. Sun, N. Arul Murugan, D. Feng, F. Wei, J. Li, X. Jiang, E. D. Clercq, C. Pannecouque, P. Zhan, X. Liu, Structure–Activity Relationship Exploration of NNIBP Tolerant Region I Leads to Potent HIV-1 NNRTIs, ACS Infect. Dis, 6, 2225(2020) (doi:10.1021/acsinfecdis.0c00327)

104. Moustafa Gabr, N. Arul Murugan, Discovery of biphenyl pyrazole scaffold for neurodegenerative diseases: A novel class of acetylcholinesterase-centered multitargeted ligands, Bioorg. Med. Chem. Lett., 30(17), , 127370 (2020)

103. N. Arul Murugan*, J.P. Chitra, J. Jeyakanthan*, Computational investigation on Andrographis paniculata phytochemicals to evaluate their potency against SARS-CoV-2 in comparison to known antiviral compounds in drug trials, J. Biomol. Struc. Dyn., xx, xxxx(2020) (DOI: 10.1080/07391102.2020.1777901)

102. K. Rajasekhar, S. Samanta, V. Bagoband, N. Arul Murugan, T. Govindaraju, Antioxidant berberine-derivative inhibits multifaceted amyloid toxicity, iScience, 23(4), 101005(2020)

101. P. Komala, R. Bappaditya, K. Rajasekhar, Y.V. Suseela, P. Nagendra, A. Chaturvedi, U.R. Satwik, N. Arul Murugan, U. Ramamurty, T. Govindaraju, Molecular Architectonics of Cyclic Dipeptide Amphiphiles and Their Application in Drug Delivery, ACS Appl. Bio Mater., 3(5), 3413–3422(2020).

100. G. Kuang, N. Arul Murugan, Yang Zhou, Agneta Nordberg, and Hans Agren, Computational Insight into the Binding Profile of the Second-Generation PET Tracer PI2620 with Tau Fibrils, ACS Chem. Neurosci.,2020 (DOI: 10.1021/acschemneuro.9b00578)

99. Charuvaka Muvva, N. Arul Murugan, C. Venkata Surya Kumar, V. Subramanian, Unraveling the Unbinding Pathways of Products Formed in Catalytic Reactions Involved in SIRT1–3: A Random Acceleration Molecular Dynamics Simulation Study, J. Chem. Inf. Model., 59, 10, 4100-4115(2019)

98. N. Arul Murugan, Konstantinos, Elena, Laetitia, Hans Ågren, A. Nordberg, Cross-interaction of tau PET tracers with monoamine oxidase B: evidence from in silico modelling and in vivo imaging, Eur. J. Nucl. Med. Mol. Imaging, 46, 1369(2019).

97. A. Grabarz, A. Skotnicka, B. Jedrzejewska, B. Osmialowski, D. Jacquemin, F. Patalas, N. Arul Murugan, W. Bartkowiak, The Impact of the Heteroatom in a Five-Membered Ring on the Photophysical Properties of Difluoroborates, Dyes and Pigments, 170, 107481(2019).

96. D. Kang, H. Zhang, Z. Wang, T. Zhao, T. Ginex, F.J. Luque, Y. Yang, G. Wu, D. Feng, F. Wei, J. Zhang, E. D. Clercq, C. Pannecouque, C.H. Chen, K.-H. Lee, N. Arul Murugan, T.A. Steitz, P. Zhan, X. Liu, Identification of Dihydrofuro[3,4-d]pyrimidine Derivatives as Novel HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors with Promising Antiviral Activities and Desirable Physicochemical Properties, J. Med. Chem., 62(3), 1484(2019).

95. M. Sathish Kumar, N. Arul Murugan*, V. Subramanian*, Hans Ågren*, Destabilization of Amyloid Fibrils on Interaction with MoS2 based Nanomaterials, RSC Adv., 9, 1613(2019).

94. Guanglin Kuang, N. Arul Murugan*, Hans Ågren, Mechanistic insight into the binding profile of DCVJ and α-synuclein fibril revealed by multi-scale simulations, ACS. Chem. Neuro., 10, 610(2019).

