58. Atsmon-Raz Y, Miller Y.*  Molecular Mechanisms of the Bindings between Non-Amyloid β Component (NAC) Oligomers and Amylin Oligomers, 2016. [Epub ahead of print]

57.Wineman-Fisher V, Simkovich R, Huppert D, Trujillo K, Remington SJ, Miller Y.* Mutagenic induction of an ultra-fast water-chain proton wire. Phys Chem Chem Phys. 18, 23089-95, 2016.

56. Wineman-Fisher V, Miller Y.*  Effect of Zn(2+) ions on the assembly of amylin oligomers: insight into the molecular mechanisms. Phys Chem Chem Phys. 18, 21590-9, 2016.

55. Ivnitski D, Amit M, Silberbush O, Atsmon-Raz Y, Nanda J, Cohen-Luria R, Miller Y, Ashkenasy G, Ashkenasy N.  The Strong Influence of Structure Polymorphism on the Conductivity of Peptide Fibrils. Angew Chem Int Ed 55, 9988-92, 2016.

54. Wineman-Fisher V., Tudorach L., Nissim E. and Miller Y.* The removals of disulfide bonds in amylin oligomers lead to the conformational change of the 'native' amylin oligomers. Phys. Chem. Chem. Phys.18, 12438 – 12442, 2016. 

53. Wineman-Fisher V., Bloch D. N. and Miller Y.* The challenges in studying the structures of metal- amyloid oligomers related to Type 2 diabetes, Parkinson's disease and Alzheimer's disease. Coord. Chem. Rev., doi:10.1016/j.ccr.2016.04.010 , 2016.  

52. Wineman-Fisher V. and Miller Y.* Structural insights into the polymorphism of self-assembled Amylin oligomers. Isr. J. Chem.  DOI: 10.1002/ijch.201500091, 2016.

51. Daschakraborty S, Kiefer PM, Miller Y, Motro Y, Pines D, Pines E, Hynes JT.  Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution I: Acid and Base Coordinate and Charge Dynamics. J Phys. Chem. B. 120, 2271-80, 2016.

50. Daschakraborty S, Kiefer PM, Miller Y, Motro Y, Pines D, Pines E, Hynes JT. Reaction Mechanism for Direct Proton Transfer from Carbonic Acid to a Strong Base in Aqueous Solution II: Solvent Coordinate-Dependent Reaction Path. J Phys. Chem. B. 120, 2281-90, 2016. 

49. Pines D, Ditkovich J, Mukra T, Miller Y, Kiefer PM, Daschakraborty S, Hynes JT, Pines E.  How Acidic Is Carbonic Acid? J. Phys. Chem. B. 120, 2440-51, 2016.

48. Brasili D, Watly J, Simonovsky E, Guerrini R, Barbosa NA, Wieczorekb R, Remellia M, Kozlowski H, Miller Y.* 2016, The unusual metal ion binding ability of histidyl tags and their mutated derivatives. Dalton Transaction, 45, 5629-39, 2016.

47. Baram M, Atsmon-Raz Y, Ma B, Nussinov R, Miller Y.*  Amylin-Aβ oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease. Phys. Chem. Chem. Phys. 18, 2330-8, 2016. Cover article.

46. Atsmon-Raz Y, Miller Y.* Non-Amyloid-β Component of Human α-Synuclein Oligomers Induces Formation of New Aβ Oligomers: Insight into the Mechanisms That Link Parkinson's and Alzheimer's Diseases. ACS Chem. Neurosci., 7, 46-55, 2016.


45. Simonovsky, E., Kozlowski H. Miller Y.* Termini capping of metal-poly-His peptide complexes induces the formation of α-helix . RSC Adv.,Communication. 2015,5, 104551-104555. 

44. Watly, J, Simonovsky, E, Barbosa, N. A., Spodzieja, M., Wieczorek, R., Rodziewicz-Motowidlo, S., Miller, Y.*, Kozlowski, H.* African viper poly-His tag peptide fragment efficiently binds metal ions and is folded into an α-helical structure. Inorg. Chem. 54:7692-702, 2015.

