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Selected Publications
  1. Size-dependent conformational features of Abeta(17-42) protofilaments from molecular simulation studies
    P. Khatua, S. K. Sinha and S. Bandyopadhyay, J. Chem. Inf. Model. **, 00000 (2017).

  2. Sensitivity of folding free energy landscapes of trpzips to mutations in the hydrophobic core
    M. Gupta, P. Khatua, C. Chakravarty and S. Bandyopadhyay, Phys. Chem. Chem. Phys. 19, 22813-22825 (2017).

  3. Interfacial water arrangement in the ice-bound state of an antifreeze protein: A molecular dynamics simulation study
    U. S. Midya and S. Bandyopadhyay, Langmuir 33, 5499-5510 (2017).

  4. Water structure around hydrophobic amino acid side chain analogs using different water models
    T. Hajari and S. Bandyopadhyay, J. Chem. Phys. 146, 225104 (2017).

  5. In-silico studies of the early stages of aggregation of Abeta-42 peptides
    P. Khatua and S. Bandyopadhyay, J. Chem. Sci. 129, 899-909 (2017).

  6. Conformational features of Abeta-42 peptide monomer and its interaction with surrounding solvent
    P. Khatua, J. C. Jose, N. Sengupta and S. Bandyopadhyay, Phys. Chem. Chem. Phys. 18, 30144-30159 (2016).

  7. Comparison of hydration behavior and conformational preferences of Trp-cage mini-protein in different rigid-body water models
    M. Gupta, D. Nayar, C. Chakravarty and S. Bandyopadhyay, Phys. Chem. Chem. Phys. 18, 32796-32813 (2016).

  8. Sensitivity of protein glass transition to the choice of water model
    M. Gupta, C. Chakravarty and S. Bandyopadhyay, J. Chem. Theory Comput. 12, 5643-5655 (2016).

  9. Exploring ion induced folding of a single-stranded DNA oligomer from molecular simulation studies
    K. Chakraborty, P. Khatua and S. Bandyopadhyay, Phys. Chem. Chem. Phys. 18, 15899-15910 (2016).

  10. Thermodynamics of complex structures formed between single-stranded DNA oligomers and the KH domains of the far upstream element binding protein
    K. Chakraborty, S. K. Sinha and S. Bandyopadhyay, J. Chem. Phys. 144, 205105 (2016).

  11. Effect of protein-DNA complex formation on the intermolecular vibrational density of states of interfacial water
    K. Chakraborty and S. Bandyopadhyay, Phys. Chem. Chem. Phys. 18, 7780-7788 (2016).

  12. Excess entropy and crystallization in Stillinger-Weber and Lennard-Jones fluids
    D. Dhabal, A. H. Nguyen, M. Singh, P. Khatua, V. Molinero, S. Bandyopadhyay and C. Chakravarty, J. Chem. Phys. 143, 164512 (2015).

  13. Dynamics of water around the complex structures formed between the KH domains of Far Upstream Element binding protein and single-stranded DNA molecules
    K. Chakraborty and S. Bandyopadhyay, J. Chem. Phys. 143, 045106 (2015).

  14. Correlated conformational motions of the KH domains of Far Upstream Element binding protein complexed with single-stranded DNA oligomers
    K. Chakraborty and S. Bandyopadhyay, J. Phys. Chem. B 119,10998-11009 (2015).

  15. Microscopic dynamics of water around unfolded structures of barstar at room temperature
    S. Pal, K. Chakraborty, P. Khatua and S. Bandyopadhyay, J. Chem. Phys. 142, 055102 (2015).

  16. Effect of temperature on the low-frequency vibrational spectrum and relative structuring of hydration water around a single-stranded DNA
    K. Chakraborty and S. Bandyopadhyay, J. Chem. Phys. 142, 015101 (2015).

  17. Microscopic hydration properties of the ABeta(1-42) peptide monomer and the globular protein ubiquitin: A comparative molecular dynamics study
    J. C. Jose, P. Khatua, N. Bansal, N. Sengupta and S. Bandyopadhyay, J. Phys. Chem. B 118, 11591-11604 (2014).

  18. In-silico studies of the properties of water hydrating a small protein
    S. K. Sinha, M. Jana, K. Chakraborty and S. Bandyopadhyay, J. Chem. Phys. 141, 22D502 (2014).

  19. Hydration behavior at the ice-binding surface of the antifreeze protein TmAFP
    U. S. Midya and S. Bandyopadhyay, J. Phys. Chem. B 118, 4743-4752 (2014).

