Publications
1. I. Ahmadabadi, A. Esfandiar, Ali A. Hassanali, and R. Ejtehadi. “Structural and dynamical fingerprints
of the anomalous dielectric properties of water under confinement” Phys. Rev. Mater., 5(2),
024008 (2021).
2. A. Stephens,M. Qaisrani,M. Ruggiero, G.Miron, U.Morzan,M. Lebrero, S. Jones, E. Poli, A. Bond,
P. Woodhams, E. Kleist, L. Grisanti, R. Gebauer, J. Zeitler, D. Credgington, Ali A. Hassanali and
G. Kaminski-Schierle. “Short hydrogen bonds enhance non-aromatic protein-related fluorescence”
bioRxiv, 2020.01. 22.915306 (2021).
3. M. Anzola, A. Painelli, Ali A. Hassanali and L. Grisanti. “Understanding Forster Energy Transfer
through the Lens of Molecular Dynamics” J. Chem. Theor. Comp., 16(12), 7281 (2020).
4. L. Grisanti, M. Sapunar, Ali A. Hassanali and N. Doslic. “Toward understanding optical properties
of amyloids: a reaction path and nonadiabatic dynamics study” J. Amer. Chem. Soc., 142(42), 18042
(2020).
5. J. Cuny, J. Calatayud, N. Ansari, Ali A. Hassanali, M. Rapacioli, and A. Simon. “Simulation of Liquids
with the Tight-Binding Density-Functional Approach and Improved Atomic Charges” J. Phys.
Chem. B, 124(34), 7421 (2020).
6. C. Pruteanu, V. Robinson, N. Ansari, Ali A. Hassanali, S. Scandolo and J. Loveday “Squeezing Oil
in Water under Pressure: Inverting the Hydrophobic Effect”, J. Phys. Chem. Letters 11(12):4826
(2020).
7. D. Shadrack, H. Swai and Ali A. Hassanali “A computational study on the role of water and conformational
fluctuations in Hsp90 in response to inhibitors” J. Mol. Graph. and Model., 96, 107510
(2020).
8. E. Poli, K. Jong and Ali A. Hassanali “Charge transfer as a ubiquitous mechanism in determining
the negative charge at hydrophobic interfaces” Nat. Comm., 11(1), 1-13 (2020).
9. N. Ansari, B. Onat, G Sosso and Ali A. Hassanali “Insights into the emerging networks of voids in
simulated supercooled water” J. Phys. Chem. B, 124(11), 2180 (2020).
10. R. Belousov, M. Qasirani, Ali A. Hassanali and E. Roldan, “First-passage fingerprints of water diffusion
near glutamine surfaces”, Soft Matter 16(40):5585 (2020).
11. G. Falciani, R. Frankin, A. Cagna, I. Sen, Ali A. Hassanali and E. Chiavazzo, “A multi-scale perspective
of gas transport through soap-film membranes”, Molecular Systems Design and Engineering
5(5):911 (2019).
12. N. Ansari, A. Laio and Ali A. Hassanali, “Spontaneously forming dendritic voids in liquid water can
host small polymers”, J. Phys. Chem. Letters 10(18):5585 (2019).
13. A. Rajabpour, R. Seif, S. Arabha, MM Heyhat, S. Merabia and Ali A. Hassanali, “Thermal transport
at a nanoparticle-water interface: A molecular dynamics and continuum modeling study”, J. Chem.
Phys. 150(11):114701 (2019).
14. M. Qasirani, L. Grisanti, R. Gebauer and Ali A. Hassanali, “Structural and dynamical heterogeneities
at glutaminewater interfaces”, Phys. Chem. Chem. Phys. 21(29):16083 (2019).
15. K.H Jong, Y.T Azar, L. Grisanti, A. Stephens, S. Jones, D. Credigington, G. S Kaminski Schierle and
Ali A. Hassanali, “Low energy optical excitations as an indicator of structural changes initiated at
the termini of amyloid proteins”, Phys. Chem. Chem. Phys. 21(43):23931 (2019).
