## A list and download of scientific papers (July 2015)

My >> Google Scholar profile.

### Shapes, energies, dynamics and thermodynamics of nanoscale objects

- M. Petrović, J. T. Sadowski,
__A. Šiber__, and M. Kralj, "Wrinkles of graphene on Ir(111): Macroscopic network ordering and internal multi-lobed structure", Carbon**94**, 856 (2015). - A. J. Perez-Berna, S. Marion, F. J. Chichon, J. J. Fernandez, D. C. Winkler, J. L. Carrascosa,
A. C. Steven,
__A. Šiber__, and C. San Martin, "Distribution of DNA-condensing protein complexes in the adenovirus core", Nucl. Acids Res.**43**, 4274 (2015). - S. Marion and
__A. Šiber__"Ejecting Phage DNA against Cellular Turgor Pressure", Biophys. J.**107**, 1924 (2014). - M. Popović and
__A. Šiber__"Lattice-gas Poisson-Boltzmann approach for sterically asymmetric electrolytes", Phys. Rev. E**88**, 022302 (2013). -
__A. Šiber__and P. Ziherl "Many-body contact repulsion of deformable disks“, Phys. Rev. Lett.**110**, 214301 (2013). - A. Lošdorfer Božič,
__A. Šiber__, and R. Podgornik "Statistical analysis of sizes and shapes of virus capsids and their resulting elastic properties“, J. Biol. Phys.**39**, 215 (2013). - A. Lošdorfer Božič,
__A. Šiber__, and R. Podgornik "How simple can a model of an empty viral capsid be? Charge distributions in viral capsids“, J. Biol. Phys.**38**, 657 (2012). -
__A. Šiber__, A. Lošdorfer Božič, and R. Podgornik "Energies and pressures in viruses: contribution of nonspecific electrostatic interactions“, Phys.Chem.Chem.Phys.**14**, 3746 (2012). -
__A. Šiber__and H. Buljan "Theoretical and experimental analysis of a thin elastic cylindrical tube acting as a non-Hookean spring“, Phys. Rev. E**83**, 067601 (2011). - A. Leforestier,
__A. Šiber__, F. Livolant, and R. Podgornik "Protein-DNA Interactions Determine the Shapes of DNA Toroids Condensed in Virus Capsids“, Biophys. J.**100**, 2209 (2011). - A. Lošdorfer Božič,
__A. Šiber__, and R. Podgornik "Electrostatic self-energy of a partially formed spherical shell in salt solution: Application to stability of tethered and fluid shells as models for viruses and vesicles“, Phys. Rev. E**83**, 041916 (2011). -
__A. Šiber__, R. Zandi and R. Podgornik "Thermodynamics of nanospheres encapsulated in virus capsids“, Phys. Rev. E**81**, 051919 (2010). -
__A. Šiber__, R.F. Rajter, R.H. French, W.Y. Ching, V.A. Parsegian, and R. Podgornik, "Optically anisotropic infinite cylinder above an optically anisotropic half space: Dispersion interaction of a single-walled carbon nanotube with a substrate", J. Vac. Sci. Technol. B**28**, C4A17 (2010). -
__A. Šiber__, R.F. Rajter, R.H. French, W.Y. Ching, V.A. Parsegian, and R. Podgornik, "Dispersion interactions between optically anisotropic cylinders at all separations: Retardation effects for insulating and semiconducting single-wall carbon nanotubes“, Phys. Rev. B**80**, 165414 (2009). -
__A. Šiber__and A. Majdandžić, "Spontaneous curvature as a regulator of the size of virus capsids“, Phys. Rev. E**80**, 021910 (2009). -
__A. Šiber__and R. Podgornik, "Stability of elastic icosadeltahedral shells under uniform external pressure: Application to viruses under osmotic pressure“, Phys. Rev. E**79**, 011919 (2009). -
__A. Šiber__and R. Podgornik, "Nonspecific interactions in spontaneous assembly of empty versus functional single-stranded RNA viruses“, Phys. Rev. E**78**, 051915 (2008). -
__A. Šiber__, M. Dragar, V.A. Parsegian, and R. Podgornik, "Packing nanomechanics of viral genomes“, Eur. Phys. J. E**26**, 317 (2008). -
__A. Šiber__and R. Podgornik, "Role of electrostatic interactions in the assembly of empty spherical viral capsids", Phys. Rev. E**76**, 061906 (2007). -
__A. Šiber__, "Continuum and all-atom description of the energetics of graphene nanocones", Nanotechnology**18**, 375705 (2007). -
__A. Šiber__, "Shapes and energies of giant icosahedral fullerenes: Onset of ridge sharpening transition", Eur. Phys. J. B**53**, 395 (2006). -
__A. Šiber__, "Energies of sp^{2}carbon shapes with pentagonal disclinations and elasticity theory", Nanotechnology**17**, 3598 (2006). -
__A. Šiber__, "Buckling transition in icosahedral shells subjected to volume conservation constraint and pressure: Relations to virus maturation", Phys. Rev. E**73**, 061915 (2006). -
__A. Šiber__, "Vibrations of closed-shell Lennard-Jones icosahedral and cuboctahedral clusters and their effect on the cluster ground-state energy", Phys. Rev. B**70**, 075407 (2004).