93. M. Sathish Kumar*, N. Arul Murugan*, Hans Ågren, Effect of Familial Mutations on the Interconversion of Alpha Helix to Beta Sheet Structures in Amyloid Forming Peptide : Insights from Umbrella Sampling Simulations, ACS. Chem. Neuro., 10, 1347(2019).

92. M. Sathish Kumar, N. Arul Murugan*, Hans Ågren, Free Energy Landscape for Alpha-Helix to Beta-Sheet Interconversion in Small Amyloid Forming Peptide under Nanoconfinement, J. Phys. Chem. B, 122, 9654(2018).

91. N. Arul Murugan*, Robert Zalesny, Hans Ågren, Unusual Binding-Site-Specific Photo-physical Properties of the Benzothiazole-Based Optical Probe in Amyloid Beta Fibrils, Phys.Chem. Chem. Phys. (communications), 20, 20334 (2018).

90. N. Arul Murugan*, Agneta Nordberg, Hans Ågren, Different Positron Emission Tomography Tau Tracers Bind to Multiple Binding Sites on the Tau Fibril: Insight from Computational Modeling, ACS Chemical Neuroscience, 9, 1757 (2018) (An ACS Editors’ Choice article).

89. S. Osella, Florent Di Meo, N. Arul Murugan, G. Fabre, M. Ameloot, P. Trouillas, S. Knippenberg, Combining (Non)linear Optical and Fluorescence Analysis of DiD To Enhance Lipid Phase Recognition , J. Chem Theory Comput., 14, 5350 (2018)

88. J. Zhang, N. Arul Murugan, Y. Tian, C. Bertagnin, Z. Fang, D. Kang, X. Kong, H. Jia, Z. Sun, R. Jia, P. Gao, V. Poongavanam, A. Loregian, W. Xu, X. Ma, X. Ding, B. Huang, P. Zhan, X. Liu, Structure-Based Optimization of N-Substituted Oseltamivir Derivatives as Potent Anti-Influenza A Virus Agents with Significantly Improved Potency against Oseltamivir-Resistant N1-H274Y Variant, J. Med. Chem., 61, 9976(2018).

87. J. Zhang, V. Poongavanam, D. Kang, C. Bertagnin, H. Lu, X. Kong, H. Ju, X. Lu, P. Gao, Y. Tian, H. Jia, S. Desta, X. Ding, L. Sun, Z. Fang, B. Huang, X. Liang, R. Jia, X. Ma, W. Xu, N. Arul Murugan, A. Loregian, B. Huang, P. Zhan, X. Liu, Optimization of N-Substituted Oseltamivir Derivatives as Potent Inhibitors of Group-1 and -2 Influenza A Neuraminidases, Including a Drug-Resistant Variant, J. Med. Chem., 61, 6379(2018)

86. V. Poongavanam, M. Vanangamudi, V. Namasivayam, H. Shamaileh, R. N. Veedu, J. Kihlberg, N. Arul Murugan, Integrative Approaches in HIV-1 Non-nucleoside Reverse Transcriptase Inhibitors Design, WIREs Computational Molecular Science, 8(1), 1-26(2018)

85. Y. K. Mishra, N. Arul Murugan, J. Kotakoski, J. Adam, Progress in Electronics and Photonics with Nanomaterials, Vacuum: E-MRS Fall 2016 speacial issue, 146, 304- 307(2017).

84. J. Bednarska, R. Zalesny, G. Tian, N. Arul Murugan, Hans Ågren and W. Bartkowiak, Nonempirical Simulations of Inhomogeneous Broadening of Electronic Transitions in Solution: Predicting Band Shapes in One- and Two-Photon Absorption Spectra of Chalcones, Molecules, 22(10), 1643(2017).

83. K. Balamurugan, N. Arul Murugan, B. Långström, A. Nordberg, H. Ågren, Effect of Alzheimer Familial Chromosomal Mutations on the Amyloid Fibril Interaction with Different PET Tracers- Insight from Molecular Modeling Studies, ACS Chemical Neuroscience, 8(12), 2655(2017).