  20. Correlated dynamical crossovers of the hydration layer of a single-stranded DNA oligomer
    K. Chakraborty and S. Bandyopadhyay, J. Phys. Chem. B 118, 413-422 (2014).

  21. Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms
    S. Pal and S. Bandyopadhyay, J. Chem. Phys. 139, 235101 (2013).

  22. Molecular dynamics simulation of a single-stranded DNA with heterogeneous distribution of nucleobases in aqueous medium
    K. Chakraborty, S. Mantha and S. Bandyopadhyay, J. Chem. Phys. 139, 075103 (2013).

  23. Molecular dynamics study of beta-cyclodextrin-phenylalanine (1:1) inclusion complex in aqueous medium
    M. Jana and S. Bandyopadhyay, J. Phys. Chem. B 117, 9280-9287 (2013).

  24. Effects of protein conformational motions in the native form and non-uniform distribution of electrostatic interaction sites on interfacial water
    S. Pal and S. Bandyopadhyay, Chem. Phys. 420, 35-43 (2013).

  25. Effects of protein conformational flexibilities and electrostatic interactions on the low-frequency vibrational spectrum of hydration water
    S. Pal and S. Bandyopadhyay, J. Phys. Chem. B 117, 5848-5856 (2013).

  26. Computer simulation studies of biomolecular hydration
    S. Pal, K. Chakraborty, U. S. Midya, P. Khatua and S. Bandyopadhyay, ISRAPS Bull. 25, 77-83 (2013).

  27. Importance of protein conformational motions and electrostatic anchoring sites on the dynamics and hydrogen bond properties of hydration water
    S. Pal and S. Bandyopadhyay, Langmuir 29, 1162-1173 (2013).

  28. Restricted dynamics of water around a protein--carbohydrate complex: Computer simulation studies
    M. Jana and S. Bandyopadhyay, J. Chem. Phys. 137, 055102 (2012).

  29. Polar solvation dynamics of lysozyme from molecular dynamics studies
    S. K. Sinha and S. Bandyopadhyay, J. Chem. Phys. 136, 185102 (2012).
    This article has been selected for publication in Virtual Journal of Biological Physics Research 23 (January 1, 2012).

  30. Conformational flexibility of a protein--carbohydrate complex and the structure and ordering of surrounding water
    M. Jana and S. Bandyopadhyay, Phys. Chem. Chem. Phys. 14, 6621-6631 (2012).

  31. Local heterogeneous dynamics of water around lysozyme: A computer simulation study
    S. K. Sinha and S. Bandyopadhyay, Phys. Chem. Chem. Phys. 14, 899-913 (2012).

  32. Conformational fluctuations of a protein--DNA complex and the structure and ordering of water around it
    S. K. Sinha and S. Bandyopadhyay, J. Chem. Phys. 135, 245104 (2011).
    This article has been selected for publication in JCP: BioChemical Physics 5 (December, 2011) and in Virtual Journal of Biological Physics Research 23 (January 1, 2012).

  33. Dynamical properties of water around a protein--DNA complex form molecular dynamics simulations
    S. K. Sinha and S. Bandyopadhyay, J. Chem. Phys. (cover page) 135, 135101 (2011).
    One of the Top 20 Most Downloaded Articles in October 2011.
    This article has been selected for publication in JCP: BioChemical Physics 5 (October, 2011) and in Virtual Journal of Biological Physics Research 22 (October 15, 2011).

  34. Vibrational spectrum of water confined in and around cyclodextrins
    M. Jana and S. Bandyopadhyay, Chem. Phys. Lett. 509, 181-185 (2011).

  35. Hydration properties of α-, β-, and γ-cyclodextrins from molecular dynamics simulations
    M. Jana and S. Bandyopadhyay, J. Phys. Chem. B 115, 6347-6357 (2011).

  36. Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules
    S. K. Sinha and S. Bandyopadhyay, J. Chem. Phys. 134, 115101 (2011).
    This article has been selected for publication in JCP: BioChemical Physics 5 (March, 2011) and in Virtual Journal of Biological Physics Research 21 (March 15, 2011).

  37. Kinetics of hydrogen bonds in aqueous solutions of cyclodextrin and its methyl-substituted forms
    M. Jana and S. Bandyopadhyay, J. Chem. Phys. 134, 025103 (2011).
    This article is selected for publication in JCP: BioChemical Physics 5 (January, 2011).
    This article is selected for publication in Virtual Journal of Biological Physics Research 21 (January 15, 2011).