6. N. Ansari, R. Dandekar, S. Caravati, G. Sosso and Ali A. Hassanali “High and low density patches
in simulated liquid water” J. Chem. Phys. 129(22:222826 (2018).
17. Rahul Dandekar and Ali A. Hassanali “Hierarchical lattice models of hydrogen-bond networks in
water” Phys. Rev. E, 97(6) (2018)
18. Yamila Perez Sirkin, Ali A. Hassanali and Damian A. Scherlis “One-Dimensional Confinement Inhibits
Water Dissociation in Carbon Nanotubes” J. Phys. Chem. Letters, 9:5029 (2018)
19. Kwang Hyok Jong and Ali A. Hassanali “A Data-Science Approach to Understanding Hydrogen
Bond Networks Around Biomolecules: The Case of Tri-Alanine in Liquid Water” J. Phys. Chem. B.
122(32):7895 (2018)
20. Kwang Hyok Jong, Narges Ansari, Luca Grisanti and Ali A. Hassanali “Understanding the quantum
mechanical properties of hydrogen bonds in solvated biomolecules from cluster calculations” J. Mol.
Liq., 263:501 (2018)
21. Sudarkodi Venkatesan, R P Vivek-Ananth, R P Sreejith, P. Mangalapandi, Ali A. Hassanali and
Areejit Samal “Network approach towards understanding the crazing in glassy amorphous polymers”
J. Stat. Mech. 2018 (2018).
22. G. Vladilo and Ali A. Hassanali “Hydrogen Bonds and Life in the Universe” Life 8(1):1 (2018).
23. K. Ulman, S. Busch and Ali A. Hassanali “Quantum mechanical effects in zwitterionic amino acids:
the case of proline, hydroxyproline and alanine in water” J. Chem. Phys. 148(22:222826 (2018).
24. Yu Kay Law and Ali A. Hassanali “The importance of nuclear quantum effects in spectral line
broadening of optical spectra and electrostatic properties in aromatic chromophores” J. Chem. Phys.
148(10:102331 (2018).
25. C. A. Daly Jr., L.M. Streacker, Y.Sun, S.R. Pattenaude, Ali A. Hassanali, P.B Petersen, S. Corcelli
and Dor-Ben Amotz “Decomposition of the Experimental Raman and Infrared Spectra of Acidic
Water Into Proton, Special Pair and Counterion Contributions” J. Phys. Chem. Letters, 8, 5246(2017).
26. Federico Giberti and Ali A. Hassanali “The excess proton at the air-water interface: The role of
instantaneous liquid interface”, J. Chem. Phys. 146:244703 (2017).
27. Kwang Hyok Jong, Luca Grisanti and Ali A. Hassanali, “Hydrogen Bond Networks and Hydrophobic
Effects in the Amyloid Beta 30-35 Chain in Water: A Molecular Dynamics Study”, J. Chem. Inf.
Model. 7, 1548-1562 (2017).
28. Bobo Shi, Yung Kyung Shin, Ali A. Hassanali and S.J Singer, “Biomolecules at the amorphous
silica/water interface: Binding and fluorescence anisotropy of peptides”, Colloids and Surfaces B:
Biointerfaces 157, 83 (2017).
29. Luca Grisanti, Dorothea Pinotsi, Ralph Gebauer, Gabriele S Kaminski Schierle and Ali A. Hassanali,
“A computational study on how structure influences optical properties in model crystal structures of
amyloid fibrils”, Phys. Chem. Chem. Phys. 19(5):4030 (2017).
30. Gabriele Cesare Sosso, Sebastiano Caravati, Grant Rotskoff, Surinyan Vaikuntanathan and Ali A.
Hassanali, “On the Role of Non-Spherical Cavities in Short Length-Scale Density Fluctuations”, J.
Phys. Chem. A 121(1):370 (2017).
