37 research outputs found
Suppression of inelastic bound state resonance effects by the dimensionality of atom-surface scattering event
We develop a multidimensional coupled channel method suitable for studying
the interplay of bound state resonance and phonon assisted scattering of inert
gas atoms from solid surfaces in one, two and three dimensions. This enables us
to get insight into the features that depend on the dimensionality of inelastic
resonant processes typically encountered in low energy He atom scattering from
surfaces, in general, and to elaborate on the observability of recently
conjectured near threshold resonances in scattering from Einstein phonons, in
particular.Comment: 2 figure
How simple can a model of an empty viral capsid be? Charge distributions in viral capsids
We investigate and quantify salient features of the charge distributions on
viral capsids. Our analysis combines the experimentally determined capsid
geometry with simple models for ionization of amino acids, thus yielding the
detailed description of spatial distribution for positive and negative charge
across the capsid wall. The obtained data is processed in order to extract the
mean radii of distributions, surface charge densities and dipole moment
densities. The results are evaluated and examined in light of previously
proposed models of capsid charge distributions, which are shown to have to some
extent limited value when applied to real viruses.Comment: 10 pages, 10 figures; accepted for publication in Journal of
Biological Physic
Phonons and specific heat of linear dense phases of atoms physisorbed in the grooves of carbon nanotube bundles
The vibrational properties (phonons) of a one-dimensional periodic phase of
atoms physisorbed in the external groove of the carbon nanotube bundle are
studied. Analytical expressions for the phonon dispersion relations are
derived. The derived expressions are applied to Xe, Kr and Ar adsorbates. The
specific heat pertaining to dense phases of these adsorbates is calculated.Comment: 4 PS figure
Vibrations of a chain of Xe atoms in a groove of carbon nanotube bundle
We present a lattice dynamics study of the vibrations of a linear chain of Xe
adsorbates in groove positions of a bundle of carbon nanotubes. The
characteristic phonon frequencies are calculated and the adsorbate polarization
vectors discussed. Comparison of the present results with the ones previously
published shows that the adsorbate vibrations cannot be treated as completely
decoupled from the vibrations of carbon nanotubes and that a significant
hybridization between the adsorbate and the tube modes occurs for phonons of
large wavelengths.Comment: 3 PS figure
Comment on "Quantum Scattering of Heavy Particles from a 10 K Cu(111) Surface"
In the original paper Althoff et al. (see ibid., vol.79, p.4429 (1997))
reported a study of scattering of thermal Ne, Ar, and Kr atoms from a Cu(111)
surface in which they assessed the corresponding Debye-Waller factor (DWF) as a
function of the particle mass m in a wide range of substrate temperature T. The
experiments were interpreted by the semiclassical DWF theory in which the
projectile moves on the classical recoilless trajectory and the surface
vibrations are quantized. Siber and Gumhalter claim that the experiments
described by Althoff et al. were carried out in the quantum scattering regime
in which the semiclassical scalings of Althoff et al. do not hold and the
semiclassical DWE significantly deviates from the exact quantum one both in the
low and high T limits. Hence, it is claimed, the quantum scattering data of
Althoff et al. cannot be reliably interpreted by the semiclassical theory.Comment: 1 page (2 figures) - comment in Phys. Rev. Let
Quantum virial expansion approach to thermodynamics of He adsorbates in carbon nanotube materials: Interacting Bose gas in one dimension
I demonstrate that He adsorbates in carbon nanotube materials can be
treated as one-dimensional interacting gas of spinless bosons for temperatures
below 8 K and for coverages such that all the adsorbates are in the groove
positions of the carbon nanotube bundles. The effects of adsorbate-adsorbate
interactions are studied within the scheme of virial expansion approach. The
theoretical predictions for the specific heat of the interacting adsorbed gas
are given.Comment: 5 PS figure
Dispersion Interactions between Optically Anisotropic Cylinders at all Separations: Retardation Effects for Insulating and Semiconducting Single Wall Carbon Nanotubes
We derive the complete form of the van der Waals dispersion interaction
between two infinitely long anisotropic semiconducting/insulating thin
cylinders at all separations. The derivation is based on the general theory of
dispersion interactions between anisotropic media as formulated in [J. N.
Munday, D. Iannuzzi, Yu. S. Barash and F. Capasso, {\sl Phys. Rev. A} {\bf 71},
042102 (2005)]. This formulation is then used to calculate the dispersion
interactions between a pair of single walled carbon nanotubes at all
separations and all angles. Non-retarded and retarded forms of the interactions
are developed separately. The possibility of repulsive dispersion interactions
and non-monotonic dispersion interactions is discussed within the framework of
the new formulation
Quantum states and specific heat of low-density He gas adsorbed within the carbon nanotube interstitial channels: Band structure effects and potential dependence
We calculate the energy-band structure of a He atom trapped within the
interstitial channel between close-packed nanotubes within a bundle and its
influence on the specific heat of the adsorbed gas. A robust prediction of our
calculations is that the contribution of the low-density adsorbed gas to the
specific heat of the nanotube material shows pronounced nonmonotonic variations
with temperature. These variations are shown to be closely related to the band
gaps in the adsorbate density of states
Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition
Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available