  38. Low-frequency vibrational spectrum of water around cyclodextrin and its methyl-substituted derivatives
    M. Jana and S. Bandyopadhyay, Langmuir 26, 14097-14102 (2010).

  39. Secondary structure specific entropy change of a partially unfolded protein molecule
    S. K. Sinha, S. Chakraborty and S. Bandyopadhyay, Langmuir 26, 9911-9916 (2010).

  40. Microscopic investigation of the hydration properties of cyclodextrin and its substituted forms
    M. Jana and S. Bandyopadhyay, Langmuir 25, 13084-13091 (2009).

  41. Effect of unfolding on the thickness of the hydration layer of a protein
    S. K. Sinha, S. Chakraborty and S. Bandyopadhyay, Ind. J. Phys. 83, 49-64 (2009).

  42. Thickness of the hydration layer of a protein from molecular dynamics simulation
    S. K. Sinha, S. Chakraborty and S. Bandyopadhyay, J. Phys. Chem. B 112, 8203-8209 (2008).

  43. Dynamics of water in the hydration layer of a partially unfolded structure of the protein HP-36
    S. Chakraborty and S. Bandyopadhyay, J. Phys. Chem. B 112, 6500-6507 (2008).

  44. Low-frequency vibrational spectrum of water in the hydration layer of a protein: A molecular dynamics simulation study
    S. Chakraborty, S. K. Sinha and S. Bandyopadhyay, J. Phys. Chem. B 111, 13626-13631 (2007).

  45. Correlation between the dynamics of hydrogen bonds and the local density reorganization in the protein hydration layer
    S. Chakraborty and S. Bandyopadhyay, J. Phys. Chem. B 111, 7626-7630 (2007).

  46. Molecular dynamics study of surfactant monolayers adsorbed at the oil/water and air/water interfaces
    J. Chanda and S. Bandyopadhyay, J. Phys. Chem. B 110, 23482-23488 (2006).

  47. Hydrogen bond lifetime dynamics at the interface of a surfactant monolayer
    J. Chanda and S. Bandyopadhyay, J. Phys. Chem. B 110, 23443-23449 (2006).

  48. Exploration of the secondary structure specific differential solvation dynamics between the native and molten globule states of the protein HP-36
    S. Bandyopadhyay, S. Chakraborty and B. Bagchi, J. Phys. Chem. B 110, 20629-20634 (2006).

  49. Coupling between hydration layer dynamics and unfolding kinetics of HP-36
    S. Bandyopadhyay, S. Chakraborty and B. Bagchi, J. Chem. Phys. 125, 084912 (2006).
    This article is selected for publication in Virtual Journal of Biological Physics Research 12(5) (2006).

  50. Perturbation of phospholipid bilayer properties by ethanol at a high concentration
    J. Chanda and S. Bandyopadhyay, Langmuir 22, 3775-3781 (2006).

  51. Sensitivity of hydrogen bond lifetime dynamics to the presence of ethanol at the interface of a phospholipid bilayer
    J. Chanda, S. Chakraborty and S. Bandyopadhyay, J. Phys. Chem. B 110, 3791-3797 (2006).

  52. Water dynamics at the surface of proteins and micelles: Understanding the fast and the slow components , in Water Properties of Food, Pharmaceutical, and Biological Materials
    S. Pal, S. Chakraborty, S. M. Bhattacharyya, S. Bandyopadhyay, S. Balasubramanian and B. Bagchi, Taylor and Francis Publisher, 11-37 (2006).

  53. Secondary structure sensitivity of hydrogen bond lifetime dynamics in the protein hydration layer
    S. Bandyopadhyay, S. Chakraborty and B. Bagchi, J. Am. Chem. Soc. 127, 16660-16667 (2005).

  54. Correlation between the dynamics of amino acid residues and water molecules in aqueous protein solutions
    S. Bandyopadhyay, Abstr. Pap. Am. Chem. Soc. 229, 335-COMP Part 1, (March, 2005). Abstract

  55. Molecular dynamics study of a surfactant monolayer adsorbed at air/water interface
    J. Chanda and S. Bandyopadhyay, J. Chem. Theory Comput. 1, 963-971 (2005).

  56. Sensitivity of polar solvation dynamics to the secondary structures of aqueous proteins and the role of surface exposure of the probe
    S. Bandyopadhyay, S. Chakraborty, S. Balasubramanian and B. Bagchi, J. Am. Chem. Soc. 127, 4071-4075 (2005).