82. S. Manchineella, N. Arul Murugan, T. Govindaraju, Cyclic Dipeptide-based Ambidextrous Supergelators: Minimalistic Rational Design, Structure-Gelation Studies and In Situ Hydrogelation, Biomacromolecules, 18(11), 3581(2017).

81. K. Rajasekhar, N. Naryanaswamy, N. Arul Murugan, K. Viccaro, H.-G. Lee, K. Shah, T. Govindaraju, Aβ plaque-selective NIR fluorescence probe to differentiate Alzheimer’s disease from tauopathies, Biosensors and Bioelectronics, 98, 54-61(2017).

80. Md. Ashaduzzaman, S.R. Deshpande, N. Arul Murugan, Y.K. Mishra, A.P.F. Turner, A. Tiwari, On/off-switchable LSPR nano-immunoassay for troponin-T, Scientific Reports, 7, 44027(2017).

79. L.J. Aaldering, V. Poongavanam, N. Langkjaer, N. Arul Murugan, P.T. Jorgensen, J. Wengel, R.N. Veedu, Development of an efficient G-quadruplex stabilized thrombin binding aptamer containing 3-carbon space, ChemBioChem, 18, 755-763(2017)

78. A.O. Osikoyaa, O. Parlak, N. Arul Murugan, E.D. Dikio, H. Moloto, L. Uzun, A.P.F. Turner, A. Tiwari, Acetylene-sourced CVD-synthesised catalytically active graphene for electrochemical biosensing, Biosensors and Bioelectronics, 89(1), 496-504(2017).

77. N.K. Jena, Å. L. Lyne, N. Arul Murugan, H. Ågren, B. Birgisson, Atomic level simulations of the interaction of asphaltene with quartz surfaces: Role of chemical modifications and aqueous environment, Materials and Structures, 50(1), 2017.

76. S. Osella, N. Arul Murugan, N.K. Jena, S. Knippenberg, An Investigation into Biological Environments through (Non)Linear Optics: a Multiscale Study of Laurdan Derivatives, J. Chem. Theory Comput., 12, 6169-6181(2016).

75. N. Arul Murugan*, C. Halldin, A. Nordberg, B. Långström, H. Ågren, The culprit is in the cave: The core sites explain the binding profiles of amyloid specific tracers, J. Phys. Chem. Letters, 7(17), 3313-3321(2016).

74. K. Balamurugan, N. Arul Murugan, H. Ågren, A Multistep Modeling Strategy to Improve the Binding Affinity Prediction of PET Tracers to Amyloid Aβ42: A Case Study with Styrylbenzoxazole Derivatives, ACS Chemical Neuroscience, 7(12), 1698-1705(2016).

73. M. Chattopadhyaya, N. Arul Murugan, Z. Rinkevicius, The Origin of the Absorption Band of Bromophenol Blue in Acidic and Basic pH: Insight from a Combined Molecular Dynamics and TD-DFT/MM Study, J. Phys. Chem. A, 120(36), 7175-7182(2016).

72. H.K. Patra, Y. Sharma, M. Islam, M.J. Jafari, N. Arul Murugan, H. Kobayashi, A.P.F. Turner, A. Tiwari, Inflammation-sensitive in situ smart scaffolding for regenerative medicine, Nanoscale, 8, 17213-17222(2016).

71. J. Bednarska, R. Zaleśny, N. Arul Murugan, W. Bartkowiak, H. Ågren, M. Odelius, Elucidating the mechanism of Zn2+ sensing by bipyridine probe based on two-photon absorption, J. Phys. Chem. B, 120(34), 9067-9075(2016).

70. K. Rajasekhar, N. Naryanaswamy, N. Arul Murugan, G. Kuang, H. Ågren, T. Govindaraju, A High Affinity Red Fluorescent and Colorimetric Probe for Amyloid Aggregation, Scientific Reports, 6, 23668(2016).

69. R. Zalesny, N. Arul Murugan, G. Tian, M. Medved, and H. Ågren, First-Principles Simulations of One- and Two-Photon Absorption Band Shapes of the Bis(BF2) Core Complex, J. Phys. Chem. B, 120(9), 2323-2332(2016).