31. A Yaya, CP Ewels, JK Efavi, B Agyei-Tuffor, K Kan-Dapaah, B Onwona-Agyeman, EKK Abavare,
Ali A. Hassanali and PR Briddon “A study of polybromide chain formation using carbon nanomaterials
via density functional theory approach”, Cogent Engineering 3(1):1261059 (2016)
32. Subrahmanyam Sappati, Ali A. Hassanali, Ralph Gebauer and Prasenjit Ghosh “Nuclear quantum
effects in a HIV/cancer inhibitor” - Editors Choice 2016, J. Chem. Phys. 145(20):205102 (2016).
33. Marie-Claire Bellisent-Funel, Ali A. Hassanali, Martina Havenith, Richard Henchman, Peter Pohl,
Fabio Sterpone, David van der Spoel, Yao Xu, Angel Garica “Water determines the structure and
dynamics of proteins” Chemical Reviews 116(13):7673(2016)
34. Noam Agmon, Huib J Bakker, R Kramer Campen, Richard Henchman, Peter Pohl, Sylvie Roke,
Martin Thamer and Ali A. Hassanali “Protons and Hydroxide Ions in Aqueous Systems” Chemical
Reviews 116(13):7642(2016)
35. Piero Gasparotto, Ali A. Hassanali and Michele Ceriotti “Probing Defects and Correlations in the
Hydrogen Bond Network of Ab Initio Water” J. Chem. Theor. Comp, 12(4):1953(2016)
36. Yanier Crespo and Ali A. Hassanali “Characterizing the local solvation environment of OH- in water
clusters using AIMD”, J. Chem. Phys. 144:074304 (2016).
37. Dorothea Pinotsi, Luca Grisanti, Pierre Mahou, Ralph Gebauer, Clemens F. Kaminski, Ali A. Has-
sanali and Gabriele S. Kaminski-Schierle. “Proton Transfer and Structure Specific Fluorescence in
Hydrogen Bond-Rich Protein Structures”, J. Amer. Chem. Soc. 138(9):3046 (2016).
38. Jerome Cuny, Yu Xie, Chris J. Pickard and Ali A. Hassanali “Ab Initio Quality NMR Parameters in
Solid-State Materials Using a High Dimensional Neural Network Representation” J. Chem. Theor.
Comp, 12(2), 765-773(2016)
39. Yu Kay Law and Ali A. Hassanali “The Role of Quantum Vibrations on the Structural, Electronic
and Optical Propertie of 9-Methylguanine” J. Phys. Chem. A, 119(44), 10816-10827(2015).
40. Bobo Shi, Yun Kyung Shin, Ali A. Hassanali and Sherwin J. Singer “DNA Binding to the Silica
Surface” J. Phys. Chem. B, 119(34), 11030-11040(2015).
41. Jan Kessler, Hossam Elgabarty, Thomas Spura, Kristof Karhan, Pouya Partovi-Azar, Ali A. Has-
sanali and Thomas D. Kuhne “Structure and Dynamics of the Instantaneous Water/Vapor Interface
Revisited by Path-Integral and Ab Initio Molecular Dynamics Simulations” J. Phys. Chem. B,
119(31), 10079-10086(2015).
42. Yanier Crespo and Ali A. Hassanali “Unveiling the Janus-like properties of OH-” J. Phys. Chem.
Letters, 2, 272-278(2015).
43. Jerome Cuny and Ali A. Hassanali “Ab Initio molecular dynamics study of the mechanism of proton
recombination with a weak base” J. Phys. Chem. B, 118(48), 13903-13912(2014).
44. Federico Giberti, Ali A. Hassanali, Michele Ceriotti and Michele Parrinello “The role of quantum
effects on structural and electronic fluctuations in neat and charged water” J. Phys. Chem. B, 118(46),
13226-13235(2014).