43. Atsmon-Raz Y, Miller Y.* A Proposed Atomic Structure of the Self-Assembly of the Non Amyloid-β Component of Human α-Synuclein as Derived by Computational Tools. J. Phys. Chem. B. 119(31):10005-15, 2015.

42. Atsmon-Raz Y, Miller Y*  Insight into Atomic Resolution of the Cross-Seeding between Tau/Mutated Tau and Amyloid-β in Neurodegenerative Diseases. Isr J Chem DOI: 10.1002/ijch.201400162.

41. Pellach M, Atsmon-Raz Y, Simonovsky E, Gottlieb H, Jacoby G, Beck R, Adler-Abramovich L, Miller Y*, Gazit E.*  Spontaneous structural transition in phospholipid-inspired aromatic phosphopeptide nanostructures. ACS Nano. 9(4):4085-95, 2015. 

40. Adhikary J, Chakraborty P, Chattopadhyay T, Prasad R, Motro Y, Koch B, Mautner FA, Miller Y*, Das D* Configuration change from cis to trans of isothiocyanato groups in nickel(II) species: Experimental verification and theoretical interpretation of reaction consequence and study on their bio-activity Polyhedron. 93: 55-65, 2015.

39.  Miller Y*, Ma B, Nussinov R.* Polymorphism in self-assembly of peptide-based β-hairpin contributes to network morphology and hydrogel mechanical rigidity. J Phys Chem B. 119(2):482-90, 2015.  

38.  Wineman-Fisher V, Atsmon-Raz Y, Miller Y.* Orientations of residues along the β-arch of self-assembled amylin fibril-like structures lead to polymorphism. Biomacromolecules. 16(1):156-65, 2015.



37.   Pontecchiani, F., Simonovsky, E., Wieczorek, R., Barbosa, N., Rowinska-Zyrek, M., Potocki, S., Remelli, M., Miller, Y*. & Kozlowski, H.  Unusual binding mechanism of Cu (II) ions to the poly-histidyl domain of a peptide found in the venom of an African viper Dalton Transactions, DOI: 10.1039/C4DT02257B, 2014.