68. S. Awasthi, N. Arul Murugan, N.T. Saraswathi, Advanced Glycation End Products Modulate Structure and Drug Binding Properties of Albumin, Mol. Pharmaceutics, 12 (9), 3312-3322(2015).

67. G. Kuang, N. Arul Murugan*, Y. Tu, A. Nordberg, H. Ågren, Investigation of the Binding Profiles of AZD2184 and Thioflavin T with Amyloid-β(1-42) Fibril by Molecular Docking and Molecular Dynamics Methods, J. Phys. Chem. B, 119(35), 11560-11567 (2015).

66. N.H. List, R. Zalesny, N. Arul Murugan, J. Kongsted, W. Bartkowiak, and H. Ågren, On the Relation Between Nonlinear Optical Properties of Push-Pull Molecules and the Metric of Charge Transfer Excitations, J. Chem. Theory Comput., 11 (9), 4182-4188(2015).

65. Md. Ashaduzzaman, A. A. Antony, N. Arul Murugan, S.R. Deshpande, A.P.F. Turner, A. Tiwari, Studies on an on/off-switchable immunosensor for troponin T, Biosensors and Bioelectronics., 73, 100-107 (2015).

64. T. Suresh, S. Sarveswari, N. Arul Murugan, V. Vijayakumar, P. Iniyavan, A. Srikanth, J.P. Jasinski, Synthesis, spectral characterization and DFT analysis for the validation of 2,6 diaryl -piperidin-4-ones as potential sunscreens and UV filters, J. Molec. Struc., 1099, 560-566(2015)

63. K. Matczyszyn, J. Olesiak-Banska, K. Nakatani, P. Yu, N. Arul Murugan, R. Zalesny, A. Roztoczynska, J. Bednarska, W. Bartkowiak, J. Kongsted, H. Ågren and M. Samoc, One- and Two-Photon Absorption of a Spiropyran/Merocyanine System: Experimental and Theoretical Studies, J. Phy. Chem. B, 119, 1515-1522(2015).

62. R. Zalesny, N. Arul Murugan, F. Gel’mukhanov, Z. Rinkevicius, B. Osmialowski, W. Bartkowiak and H. Ågren, Towards Fully Nonempirical Simulations of Optical Band Shapes Of Molecules in Solution: A Case Study of Heterocyclic Ketoimine Difluoroborates, J. Phy. Chem. A, 119, 5145-5152(2015).

61. S. K. Mudedla, E. R. A. Singam, J. Vijay Sundar, M. N. Pedersen, N. Arul Murugan, J. Kongsted, H. Ågren, S. Subramanian, Enhancement of Internal Motions of Lysozyme by the Interaction of Gold Nano Cluster and Its Optical Imaging, J. Phy. Chem. C, 119, 653(2015).

60. S. Sarveswari, A. Srikanth, N. Arul Murugan, V. Vijayakumar, J.P. Jasinski, H. C. Beauchesne, E. E. Jarvis, Synthesis, characterization of (3E)-1-(6-chloro-2-methyl-4-phenyl quinolin-3-yl)-3-aryl prop-2-en-1-ones through IR, NMR, single crystal X-RAY diffraction and insights into their electronic structure using DFT calculations , Spectrochimica Acta, 136, 1010(2015).

59. N. Arul Murugan*, R. Zaleśny, J. Kongsted, A. Nordberg, H. Ågren, Promising two-photon probes for in-vivo detection of β amyloid deposits. Chem. Commun., 50, 11694(2014).

58. N. Arul Murugan*, Sigurd Schrader and H. Ågren, Role of Protonation State and Solvation on the pH Dependent Optical Properties of Bromocresol Green, J. Chem. Theory Comput., 10 (9), 3958(2014).

57. I. Harczuk, N. Arul Murugan, O. Vahtras, H. Ågren, Studies of pH-sensitive optical properties of the deGFP1 green fluorescent protein using a unique polarizable force field. J. Chem. Theory Comput., 10 (8), 3492(2014).

56. N. Arul Murugan*, Solvatochromism in a Pyridinium Cyclopentadienylide Studied Using a Sequential Car-Parrinello QM/MM and TD-DFT/semicontinuum approach. J. Phy. Chem. B, 118 (26), 7358(2014).