### Quantum dynamics

- B. Gumhalter, A. Šiber, H. Buljan, and T. Fauster,
“Nonadiabatic dynamics of electron scattering from adsorbates in surface bands”, Phys. Rev. B
**78**, 155410 (2008). - A. Šiber, "Dynamics and (de)localization in a one-dimensional tight-binding chain", Am. J. Phys. 74, 692 (2006). Copyright (2006) American Association of Physics Teachers. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Association of Physics Teachers.

### Adsorption and (thermo)dynamics of gases in carbon nanotube based materials

- A. Šiber and H. Buljan, "Quantum states
and specific heat of low-density He gas adsorbed within the carbon nanotube interstitial channels: Band
structure effects and potential dependence", Phys. Rev. B
**66**, 075415 (2002). - A. Šiber, "Adsorption of He atoms in external
grooves of single wall carbon nanotube bundles", Phys. Rev. B
**66**, 205406 (2002). - A. Šiber, "Phonons and specific heat of linear
dense phases of atoms physisorbed in the grooves of carbon nanotube bundles",
Phys. Rev. B
**66**, 235414 (2002). - A. Šiber, "Quantum virial expansion approach to
thermodynamics of
^{4}He adsorbates in carbon nanotube bundles: Interacting Bose gas in one dimension", Phys. Rev. B**67**, 165426 (2003). - M. T. Cvitaš and A. Šiber, "Vibrations of a chain
of Xe atoms in a groove in a carbon nanotube bundle", Phys. Rev. B
**67**, 193401 (2003). - A. Šiber, "Coating carbon nanotubes: geometry of
incommensurate long-range-ordered physisorbed monolayers", Phys. Rev. B
**68**, 033406 (2003). - A. Šiber, "Reply to 'Comment on `Quantum virial
expansion approach to thermodynamics of
^{4}He adsorbates in carbon nanotube materials: Interacting Bose gas in one dimension'", Phys. Rev. B**70**, 016502(2004).

### Physics of "white" light in nonlinear optical materials

- H. Buljan, A. Šiber, M. Soljačić, and M.Segev,
"Propagation of incoherent ''white'' light and modulation instability in non-instantaneous nonlinear
media", Phys. Rev. E
**66**, 035601(R) (2002). - H. Buljan, A. Šiber, M. Soljačić, T. Schwartz, M. Segev, and D. N. Christodoulides,
"Incoherent white light solitons in logarithmically
saturable noninstantaneous nonlinear media", Phys. Rev. E
**68**, 036607 (2003).

### Valence hole-phonon interaction: surface quantum well states

- T. Valla, M. Kralj, A. Šiber, M. Milun, P. Pervan, P. D. Johnson, and D. P. Woodruff,
"Oscillatory electron-phonon coupling
in ultra-thin silver films on V(100)", J. Phys.: Condens. Matter
**12**, L477 (2000). - M. Kralj, A. Šiber, P. Pervan, M. Milun, T. Valla, P. D. Johnson, and D. P. Woodruff,
"Temperature dependence of photoemission
from quantum-well states in Ag/V(100): Moving surface-vacuum barrier effect",
Phys. Rev. B
**64**, 085411(2001).

