Current Collaborators

Selected Publications of J. Akola

1. M. Wilding, M. Guthrie, S. Kohara, C.L. Bull, J. Akola and M.G. Tucker,
   The structure of MgO-SiO₂ glasses at elevated pressure
   J. Phys.: Condens. Matter 24, 225403 (2012).
   Abstract
2. E. Heikkilä, A.A. Gurtovenko, H. Martinez-Seara, H. Häkkinen, I. Vattulainen, and J. Akola
   Atomistic Simulations of Functional Au₁₄₄(SR)₆₀ Gold Nanoparticles in Aqueous Environment
   J. Phys. Chem. C 116, 9805 (2012).
   Abstract
3. J. Akola and R.O. Jones,
   Structure and dynamics in amorphous tellurium and Te_n clusters: A density functional study
   Phys. Rev. B 85, 134103 (2012).
   Abstract
4. J. Kalikka, J. Akola, R.O. Jones, S. Kohara, and T.Usuki,
   Amorphous Ge₁₅Te₈₅: density functional, high-energy x-ray and neutron diffraction study
   J. Phys.: Condens. Matter 24, 015802 (2012).
   Abstract
5. S. Kohara, J. Akola, H. Morita, K. Suzuya, J. K. R. Weber, M. C. Wilding, and C. J. Benmore,
   Relationship between topological order and glass forming ability in densely packed enstatite and forsterite composition glasses
   Proc. Natl. Acad. Sci. 108, 14780 (2011). [doi: 10.1073/pnas.1104692108]
   Abstract
6. J. Akola and R.O. Jones,
   JUGENE unravels Structures in Phase Change Materials,
   inSiDE (Innovatives Supercomputing in Deutschland) Vol. 9 No. 2, Autumn 2011.
   pdf
7. A. J. Logsdail and J. Akola,
   Interaction of Au₁₆ Nanocluster with Defects in Supporting Graphite: A Density-Functional Study
   J. Phys. Chem. C 115, 15240 (2011).
   Abstract
8. V. V. Brazhkin, J. Akola, Y. Katayama, S. Kohara, M. V. Kondrin, A. G. Lyapin, S. G. Lyapin, G. Tricot and O. F. Yagafarov ,
   Densified low-hygroscopic form of P₂O₅ glass
   J. Mater. Chem. 21, 10442 (2011).
   Abstract
9. T. Matsunaga, J. Akola, S. Kohara, T. Honma, K. Kobayashi, E. Ikenaga, R.O. Jones, N. Yamada, M. Takata, and R. Kojima,
   From local structure to nanosecond recrystallization dynamics in AgInSbTe phase-change materials
   Nature Materials 10, 129 (2011).
   Abstract
10. J. Akola, J. Larrucea, and R.O. Jones,
    Polymorphism in phase-change materials: melt-quenched and as-deposited amorphous structures in Ge₂Sb₂Te₅ from density functional calculations
    Phys. Rev. B 83, 094113 (2011).
    Abstract
11. J. Kalikka and J. Akola,
    Steered molecular dynamics simulations of ligand-receptor interaction in lipocalins
    Eur. Biophys. J. 40, 181 (2011).
    Abstract
12. O. Lopez-Acevedo, K.A. Kacprzak, J. Akola, and H. Häkkinen,
    Quantum size effects in ambient CO oxidation catalysed by ligand-protected gold clusters
    Nature Chemistry 2, 329 (2010).
    Abstract
13. S. Kohara, H. Ohno, M. Takata, T. Usuki, H. Morita, K. Suzuya, J. Akola, and L. Pusztai,
    Lead silicate glasses: Binary network-former glasses with large amounts of free volume
    Phys. Rev. B 82, 134209 (2010).
    Abstract
14. J. Akola, R. O. Jones, S. Kohara, T. Usuki, and E. Bychkov,
    Density variations in liquid tellurium: Roles of rings, chains, and cavities
    Phys. Rev. B 81, 094202 (2010).
    Abstract
15. J. Akola and R.O. Jones,
    Comment on "Formation of Large Voids in the Amorphous Phase-Change Memory Ge₂Sb₂Te₅ Alloy"
    Phys. Rev. Lett. 104, 019603 (2010).
    Comment Reply
16. J. Akola, K.A. Kacprzak, O. Lopez-Acevedo, M. Walter, H. Häkkinen, and H. Grönbeck,
    Thiolate-Protected Au₂₅ Superatoms as Building Blocks: Dimers and Crystals
    J. Phys. Chem. C 114, 15986 (2010).
    Abstract
17. D. Jiang, M. Walter, and J. Akola,
    On the Structure of a Thiolated Gold Cluster: Au₄₄(SR)₂₈^2-
    J. Phys. Chem. C 114, 15883 (2010).
    Abstract
18. J. Akola, J. Larrucea, and R. O. Jones,
    Polymorphism in amorphous Ge₂Sb₂Te₅: comparison of melt-quenched and as-deposited structures
    Proceedings, E*PCOS 2010, European Phase Change and Ovonics Symposium, Politecnico di Milano, Edited by R. Bez, A. Lacaita, pp. 126 - 133 (2010).
    pdf
19. K. Kobayashi, J.J. Kim, J. Akola, R.O. Jones, E. Ikenaga, M. Kobata, S. Ueda, T. Matsunaga, K. Kifune, S. Kohara, R.Kojima, and N. Yamada,
    Hard X-ray Photoelectron Spectroscopy, Chemical Bonding, and First-Principle Calculations in Phase Change Memory Materials
    Proceedings, E*PCOS 2010, European Phase Change and Ovonics Symposium, Politecnico di Milano, Edited by R. Bez, A. Lacaita, pp. 158 - 159 (2010).
    pdf
20. Z.W. Wang, O. Toikkanen, B.M. Quinn, J. Akola, O. Lopez-Acevedo, H. Häkkinen, and R.E. Palmer,
    Probing the Atomic-scale Structure of Monolayer-Protected Au₃₈ Clusters
    Microscopy & Microanalysis 2010, Proceedings, 16 (Suppl. 2): pp. 1652-1653 (2010).
21. J.-H. Lin, J. Akola, and R.O. Jones,
    Structure and Dynamics of Large Biological Molecules
    NIC Symposium 2010, Proceedings, G. Münster, D. Wolf, and M. Kremer (Editors), John von Neumann Institute for Computing, Jülich, IAS Series Volume 3 ISBN 978-3-89336-606-4, pp. 84-91 (2010).
    pdf
22. R. O. Jones and J. Akola,
    Phase change materials: an update
    IFF Scientific Report 2009, pp. 64-65 (2010).
    pdf
    