55. Thomas Hede, N. Arul Murugan, J. Kongsted, C. Leck and H. Ågren, Simulations of light absorption of carbon particles in nanoaerosol clusters. J. Phy. Chem. A, 118, 1879(2014).

54. D.L. Silva, N. Arul Murugan, J. Kongsted, H. Ågren, S. Canuto, Self-aggregation and optical behavior of stilbazolium merocyanine in chloroform. J. Phy. Chem. B, 118, 1715(2014).

53. N. Arul Murugan*, R. Zaleśny, J. Kongsted and H. Ågren, Chelation-induced quenching of two-photon absorption properties of azacrown ether substituted distyryl benzene for metal ion sensing, J. Chem. Theory Comput., 10(2), 778(2014).

52. A.R. Pavankumar, R. Kayathri, N. Arul Murugan, Q. Zhang, H. Ågren, G. K. Rajarao, Experimental evidence for dimerization of flocculent protein from Moringa Oleifera seed and its in-silico interpretation. J. Biomol. Struct. Dyn., 32 (3), 406(2014).

51. Naresh Kumar Jena and N. Arul Murugan*, Solvent Dependent Shuttle Dynamics of[2]Rotaxane Molecule: A Molecular Dynamics Perspective, J. Phy. Chem. C, 117(47), 25059(2013).

50. J. Olesiak-Banska, K. Matczyszyn, R. Zalesny, N. Arul Murugan, J. Kongsted, H. Ågren, W. Bartkowiak, and M. Samoc, Revealing Spectral Features in the Two-Photon Absorption Spectrum of the Hoechst 33342 dye: A Combined Experimental and Quantum-Chemical Study. J. Phy. Chem. B, 117(40), 12013(2013).

49. N. Arul Murugan, R. Apostolov, Z. Rinkevicius, J. Kongsted, Erik Lindahl and H. Ågren, Association dynamics, linear and non-linear optical properties of an N-acetylaladanamide probe in a POPC membrane. J. Am. Chem. Soc., 135 (36), 13590(2013).

48. M. Wielgus, R. Zalesny, N. Arul Murugan, J. Kongsted, H. Ågren, M. Samoc, W. Bartkowiak, Two-photon solvatochromism. II. Experimental and theoretical study of solvent effects on the two-photon absorption spectrum of Reichardt’s dye. Chem. Phys. Chem., 14, 3731(2013).

47. C. Okoli, S. Selvaraj, N. Arul Murugan, A.R. Pavankumar, H. Ågren, G. K. Rajarao, In- silico modeling and experimental evidences of coagulant protein interaction with precursors for nanoparticle functionalization. J. Biomol. Struct. Dyn., 31(10), 1182(2013).

46. N. Arul Murugan*, J. Kongsted and H. Ågren, pH induced modulation in one and two photon absorption properties of a napthalene based probe. J. Chem. Theory Comput., 9(8), 3660(2013).

45. Boris F. Minaev, N. Arul Murugan and H. Ågren, Dioxygen Spectra and Bioactivation. Int. J. Quant. Chem., 113(14), 1847(2013).

44. B. Frecus, Z. Rinkevicius, N. Arul Murugan, O. Vahtras, J. Kongsted and H. Ågren, EPR spin Hamiltonian parameters of encapsulated spin-labels: Impact of the hydrogen bonding topology. Phys. Chem. Chem. Phys., 15, 2427(2013).

43. N. Arul Murugan*, Magnus, J. Kongsted, Z. Rinkevicius, K. Aidas and H. Ågren, Amyloid fibril induced structural and spectral modifications in Thioflavin-T optical probe. J. Phys. Chem. Lett., 4, 70(2013).

42. C. Mausumi, N. Arul Murugan, Alam. Md. Mehboob, S. Chakrabarti, Spatial spin-charge separation in neutral endohedral metallofullerene: A combined restricted open-shell MP2 and Car-Parrinello molecular dynamics study. Chem. Phys. Lett., 557, 71(2013).

41. J. Niskanen, N. Arul Murugan, Z. Rinkevicius, O. Vahtras, C. Li, S. Monti, V. Carravetta and H. Ågren, Hybrid density functional – molecular mechanics calculations for core-electron binding energies of glycine in water solution. Phys. Chem. Chem. Phys., 15, 244(2013).