36.   Linnewiel-Hermoni K, Motro Y, Miller Y, Levy J, Sharoni Y.  Carotenoid derivatives inhibit nuclear factor kappa B activity in bone and cancer cells by targeting key thiol groups. Free Radic Biol Med. 75C:105-120, 2014.
35.  Watly J, Simonovsky E, Wieczorek R, Barbosa N, Miller Y*, Kozlowski H. Insight into the coordination and the binding sites of Cu(2+) by the histidyl-6-tag using experimental and computational tools. Inorg Chem. 53(13):6675-83, 2014.
34. Zeytuni N, Uebe R, Maes M, Davidov G, Baram M, Raschdorf O, Friedler A, Miller Y, Schüler D, Zarivach R. Bacterial Magnetosome Biomineralization-A Novel Platform to Study Molecular Mechanisms of Human CDF-Related Type-II Diabetes. PloS one9(5), e97154., 2014.
33.  Wineman-Fisher V, Simkovitch R, Shomer S, Gepshtein R, Huppert D, Saif M, Kallio K, Remington SJ, Miller Y.*   Insight into the structure and the mechanism of the slow proton transfer in the GFP double mutant T203V/S205A. Phys Chem Chem Phys16(23), 11211-11223., 2014.
32.  Zeytuni N, Uebe R, Maes M, Davidov G, Baram M, Raschdorf O, Nadav-Tsubery M, Kolusheva S, Bitton R, Goobes G, Friedler A, Miller Y, Schüler D, Zarivach R.  Cation Diffusion Facilitators Transport Initiation and Regulation is Mediated by Cation Induced Conformational Changes of the Cytoplasmic Domain. PloS one9(3), e92141., 2014.
31.  Raz Y, Adler J, Vogel A, Scheidt HA, Häupl T, Abel B, Huster D, Miller Y.*  The influence of the ΔK280 mutation and N-or C-terminal extensions on the structure, dynamics, and fibril morphology of the tau R2 repeat. Phys Chem Chem Phys. Cover article. 16(17), 7710-7717, 2014.
30.  Simkovitch R., Huppert A., Huppert D., Remington S.J. and Miller Y.*: Proton Transfer in Wild-Type GFP and S205V Mutant is Reduced by Conformational Changes of Residues in the Proton-Wire. J. Phys. Chem. B., 117, 11921-31, 2013.
29.  Raz Y., and Miller, Y.*: Interactions between Aβ and mutated tau lead to polymorphism and induce aggregation of Aβ-mutated tau oligomeric complexes. PLOS ONE, 8(8): e73303. doi:10.1371/journal.pone.0073303, 2013.
28. Pimentel A.S.*, Guimarães Cristiano R. W., and Miller, Y.*: Molecular Modeling: Advancements and Applications. J. Chem., Editorial article for a special issue, DOI: 10.1155/2013/875478, 2013.
27.  Raz Y., Rubinov, B., Matmor M., Rapaport, H., Ashkenasy, G.,* and Miller, Y*:  Effects of mutations in de novo designed synthetic amphiphilic β-sheet peptides on self-assembly of fibrils. Chem. Comm. 49, 6561-6563, 2013.
26.  Miller, Y.*, Ma, B., and Nussinov, R.*: Metal binding sites in amyloid oligomers: complexes and mechanisms. Coord. Chem. Rev., 256: 2245-2252, 2012.
25.  Miller, Y., Ma, B., and Nussinov R.: Stability of fibrils and annular species using all-atom molecular dynamics (MD) simulations in solvent: insight into polymorphism. Derreumaux, P. (Ed.): Alzheimer’s disease: Molecular Basis of Amyloid-beta protein aggregation and fibril formation Insights into low molecular weight and cytotoxic aggregates from computer simulations. Imperial College press, 2012, Chapter 3.
24. Liessmann M., Miller Y., Gerber R.B., and Abel B.: Reaction of OH and NO at low temperatures in the presence of water: The role of clusters. Zeitschrift für Physikalische Chemie, 225: 1129-1144, 2011.
22. Parthasarathy, S., Long, F., Miller, Y., Xiao, Y., McElheny, D., Thurber, K., Ma, B., Nussinov, R., and Ishii, Y.: Molecular-level examination of Cu2+ binding structure for amyloid fibrils of 40-residue Alzheimer’s β by solid-state NMR spectroscopy. J. Am. Chem. Soc. 133: 3390-3400, 2011.
21. Miller, Y., Ma, B., and Nussinov, R.: The unique Alzheimer’s β-amyloid triangular fibril has a cavity along the fibril axis under physiological conditions.  J. Am. Chem. Soc. 133, 2742-2748, 2011. Platinum Highlight
20. Shmilovits-Ofir, M., Miller, Y., and Gerber R.B.: Conformational transitions of glycine induced by vibrational excitation of the O-H stretch. Phys. Chem. Chem. Phys, 2010, DOI: 10.1039/C0CP01385D. Advance article in a special issue
19. Miller, Y., Ma, B., Tsai, C.-J., and Nussinov, R.: The hollow core of Alzheimer Aβ42 amyloid observed by cryoEM is relevant at physiological pH. Proc. Natl. Acad. Sci. USA, 107:14128-14133, 2010.