23. J. Akola and R.O. Jones,
    Structure of liquid phase change material AgInSbTe from density functional / molecular dynamics simulations
    Appl. Phys. Letters 94, 251905 (2009).
    Abstract
24. J. Akola, R. O. Jones, S. Kohara, S. Kimura, K. Kobayashi, M. Takata, T. Matsunaga,
    R. Kojima, and N. Yamada,
    Experimentally constrained density-functional calculations of the amorphous structure of the prototypical phase-change material Ge₂Sb₂Te₅
    Phys. Rev. B 80, 020201(R) (2009).
    Rapid Communication
25. J. Akola and R.O. Jones,
    Structure of amorphous Ge₈Sb₂Te₁₁: GeTe-Sb₂Te₃ alloys and optical storage
    Phys. Rev. B 79, 134118 (2009).
    Editors' Suggestion
26. F. Yin, J. Akola, P. Koskinen, M. Manninen, and R.E. Palmer,
    Bright Beaches of Nanoscale Potassium Islands on Graphite in STM Imaging,
    Phys. Rev. Lett. 102, 106102 (2009).
    Editors' Suggestion
27. J. Akola and R.O. Jones,
    Density functional simulations of phase change materials: disordered phases of Ge₈Sb₂Te₁₁ and Ag/In/Sb/Te alloys,
    E\PCOS2009 Proceedings (RWTH Aachen University, Germany, 2009),
    M. Salinga (Editor), pp. 57-63 (2009).
    Full text
28. S. Kohara, Y. Tanaka, Y. Fukuyama, N. Yasude, J. Kim, H. Murayama, S. Kimura, K. Kato, Y. Moritomo, T. Marsunaga, R. Kojima, N. Yamada, H. Tanaka, T. Ohshima, J. Akola, R. O. Jones, and M. Takata,
    The amorphous structural basis of the rapid phase-change mechanism in DVD materials,
    E\PCOS2009 Proceedings (RWTH Aachen University, Germany, 2009),
    M. Salinga (Editor), pp. 75-82 (2009).
    Full text
29. K.A. Kacprzak, L. Lehtovaara, J. Akola, O. Lopez-Acevedo, and H. Häkkinen,
    A density functional investigation of thiolate-protected bimetal PdAu₂₄(SR)₁₈^z clusters: Doping the superatom complex,
    Phys. Chem. Chem. Phys. 11, 7123 (2009).
    Abstract
30. K.A. Kacprzak, J. Akola, and H. Häkkinen,
    First-principles simulations of hydrogen peroxide formation catalyzed by
    small gold clusters,
    Phys. Chem. Chem. Phys. 11, 6359 (2009).
    Abstract
31. O. Lopez-Acevedo, J. Akola, R.L. Whetten, H. Grönbeck, and H. Häkkinen,
    Structure and Bonding in the Ubiquitous Icosahedral Metallic Gold Cluster
    Au₁₄₄(SR)₆₀, J. Phys. Chem. C 113, 5035 (2009).
    Cover Article in JPC-C
32. M. Manninen, H.P. Heiskanen, and J. Akola,
    Electronic shell and supershell structure in graphene flakes,
    Eur. Phys. J. D 52, 143 (2009).
    abstract
33. R.O. Jones and J. Akola,
    Nanoscale phase transitions in phase change materials: What's new?,
    IFF Scientific Report 2008, pp. 76-77 (2009).
    pdf
34. J. Akola and R.O. Jones,
    Density functional study of amorphous, liquid and crystalline Ge₂Sb₂Te₅:
    Homopolar bonds and/or AB alternation?
    J. Phys.: Condens. Matter 20, 465103 (2008).
    abstract
    