40. N. Arul Murugan*, I. Dasgupta, A. Chakraborthy, N. Ganguly, J. Kongsted, and H. Ågren, How crucial are the finite-temperature and solvent effects on structure and absorption spectra of Si10 cluster. J. Phys. Chem. C, 116, 26618(2012).

39. A.R.K. Selvaraj*, N. Arul Murugan* and H. Ågren*, Solvent Polarity Induced Conformational Unlocking of Asparagine. J. Phys. Chem. A, 116, 11702(2012).

38. Xin Li, Z. Rinkevicius, J. Kongsted, N. Arul Murugan and H. Ågren, Binding Mechanism and Magnetic Properties of Spin Labels for Targeted EPR Imaging of Amyloid Proteins: Insight from Atomistic First-Principles Calculations. J. Chem. Theory Comput., 8, 4766(2012).

37. D. L. Silva*, N. Arul Murugan, J. Kongsted, Z. Rinkevicius, S. Canuto and H Ågren, The role of molecular conformation and polarizable embedding for one- and two-photon absorption of disperse orange 3 in solution. J. Phys. Chem. B, 116(28), 8169(2012).

36. N. Arul Murugan*, K. Aidas, J. Kongsted, Z. Rinkevicius and H. Ågren, NMR spin- spin coupling constants in a polymethine dye as polarity indicators. Chem. Eur. J., 18, 11677(2012).

35. M. Rovira-Esteva*, N. Arul Murugan, L. C. Pardo, S. Busch, J. Ll. Tamarit, G. J. Cuello, and F.J. Bermejo, Are the differences in first neighbor orientation behind the anomalies in the low and high density trans-1,2-dichloroethene liquid? J. Chem. Phys., 136, 124514(2012).

34. S. Selvaraj, N. Arul Murugan* and H. Ågren, Al3+ induced planarization, conformational arrest and metallochromic shift in a pyrimidine dione dye: Insight from integrated quantum-classical simulations. Phys. Chem. Chem. Phys., 14, 2339(2012).

33. Z. Rinkevicius*, B. Frecus, N. Arul Murugan, J. Kongsted, O. Vahtras, and H. Ågren, Encapsulation influence on EPR parameters of spin-labels: 2,2,6,6-tetramethyl-4-methoxypiperidine- 1-oxyl in cucurbit[8]uril. J. Chem. Theory Comput., 8, 257(2012).

32. N. Arul Murugan*, J. Kongsted, Z. Rinkevicius, and H. Ågren, Color modeling of protein optical probes. Phys. Chem. Chem. Phys. (Communication), 14, 1107(2012).

31. Z. Rinkevicius, N. Arul Murugan, J. Kongsted, F. Bogdan, A. Steindal and H. Ågren, Density functional restricted-unrestricted/molecular mechanics theory for hyperfine coupling constants of molecules in solution. J. Chem. Theory Comput., 7, 3261(2011).

30. M. Rovira-Esteva*, N. Arul Murugan, L. C. Pardo, S. Busch, J. Ll. Tamarit, G. J. Cuello, and F.J. Bermejo, Interplay of intramolecular and intermolecular structure of 1,1,2,2- tetrachloro-1,2-difluoroethane. Phys. Rev. B, 84, 064202(2011).

29. N. Arul Murugan*, J. Kongsted, Z. Rinkevicius, K. Aidas, K. V. Mikkelsen and H. Ågren, Hybrid density functional - molecular mechanics calculations of two-photon absorption of dimethylamino nitro stilbene in solution. Phys. Chem. Chem. Phys., 13, 12506(2011).

28. Z. Rinkevicius*, N. Arul Murugan, J. Kongsted, K. Aidas and H. Ågren, A density functional theory/molecular mechanics approach for electronic g-tensors of solvated molecules. J. Phys. Chem. B, 115, 4350(2011).

27. N. Arul Murugan*, S. Chakrabarti and H. Ågren, Solvent Dependence of Structure, Charge Distribution and Absorption Spectrum in the Photochromic Merocyanine-Spiropyran Pair. J. Phys. Chem. B, 115, 4925(2011).