45. Ali A. Hassanali, Federico Giberti, Gabriele Sosso and Michele Parrinello “The role of the umbrella
inversion mode in proton diffusion” Chem. Phys. Letters. 10, 1420-1425 (2014)
46. Yun Ding, Ali A. Hassanali and Michele Parrinello “Anomalous water diffusion in salt solutions”
PNAS 111(9) 3310-3315 (2014)
47. Ali A. Hassanali, Jerome Cuny, Vincenzo Verdolino and Michele Parrinello. “Aqueous solutions:
state of the art in ab initio molecular dynamics” Phil. Trans. R. Soc. A 372(2011), 20120482 (2014)
48. Ali A. Hassanali, Federico Giberti, Jerome Cuny, Thomas Kuhne and Michele Parrinello. “Proton
Transfer through the Water Gossamer” PNAS 110(34) 13723-13728 (2013)
49. Yating Kao, Xumin Guo, Yi Yang, Zheyun Liu, Ali A. Hassanali, Qin Hua Song, Lijuan Wang
and Dongping Zhong “Ultrafast dynamics of nonequilibrium electron transfer in photoinduced redox
cycle: Solvent mediation and conformational flexibility”, J. Phys. Chem. B, 116, 9130-40(2012) .
50. Ali A. Hassanali, Jerome Cuny, Michele Ceriotti and Michele Parrinello. “The Fuzzy Quantum
Proton in the Hydrogen Chloride Hydrates”, J. Amer. Chem. Soc. 134(20):8557 (2012).
51. Ali A. Hassanali, Meher Prakash, Hagai Eshet and Michele Parrinello. “On the Recombination of
Hydronium and Hydroxide ions in water”, PNAS 108(51):20410 (2011).
52. Ali A. Hassanali, Dongping Zhong and Sherwin J. Singer. “An AIMD study of the CPD Dimer
Repair Mechanism in Water: Role of Solvent in Ring Splitting”, J. Phys. Chem. B115(14):3860
(2011).
53. Ali A. Hassanali, Dongping Zhong and Sherwin J. Singer. “An AIMD study of the CPD Dimer
Repair Mechanism in Water: Reaction Free energy Surface and Mechanistic implications”, J. Phys.
Chem. B115(14):3848 (2011).
54. Ali A. Hassanali, Hui Zhang, Yun Kyung Shin, Chris Knight and Sherwin J. Singer. “The Dissociated
Amorphous Silica Surface: Model development and evaluation”, J. Comput. Theoretical. Chem.
6(11):3456 (2010).
55. Hui Zhang, Ali A. Hassanali, Yun Kyung Shin, Chris Knight and Sherwin J. Singer. “The Water-
Amorphous Silica Interface: Analysis of the Stern layer and Surface conduction”, J. Chem. Phys.
134(2):024705 (2010).
56. Tanping Li, Ali A. Hassanali and Sherwin J. Singer. “Origin of Slow Relaxation Following Photoexcitation
ofW7 inMyoglobin and the Dynamics of its Hydration Layer”, J. Phys. Chem. B112(50):16121
(2008).
57. Ali A. Hassanali and Sherwin J. Singer. “Model for the Water-Amorphous Silica Interface: The
Undissociated Surface”, J. Phys. Chem. B111(38):11181 (2007).
58. Tanping Li, Ali A. Hassanali, Ya-Ting Kao, Dongping Zhong and Sherwin J. Singer. “Hydration Dynamics
and Time Scales of Coupled Water-Protein Fluctuations”, J. Amer. Chem. Soc. 129(11):3376
(2007).
59. Ali A. Hassanali and Sherwin J. Singer. “Static and Dynamic Properties of theWater/Amorphous Silica
Interface: A model for the Undissociated Surface”, J. Computer-AidedMaterials Design. 14(1):53
(2007).
60. Ali A. Hassanali, Tanping Li, Dongping Zhong and Sherwin J. Singer. “A Molecular Dynamics
Study of Lys-Trp-Lys: Structure and Dynamics in Solution Following Photoexcitation”, J. Phys.
Chem. B110(21):10497 (2006).