### Scattering of thermal energy atoms from surfaces

- A. Šiber and B. Gumhalter, "Debye-Waller factor in He -> Cu(001) collisions revisited: the role of the interaction potentials", Surf. Sci. 385, 270 (1997).
- J. Braun, D. Fuhrmann, A. Šiber, B. Gumhalter, and Ch. Wöll, "Observation
of a zonecenter gap in the longitudinal mode of an adsorbate overlayer: Xenon on Cu(111)",
Phys. Rev. Lett.
**80**, 125 (1998). - A. Šiber and B. Gumhalter, "Comment on ''Quantum scattering of
heavy particles from a 10 K Cu(111) surface''", Phys. Rev. Lett.
**81**, 1742 (1998). - A. Šiber, B. Gumhalter, J. Braun, A. P. Graham, M. Bertino, J. P. Toennies, D. Fuhrmann,
and Ch. Wöll, "Combined He-atom scattering and theoretical study of the low-energy
vibrations of physisorbed monolayers of Xe on Cu(111) and Cu(001)", Phys. Rev. B
**59**, 5898 (1999). - A. Šiber, B. Gumhalter and J. P. Toennies, "Study of energy transfer in helium atom scattering from surfaces", Vacuum 54, 315 (1999).
- B. Gumhalter, A. Šiber and J. P. Toennies, "Recovery
temperature for nonclassical energy transfer in atom-surface scattering", Phys. Rev. Lett.
**83**, 1375 (1999). - A. Šiber, B. Gumhalter, A. P. Graham, and J. P. Toennies,
"He atom scattering and theoretical study of the surface phonons of a simple benchmark system: Xe(111)",
Phys. Rev. B
**63**, 115411 (2001). - A. Šiber and B. Gumhalter, "Zone edge focused two-phonon processes in He atom scattering from a simple prototype system: Xe(111)", Surf. Sci. 502-503, 422(2002).
- A. Šiber, B. Gumhalter and Ch. Wöll, "Kinematic effects in
the Debye-Waller factor and sticking probabilities in low-energy atom-surface scattering",
J. Phys.: Condens. Matter
**14**, 5913 (2002). - A. Šiber and B. Gumhalter, "Linear versus Nonlinear
Coupling Effects in Single- and Multiphonon Atom-Surface Scattering", Phys. Rev. Lett.
**90**, 126103(2003). -
__A. Šiber__and B. Gumhalter, "Diffraction of He atoms from Xe monolayer adsorbed on the graphite (0001) revisited: the importance of multiple scattering processes", Surf. Sci. 529, L269 (2003). - A. Šiber and B. Gumhalter, "Interactions of He atoms with Xe plated graphite: Unified treatment of scattering and adsorbate dynamics based on method of coupled channels", Prog. Surf. Sci. 74, 375 (2003).
- A. Šiber and B. Gumhalter,
"Suppression of inelastic bound-state resonance effects by the
dimensionality of an atom-surface scattering event", Phys. Rev. B
**71**, 081401(R) (2005). - A. Šiber, C. Boas, M.W. Cole. and C. Wöll, "Anomalously low probabilities for rotational excitation in HD-surface scattering", ChemPhysChem 7, 1015 (2006).
- A. Šiber and B. Gumhalter,
"Reply to “Comment on `Suppression of inelastic bound-state
resonance effects by the dimensionality of an atom-surface scattering event'”", Phys. Rev. B
**75**, 046402 (2007). - A. Šiber and B. Gumhalter, "Phonon-mediated bound
state resonances in inelastic atom-surface scattering“, Journal of Physics: Condensed Matter
**20**, 224002 (2008).

## Msc and PhD theses:

- A. Šiber, Theory of thermal energy inert atom scattering from surface vibrations, Msc thesis (1999).
- A. Šiber, Theory of thermal energy He atom scattering from ordered submonolayers on solid surfaces, Phd thesis (2002).