  57. Bimodal water dynamics at the surface of micelles and proteins
    S. Balasubramanian, S. Chakraborty,S. Bandyopadhyay, S. Pal and B. Bagchi, Ultrafast Phenomena XIV (Proceedings of the 14th International Conference) Eds. T. Kobayashi, T. Okada, T. Kobayashi, K. A. Nelson, S. De Silvestri, Springer Series in Chemical Physics 79, (2005).

  58. Monolayer of Aerosol-OT surfactants adsorbed at the air/water interface : An atomistic computer simulation study
    J. Chanda, S. Chakraborty and S. Bandyopadhyay, J. Phys. Chem. B 109 , 471-479 (2005).

  59. Molecular modeling and simulations of AOT-water reverse micelles in iso-octane: Structural and dynamical properties
    S. Abel, F. Sterpone, S. Bandyopadhyay and M. Marchi, J. Phys. Chem. B 108, 19458-19466 (2004).

  60. Atomistic simulation study of the coupled motion of amino acid residues and water molecules around protein HP-36 : Fluctuations at and around the active sites
    S. Bandyopadhyay, S. Chakraborty, S. Balasubramanian, S. Pal and B. Bagchi, J. Phys. Chem. B 108, 12608-12616 (2004).

  61. Distribution of ethanol in a model membrane: A computer simulation study
    J. Chanda and S. Bandyopadhyay, Chem. Phys. Lett. 392, 249-254 (2004).

  62. Dynamics of water at surface of complex systems: Study of aqueous micelles and proteins, in Femtochemistry and Femtobiology: Ultrafast Events in Molecular Science
    S. Pal, S. Bandyopadhyay, S. Balasubramanian and B. Bagchi, Eds. M. M. Martin and J. T. Hynes, Elsevier Publisher (ISBN: 0444516565), 213-220 (2004).

  63. Effect of the pore region of a transmembrane ion channel on the physical properties of a simple membrane
    L. Saiz, S. Bandyopadhyay and M. L. Klein, J. Phys. Chem. B 108, 2608-2613 (2004).

  64. Computer simulation studies of surfactant assemblies and complex biological systems
    S. Bandyopadhyay, Res. and Innovation 11, 21-25 (2003).

  65. Dynamics of water at the interface of a small protein, enterotoxin
    S. Balasubramanian, S. Bandyopadhyay, S. Pal and B. Bagchi, Curr. Sci. 85, 101-108 (2003).

  66. Effect of the pore region of a transmembrane ion-channel on the physical properties of a simple membrane
    L. Saiz, S. Bandyopadhyay and M. L. Klein, Biophys J. 84 (2), 382A-382A Part 2 Suppl. S, (February, 2003).

  67. Monolayer of monododecyl diethylene glycol surfactants adsorbed at the air/water interface: A molecular dynamics study
    S. Bandyopadhyay and J. Chanda, Langmuir 19, 10443-10448 (2003).

  68. Effects of the nonimmobilizer hexafluoroethane on the model membranes dimyristoylphosphatidylcholine
    L. Koubi, M. Tarek, S. Bandyopadhyay, M. L. Klein and D. Scharf, Anesthesiology 97, 848-855 (2002).

  69. Towards an understanding of complex biological membranes from atomistic molecular dynamics simulations
    L. Saiz, S. Bandyopadhyay and M. L. Klein, Bioscience Reports 22, 151-173 (2002).

  70. A coarse grain model for phospholipid simulations
    J. C. Shelley, M. Y. Shelley, R. C. Reeder, S. Bandyopadhyay and M. L. Klein, J. Phys. Chem. B 105, 4464-4470 (2001).

  71. Molecular dynamics simulation studies of surfactant systems
    R. Allen, S. Bandyopadhyay, J. C. Shelley, M. Y. Shelley and M. L. Klein, Abstr. Pap. Am. Chem. Soc. 221, 15-Coll Part 1, (April, 2001).

  72. Molecular dynamics study of the effect of surfactant on a biomembrane
    S. Bandyopadhyay, J. C. Shelley and M. L. Klein, J. Phys. Chem. B 105, 5979-598 6 (2001).

  73. Simulations of phospholipids using a coarse grain model
    J. C. Shelley, M. Y. Shelley, R. C. Reeder, S. Bandyopadhyay, P. B. Moore and M. L. Klein, J. Phys. Chem. B 105, 9785-9792 (2001).

