Computational Molecular Nanostructures and Mechanical Properties of

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Computational Molecular Nanostructures and
Mechanical Properties of
Hydroxyapatite  
Bystrov V., Paramonova E., Bystrova N.,
Sapronova A., Filippov S. Institute of
Mathematical Problems of Biology RAS,
Pushchino, 142290, Moscow region, Russia e-mail
bystrov_at_impb.psn.ru , vsbys_at_yahoo.co.uk
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Computational Molecular Nanostructures and
Mechanical Properties of Hydroxyapatite
Bystrov V., Paramonova E., Bystrova N.,
Sapronova A., Filippov S. Institute of
Mathematical Problems of Biology RAS, Pushchino,
142290, Moscow region, Russia e-mail
bystrov_at_impb.psn.ru vsbys_at_yahoo.co.uk
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PERCERAMICS Project NMP3-CT-2003-504937 of FP6 (
EC ) on 2004-2006 years.   Multifunctional
percolated nanostructured ceramics fabricated
from hydroxylapatite    The project will develop
a percolated nanostructured electrically
polarized ceramics (CER) fabricated from
hydroxylapatite (HAP) to improve quality of bone
eligible bioimplants, work out new material for
immobilization of microorganisms for their
further use to product of various biologically
active compounds (BAC) and purify the
environment. A surface of CER will provide a
relevant biological non-biological interface to
adhere cells/microorganisms. A surface morphology
of CER will be supplied at a nano scale eligible
for a cell receptor tail size and will be
packed from HAP nanoparticles. The CER surface
will be charged and supplied with a web of the
canals. Engineering support employing knowledge
acquired from computational physics research on
charging and adhesion/cohesion by HAP
nanoparticles will be provided. To meet CER
applications the project is focused to
investigation of yeast cell physiology in
biofilms immobilised in novel matrices
immobilization of bacterial cells and yeasts for
the purification of the environment,
bioremediation and industrial biotechnological
processes working out of active dry preparations
of immobilized microorganisms fabrication of
bone eligible implants. The results are planned
to implement in industry, medicine, environment
and biotechnologies. New benefits in safety of
environment, health and biotechnologies will be
challenged. Professionals from computational and
material physics, chemistry, engineering of
materials and their characterization,
microbiology, biotechnology, wastewater
treatment, orthopaedics and industries will be
involved on a multidisciplinary approach and a
critical mass of the project. A sustainable
development at relevant industries and research
will spurt. The project partners cooperation
will become stronger and reach European
networking scale to strengthen and integrate the
European Research Area.?
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• Hydroxyapatite Ca5(PO4)3OH (HAP)
• corresponds to structure of mineral bones
  component
• leads to the new bone formation generated by
  osteoblasts on its surface
• if charged and polarized
• has specific surface characteristics
• improves adhesion properties
• provide additional stimulation of the interaction
  with living cells
• Processes of a charge transfer in the HAP
  structure cause the arising of the polarization
  and have electrets-like character
• Mechanism of polarization and surface electrical
  / mechanical (adhesion) properties changes are
  not clear

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Purpose Investigation of the HAP structural
changes and analyse mechanisms of charge
transfer using the computer simulation of HAP
crystal nanostructures Software Voxel
HyperChem Crystals Babel Gaussian-98

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Used experimental data on HAP structure from
ftp//ftp.geo.arizona.edu/pub/xtal/data/AMCfiles/0
1209.amc

In the program Crystals http//www.xtl.ox.ac.uk/c
rystals.html are received the .pdb file with
coordinates of all atoms (for one and several
channels) and qualitative images of HAP
structure.
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Parameters of the elementary crystal cell unit
a b 9,4166 Angstrem 0,94166 nm, c 6,8745
Angstrem 0,68745 nm.
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Parameters of cell unit
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HAP structure

channels (parallel with c axes )
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polarization / depolarization are attributed to
rotation of a proton around OH- in the colon-like
channels proton turns around O22- ion, then
moves to the next vacancy O- proton transfer on
the large distances in the channels

H ion rotation model
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Proton transfer as possible mechanism of HAP
polarization
Mathematical description of the system 1.
Model of a discrete medium

(1)

m - proton mass, un - proton displacement
Varying (1) yields the EulerLagrange equations
of motion
(2)
G1 - damping in the system, F  qE - external
field (q charge, E - electric field),
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Quantum-chemical calculations of proton transport
between two methylamine molecules with and
without external electric field, carried out with
the GAUSSIAN-98 code http//www.gaussian.com (as
example)
Change of spacing
Change of electric field  
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2.Continuous medium model
N   and l0  c0/w0  0

(3)
Potential energy
(N   and l0  c0/w0  0
(4)
equation of motion
(5)
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proton subsystem
ion subsystem
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Sofware for computational visualization and
animation of Hydroxyapatite
structure   1.The CRYSTALS software package for
single crystal X-ray structure refinement and
analysis consists of CRYSTALS, Cameron and
specially recompiled versions of SIR92 and
SHELXS.    2. The CINEMA 4D XL Bundle includes
advanced tools for professional users, including
character animation utilities and advanced
rendering and particle features.

To visualize molecular structures we have used a
plug-in for Cinema 4D developed in the
Institute of Mathematical Problems of Biology
RAS.


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Cinema 4D equipped with the plug-in can build
molecular models from PDB-files and has enabled
us to employ in the visualization the following
technologies of professional computer
3D-graphics
1.. Use of character animation (forward and
inverse kinematics) for modeling
conformational changes.
2.. Use of expressions for modeling the behavior
of molecular groups.
3.. Use of particle systems for special effects
to visualize objects without clearly
defined shape.  
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Explored initial HAP structure (group of
symmetry are P6/m and P63/m.)
P 6/m

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CONCLUSION
As results were obtained detailed
computational structural models
(quantum-chemical, soliton and continual) and
calculated parameters of HAP nanoparticles for
different symmetry groups. These results were
obtained by using and adaptation of HyperChem,
Crystals, Gaussian-98 and several special
elaborated software of Dr. Bystrov group from
IMPB. The calculated structural HAP
properties and peculiarities allow us to
understand (to clarify) the mechanism of charge
(proton) transport (transfer) and surface
charging of HAP nanoparticles. The estimated
values of surface charge is 0.1 C/m2 which is
corresponded to known experimental data.