35. J. Akola and R.O. Jones,
    Binary alloys of Ge and Te: Order, voids, and the eutectic composition,
    Phys. Rev. Lett. 100, 205502 (2008).
    abstract
    [selected for Virtual Journal of Nanoscale Science and Technology, 2 June 2008. http://www.vjnano.org]
36. H.P. Heiskanen, M. Manninen, and J. Akola,
    Electronic structure of triangular, hexagonal and round graphene flakes near
    the Fermi level,
    New J. Phys 10, 103015 (2008).
    Full text
    
37. M. Walter, J. Akola, O. Lopez-Acevedo, P. D. Jadzinsky, G. Calero, C. J. Ackerson,
    R. L. Whetten, H. Grönbeck, and H. Häkkinen,
    A unified view of ligand-protected gold clusters as superatoms,
    Proc. Natl. Acad. Sci. 105, 9157 (2008).
    OPEN ACCESS ARTICLE
    See also: "Gilding the superatom model", Editor's Choice, Science 18 July 2008.
    News item at Georgia Tech website: Divide and Protect: Study Reveals Principles Behind Stability and Electronic Properties of Gold Nanoclusters (link)
38. J. Akola, M. Walter, R.L. Whetten, H. Häkkinen, and H. Grönbeck,
    On the structure of thiolate-protected Au₂₅,
    J. Am. Chem. Soc. 130, 3756 (2008).
    abstract
39. J. Akola and R.O. Jones,
    Density functional simulations of Te-based phase change materials,
    E\PCOS2008 Proceedings (University of Pardubice, Czech Republic, 2008),
    N. Yamada and T. Wagner (Editors), ISBN 978-80-7395-111-5, pp. 6-13.
    Full text
40. J. Akola, H.P. Heiskanen, and M. Manninen,
    Edge-dependent selection rules in magic triangular graphene flakes,
    Phys. Rev. B 77, 193410 (2008).
    Abstract
    [selected for Virtual Journal of Nanoscale Science and Technology, 9 June 2008. http://www.vjnano.org]
41. R.O. Jones and J. Akola,
    Nanoscale Phase Transitions in Phase Change Materials,
    IFF Scientific Report 2007, pp. 158-159 (2008).
    pdf
42. J. Akola and R.O. Jones,
    Structural patterns in Ge/Sb/Te phase-change materials,
    NIC Symposium 2008 - Proceedings, G. Münster, D. Wolf, and M. Kremer (Editors),
    John von Neumann Institute for Computing, Jülich, NIC Series Volume 39 ISBN 978-3-9810842-5-1, pp. 179-186 (2008).
    pdf
43. J. Akola and R.O. Jones,
    Structural phase transitions on the nanoscale: The crucial pattern in the phase-change materials Ge₂Sb₂Te₅ and GeTe,
    Phys. Rev. B 76, 235201 (2007).
    abstract
44. K. Rytkönen, J. Akola, and M. Manninen,
    Density functional study of alkali metal atoms and monolayers on graphite (0001),
    Phys. Rev. B 75, 075401 (2007).
    