  74. Comparing non-immobilizer to anesthetic distribution in a model membrane
    D. Scharf, L. Koubi, M. Tarek, S. Bandyopadhyay and M. L. Klein, Biophys J. 80 (1), 2154 Part 2, (January, 2001).
  75. Membrane structural perturbations caused by anesthetics and non-immobilizers : A molecular dynamics investigation
    L. Koubi, M. Tarek, S. Bandyopadhyay, M. L. Klein and D Scharf, Biophys. J. 81, 3339-3345 (2001).

  76. Molecular dynamics study of the poly(oxyethylene) surfactant C12E2 and water
    S. Bandyopadhyay, M. Tarek, M. Lynch and M. L. Klein, Langmuir 16, 942-946 (2000).

  77. C12E2 reverse micelle : A molecular dynamics study
    R. Allen, S. Bandyopadhyay and M. L. Klein, Langmuir 16, 10547-10552 (2000).

  78. Computer simulation studies of surfactant systems
    S. Bandyopadhyay, M. Tarek and M. L. Klein, in New approaches to Problems in Liquid State Theory, Eds. C. Caccamo, J.-P. Hansen and G. Stell, Kluwer Academic Publishers, Netherlands, v. 529, p.347-354 (1999).

  79. Molecular dynamics study of a lipid-DNA complex
    S. Bandyopadhyay, M. Tarek and M. L. Klein, J. Phys. Chem. B 103, 10075-10080 (1999).

  80. Effect of variation of the size of CH3 and CH2 groups on cage-to-cage migration of n-butane in zeolite NaCaA
    S. Bandyopadhyay, Chem. Phys. Lett. 293, 378-382 (1998).

  81. Computer simulation studies of amphiphilic interfaces
    S. Bandyopadhyay, M. Tarek and M. L. Klein, Curr. Opin. Colloid & Intarface Sci. 3, 242-246 (1998).

  82. Surfactant aggregation at a hydrophobic surface
    S. Bandyopadhyay, J. C. Shelley, M. Tarek, P. B. Moore and M. L. Klein, J. Phys. Chem. B 102, 6318-6322 (1998).

  83. Molecular dynamics studies of aqueous surfactant systems
    M. Tarek, S. Bandyopadhyay and M. L. Klein, J. Mol. Liqs. 78, 1-6 (1998).

  84. Molecular dynamics studies of the hexagonal mesophase of sodium dodecylsulphate in aqueous solution
    S. Bandyopadhyay, M. L. Klein, G. J. Martyna and M. Tarek, Mol. Phys. 95 , 377-384 (1998).

  85. Monte Carlo and molecular dynamics simulation of argon clusters and n-alkanes in the confined regions of zeolites
    R. Chitra, S. Bandyopadhyay and S. Yashonath, Bull. Mater. Sci. 20, 845-878 (1997).

  86. A Monte Carlo method for estimation of pore volumes of zeolites
    S. Bandyopadhyay and S. Yashonath, Zeolites 19, 51-56 (1997).

  87. Conformational analysis of n-butane in zeolite NaCaA: Temperature and concentration dependence
    S. Bandyopadhyay and S. Yashonath, J. Phys. Chem. B 101, 5675-5683 (1997).

  88. Conformation of confined alkanes: n-butane in zeolite Y
    S. Bandyopadhyay and S. Yashonath, J. Chem. Phys. 105, 7223-7226 (1996).

  89. Diffusion anomaly in silicalite and VPI-5 from molecular dynamics simulations
    S. Bandyopadhyay and S. Yashonath, J. Phys. Chem. 99, 4286-4292 (1995).

  90. CHIPPS: A data parallel computer for analysis of molecular dynamics trajectories
    S. Bandyopadhyay, S. Yashonath, T. C. Subramanian and M. Periasamy, Trans. Mat. Res. Soc. Jpn. 16A, 157 (1994).

  91. Anomalous behavior of cage-to-cage diffusion of methane in zeolite A and Y
    S. Bandyopadhyay and S. Yashonath, Chem. Phys. Lett. 223, 363-368 (1994).

  92. Sorbate properties of xenon in Cloverite. A molecular dynamics study
    S. Bandyopadhyay and S. Yashonath, J. Solid State Chem. 111, 151-156 (1994).

  93. Surprising diffusion behavior in the restricted regions of silicalite
    S. Yashonath and S. Bandyopadhyay, Chem. Phys. Lett. 228, 284-288 (1994).

 

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