26. N. Arul Murugan*, Modeling solvatochromism of a quinolinium betaine dye in water solvent using sequential hybrid QM/MM and semicontinuum approach. J. Phys. Chem. B, 115, 1056(2011).

25. N. Arul Murugan*, J. Kongsted, Z. Rinkevicius and H. Ågren, Demystifying the solvatochromic reversal in Brooker’s merocyanine dye. Phys. Chem. Chem. Phys (Communications), 13, 1290(2011). (Selected for ”Editor’s Choice: Theoretical and Computational Chemistry”)

24. N. Arul Murugan*, Z. Rinkevicius and H. Ågren, Modeling of solvatochromism of Nile red in water. Int. J. Quant. Chem, 111, 1521(2011).

23. N. Arul Murugan*, J. Kongsted, Z. Rinkevicius, K. Aidas and H. Ågren, Modeling the structure and absorption spectra of stilbazolium merocyanine in polar and nonpolar solvents using hybrid QM/MM techniques. J. Phys. Chem. B, 114(32), 13349(2010).

22. N. Arul Murugan, J. Kongsted, Z. Rinkevicius and H. Ågren*, Break-down of the ”first hyperpolarizability/ bond-length alternation parameter relationship. Proc. Natl. Acad. Sci. USA, 107 (38) 16453(2010).

21. N. Arul Murugan*, P.C. Jha, Z. Rinkevicius, K. Ruud and H. Ågren, Modeling of solvatochromism of phenol blue in water using hybrid-QM/MM and Zindo calculation. J. Chem. Phys., 132, 234508(2010). (This article has been selected for Virtual Journal of Biological Physics Research, Volume 20, Issue 1, July 1, 2010)

20. M. Rovira-Esteva*, N. Arul Murugan, L. C. Pardo, S. Busch, M. D. Ruiz-Martin, M.-S. Appavou, J. Ll. Tamarit, C. Smuda, T. Unruh, F. J. Bermejo, G. J. Cuello, and S. J. Rzoska, Microscopic structures and dynamics of high- and low-density liquid trans-1,2- dichloroethylene. Phys. Rev. B. (Brief reports), 81, 092202(2010)

19. N. Arul Murugan* and A. Sayeed, Thermal behavior of disordered phase of caffeine molecular crystal: A variable shape Monte Carlo simulation study. J. Chem. Phys., 130, 204514(2009).

18. N. Arul Murugan*, P.C. Jha and H. Ågren, Solvation shell structure of cyclooctylpyranone in water solvent and its comparative structure, dynamics and dipole moment in HIV Protease. Phys. Chem. Chem. Phys., 3, 508(2009). (This article has been selected for Highlights in Chemical Biology: Research Articles, issue 9, 2009)

17. N. Arul Murugan* and P.C. Jha, Pressure dependence of crystal structure and molecular packing in anthracene. Molecular Physics, 107, 1689(2009).

16. N. Arul Murugan*, Z. Rinkevicius and H. Ågren, Solvent Dependence on Bond Length Alternation and Charge Distribution in Phenol Blue: A Car-Parrinello Molecular Dynamics Investigation. J. Phys. Chem. A. (Letter), 113, 4833(2009).

15. N. Arul Murugan* and H. Ågren, 1,2-Dichloroethane in Haloalkane Dehalogenase Protein and in Water Solvent: A Case Study of the Confinement Effect on Structural and Dynamical Properties. J. Phys. Chem. B. (Letter), 113, 3257(2009).

14. N. Arul Murugan* and H. Ågren, Role of Dynamic Flexibility in Computing Solvatochromic Properties of Dye-Solvent Systems: o-Betaine in Water. J. Phys. Chem. A., 113, 2572(2009).

13. N. Arul Murugan* and H. Hugosson, Solvent Dependence of Conformational Distribution, Molecular Geometry, and Electronic Structure in Adenosine. J. Phys. Chem. B., 113, 1012(2009).