18. Miller, Y., Ma, B., and Nussinov, R.: Zinc ions promote Alzheimer Aβ aggregation via population shift of polymorphic states. Proc. Natl. Acad. Sci. USA, 107: 9490-9495, 2010.
17.  Miller, Y., Ma, B., and Nussinov, R: Polymorphism in Alzheimer Aβ amyloid organization reflects conformational selection in a rugged energy landscape. Chem. Rev., DOI: 10.1021/cr900377t, 2010.
16.  Miller, Y., Ma, B., and Nussinov, R.:  Polymorphism of Alzheimer’s Aβ17-42 (p3) oligomers:  The importance of the turn location and its conformation.  Biophys. J. 97(4):  1168-1177, 2009.
15. Miller, Y., Thomas, J.L., Kemp, D.D., Finlayson-Pitts, B.J., Gordon, M.S., Tobias, D.J. and Gerber, R.B.: Structure of large nitrate-water clusters at ambient temperatures: Simulations with effective fragment potentials and force fields with implications for atmospheric chemistry. J. Phys. Chem. A, 113 (46): 12805, 2009.
14. Miller, Y., Finlayson-Pitts, B. J., and Gerber, R. B.:  Ionization of N2O4 in contact with water:  Mechanism, timescales and atmospheric implications.  J. Am. Chem. Soc.  131: 12180, 2009. Cover article.
13.  Link, O., Vöhringer-Martinez, E., Lugovoj, E., Liu, Y., Siefermann, K., Faubel, M., Grubmuller, H., Gerber, R.B., Miller, Y., Abel, B.; Ultrafast phase transitions in metastable water near liquid interfaces. Faraday Discuss. 141: 67-79, 2009. DOI: 10.1039/b811659h
12. Kamboures, M. A., Raff, J. D., Miller, Y., Philips, L. F., Finlayson-Pitts, B. J., and Gerber, R. B.:  Complexes of HNO3 and NO2 and N2O4 and their potential role in atmospheric HONO formation.  Phys. Chem. Chem. Phys. 10: 6019, 2008.
11. Wolf, I., Shapira, A., Giniger, R., Miller, Y., Gerber, R. B., and Cheshnovsky, O.:  Critical size for intracluster proton transfer from water to an anion.  Communication.  Angew. Chem. Int. Ed. 47:  10.1002/ange.200800542, 2008.
10.  Miller, Y. and Gerber, R. B.:  Dynamics of proton recombination with NO3- anions in water clusters.  Phys. Chem. Chem. Phys. 10:  1091, 2008.  Cover communication article.
9.  Miller, Y., Vaida, V., and Gerber, R. B.:  Photodissociation yields for high vibrational excitations of H2SO4 in atmospheric conditions.  Geophys. Res. Lett. 34:  Art No. L16820, 2007. Featured as a scientific highlight article.
8. Miller, Y., Chaban, G. M., Zhou, J., Asmis, K. R., Neumark, D. M., and Gerber, R. B.:  Vibrational spectroscopy of SO42-· (H2O)n cluster, n=1.5:  Harmonic and anharmonic calculations, and experiment.  J. Chem. Phys. 127:  Art No. 094305, 2007.
7.  Ramazan, K. A., Wingen, L. M., Miller, Y., Chaban, G. M., Gerber, R. B., Xantheas, S., and Finlayson-Pitts, B. J.:  A new experimental and theoretical approach to the heterogeneous hydrolysis of NO2:  The key role of molecular nitric acid and its complexes with water.  J. Phys. Chem. A 110:  6886, 2006.
6. Miller, Y. and Gerber, R. B.:  Dynamics of vibrational overtone excitations of H2SO4, H2SO4-H2O:  Hydrogen – Hopping and photodissociation processes.  J. Am. Chem. Soc. 128:  9594, 2006.
5. Miller, Y., Chaban, G. M., Finlayson-Pitts, B. J., and Gerber, R. B.:  Photochemical processes-induced by vibrational overtone excitations:  Dynamics simulations for cis HONO, trans HONO, HNO3 and HNO3-H2O.  J. Phys. Chem. A 110:  5342, 2006.
4.  Gerber, R. B., Chaban, G. M., Brauer, B., and Miller, Y.:  First principles calculations of anharmonic vibrational spectroscopy of large molecules.  In Dykstra, C. E., Kim, K. S., Fleming, G., and Scuseria, G. E. (Eds.):  Theory and Applications of Computational Chemistry:  The First 40 Years.  Amsterdam, Netherlands, Elsevier Publications, 2005, Chapter 9, pp. 165-193
3.  Miller, Y., Chaban, G. M., and Gerber, R. B.:  Ab initio vibrational calculations for H2SO4 and H2SO4-H2O:  Spectroscopy and the nature of the anharmonic couplings.  J. Phys. Chem. A 109:  6565, 2005.
2. Miller, Y., Chaban, G. M., and Gerber, R. B.:  Theoretical study of anharmonic vibrational spectra of HNO3, HNO3-H2O, HNO4, cis HONO and trans HONO:  Fundamental, overtone and combination excitations.  Chem. Phys. 313:  213, 2005.
1. Miller, Y., Fredj, E., Harvey, J. N., and Gerber, R. B.:  UV spectroscopy of large water clusters:  Model and Calculations for (H2O)n, n=8, 11, 20, 40 and 50.  J. Phys. Chem. A 108:  4405, 2004.