45. R.O. Jones and J. Akola,
    Phase change memory: the future of computer memory,
    IFF Scientific Report 2006, pp. 138-139 (2007).
    pdf
46. J. Akola and H. Häkkinen,
    Density functional study of gold atoms and clusters on graphite (0001) surface with defects,
    Phys. Rev. B 74, 165404 (2006).
    
47. J. Akola and R.O. Jones,
    Density functional calculations of ATP systems II: ATP hydrolysis at the active site of actin,
    J. Phys. Chem. B 110, 8121 (2006).
    
48. J. Akola and R.O. Jones,
    Density functional calculations of ATP systems I: Crystalline ATP hydrates and related molecules,
    J. Phys. Chem. B 110, 8110 (2006).
    
49. J. Akola, K. Rytkönen, and M. Manninen,
    Electronic properties of single-walled carbon nanotubes inside cyclic supermolecules,
    J. Phys. Chem. B 110, 5186 (2006).
    
50. R.O. Jones, J. Akola, and P. Ballone,
    Ring-opening polymerization and branching in polycarbonates: a density functional/Monte Carlo study, Advances in Polycarbonates. ACS Symposium Series, No. 898, D. J. Brunelle and M. R. Korn (Editors) ISBN 0-8412-3887-1, pp. 200-213 (2005).
    
51. K. Rytkönen, J. Akola, and M. Manninen,
    Sodium atoms and clusters on graphite: a density functional study,
    Phys. Rev. B 69, 205404 (2004).
    
52. R.O. Jones and J. Akola,
    Calculation and prediction of molecular structures and reaction rates,
    inSiDE (Innovatives Supercomputing in Deutschland) Vol. 1 No. 2, Autumn 2003.
    pdf
53. K. Manninen, J. Akola, and M. Manninen,
    Close-Packing of Clusters: Application to Al₁₀₀,
    Phys. Rev. B 68, 235412 (2003).
    
54. J. Akola and R.O. Jones,
    ATP Hydrolysis in Water: A Density Functional Study,
    J. Phys. Chem. B 107, 11774 (2003).
    
55. J. Akola and R.O. Jones,
    Branching Reactions in Polycarbonate: A Density Functional Study,
    Macromolecules 36, 1355 (2003).
    
56. J. Akola and M. Manninen,
    Aluminum-lithium clusters: First-principles simulation of geometries and electronic properties,
    Phys. Rev. B 65, 245424 (2002).
    
57. J. Akola, P. Ballone, and R.O. Jones,
    Reactions of Polycarbonate with Cyclohexene Oxide and Phosphites - A Density Functional Study,
    Macromolecules 35, 2327 (2002).
    
58. J. Akola, K. Rytkönen, and M. Manninen,
    Metallic evolution of small magnesium clusters,
    Eur. Phys. J. D 16, 21 (2001).
    
59. J. Akola and M. Manninen,
    Heating of Al ₁₃^- and Al ₁₄ clusters,
    Phys. Rev. B 63, 193410 (2001).
    
60. J. Akola,
    Electronic structure calculations of aluminum and sodium clusters,
    (Ph.D. Thesis, University of Jyväskylä, 2000).
    
61. J. Akola, M. Manninen, H. Häkkinen, U. Landman, X. Li, and L.-S. Wang,
    Aluminum cluster anions: Photoelectron spectroscopy and ab initio simulations,
    Phys. Rev. B. 62, 13216 (2000).
    
62. S. Kümmel, J. Akola, and M. Manninen,
    Thermal expansion in small metal clusters and its impact on the electric polarizability,
    Phys. Rev. Lett. 84, 3827 (2000).
    
63. J. Akola, M. Manninen, H. Häkkinen, U. Landman, X. Li, and L.-S. Wang,
    Photoelectron spectra of aluminum cluster anions: Temperature effects and ab initio simulations,
    Phys. Rev. B 60, 11297 (1999).
    
64. J. Akola, A. Rytkönen, H. Häkkinen, and M. Manninen,
    Temperature-dependent ionization potential of sodium clusters,
    Eur. Phys. J. D 8, 93 (2000).
    
65. J. Akola, H. Häkkinen, and M. Manninen,
    Ionization potential of Al₆ and Al₇ as a function of temperature,
    Eur. Phys. J. D 9, 179 (1999).
    
66. J. Akola, H. Häkkinen, and M. Manninen,
    Ionization potential of aluminum clusters,
    Phys. Rev. B 58, 3601 (1998).