12. K. J. de Almeida, N. Arul Murugan*, Z. Rinkevicius, H. Hugosson, O. Vahtras, H. Ågren and Amary Cesar, Conformations, structural transitions and visible near-infrared absorption spectra of four-, five- and six-coordinated Cu(II) aqua complexes. Phys. Chem. Chem. Phys., 3, 508(2009).

11. N. Arul Murugan*, H. Hugosson and H. Ågren, Solvent Dependence on Conformational Transition, Dipole Moment, and Molecular Geometry of 1,2-Dichloroethane: Insight from Car-Parrinello Molecular Dynamics Calculations. J. Phys. Chem. B. (Letter), 112, 14673(2008).

10. N. Arul Murugan* and H. Hugosson, Investigations into conformational transitions and solvation structure of a 7-piperidino-5,9-methanobenzo[8] annulene in water. Phys. Chem. Chem. Phys., 40, 6135(2008).

9. N. Arul Murugan*, What does pressure decide to cook with orientationally disordered plastic phase of cubane molecular crystal: an orientational glass or crystal? J. Chem. Phys., 123, 244514(2005).

8. N. Arul Murugan*, Temperature induced dynamical conformational disorder in 4-vinyl benzoic acid molecular crystals: A Monte Carlo simulation study. J. Chem. Phys., 123, 094508(2005).

7. N. Arul Murugan*, Orientational melting and reorientational motion in cubane molecular crystal: a molecular simulation study. J. Phys. Chem. B., 109, 23955(2005).

6. N. Arul Murugan, S. Yashonath*, R.S.Rao, S. Ramasesha and B.K.Godwal, High pressure study of adamantane: variable shape simulations up to 26 GPa. J. Phys. Chem. B., 109, 17296(2005).

5. N. Arul Murugan and S. Yashonath*, Effect of pressure on pedal motion in stilbene molecular crystals and its dependence on crystallographic site. J. Phys. Chem. B., 109, 12107(2005).

4. N. Arul Murugan and S. Yashonath*, Pressure induced orientational ordering in p-terphenyl. J. Phys. Chem. B., 109, 1433(2005).

3. N. Arul Murugan and S. Yashonath*, Pressure Induced Ordering Transition in Adamantane : A Monte Carlo Simulation Study. J. Phys. Chem. B., 109, 2014(2005).

2. N. Arul Murugan and S. Yashonath*, Structure, energetics and dynamics of pedal-like motion in stilbene from molecular simulation and ab initio calculations. J. Phys. Chem. B., 108, 17403(2004).

1. N. Arul Murugan*, P.C. Jha, S. Yashonath and S. Ramasesha, High Pressure phase of biphenyl in room temperature: A Monte Carlo study, J. Phys. Chem. B., 108, 4178(2004).

Book Chapter and edited book:

1. Peptide based antiviral drugs, N. Arul Murugan*, K. Muruga Poopathi Raja*, N.T.Saraswathi, a chapter in a book entitled “Antiviral Drug Discovery and Development”, (Edited by Luis, Nathan and Peng Zhan) Springer Nature, 2020.

2. Recent Advancements in Computing Reliable Binding Free Energies in Drug Discovery Projects, N. Arul Murugan*, V. Poongavanam, D. Priyakumar, in book entitled Structural Bioinformat Applications in Preclinical Drug Discovery Process and edited by Gopi Mohan for Springer Nature, 221-246 (2019)

3. Advanced Engineering Materials and Modeling, Edited by Ashutosh Tiwari, N. Arul Murugan, Rajeev Ahuja, Wiley-Scrivener Publishing, 2016.

Research works appeared in popular news:
• e-Science of importance for Nobel prize: http://www.e-science.se/news/e-science-
importance-nobel-prize
• N. Arul Murugan, Z. Rinkevicius, H. Ågren, Multiscale Modelling in the Material and
Life Sciences (https://www.pdc.kth.se/research/publications/pdc-newsletter)

Citations data (Based on google scholar)::
h-index : 22, i10-index: 65
ResearchGate score : 40.5
Citations as per Google scholar on July, 2020 : ≈1635
Number of publications as first author : 40
Number of publications as senior author / corresponding author: 44
(Papers published as corresponding author are indicated by *)

Murugan Natarajan Arul,
murugan@kth.se

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