Chemical and optical characterization of

Psammodictyon panduriforme (Gregory) Mann

comb. nov. (Bacillariophyta) frustules
Ed Camargo,1 Perez Coca John Jaime,1 Chia-Feng Lin,2,* Ming-Shiou Lin,2 Tzu-Yun
Yu,2 Meng-Chuan Wu,1 Su-Yuan Lai,3 and Min-Ying Wang1
1
Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
2
Department of Materials Science and Engineering, National Chung Hsing University, Taichung 402, Taiwan
3
Department of Food Science, Central Taiwan University of Science and Technology, Taichung 40605, Taiwan
*cflin@dragon.nchu.edu.tw

Abstract: The amorphous frustule with a mesopore pattern of the peanut-

shaped marine diatom Psammodictyon panduriforme (Gregory) Mann
comb. nov. (Bacillariophyta) was analyzed. Two dominating
photoluminescence emission peaks in P. panduriforme were observed at
417 nm and 534 nm, and are attributed to radiative luminescence caused by
oxygen-vacancy defects on the diatom frustules. Under the 355 nm pulse
laser illumination, a narrow PL spectrum of frustules from the diatom P.
panduriforme was observed at 475 nm with a 9.3 nm linewidth that may be
caused by the resonance cavity effect on the quasi-regular pore structure on
the frustules. Diatom frustules from Psammodictyon panduriforme
(Gregory) Mann comb. nov. (Bacillariophyta) have quasi-regular pore
patterns on the biosilica valves that can be utilized in optoelectronic devices
with mesoporous structures.
©2016 Optical Society of America
OCIS codes: (160.1435) Biomaterials; (170.0170) Medical optics and biotechnology.

References and links

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1. Introduction
Diatoms are unicellular algae with a cell wall (also named as frustules) composed primarily of
glass-like SiOx [1]. The diatomic frustules are distinct, highly ornamented because they are
perforated with unique pores that vary greatly depending on the species. As a result of their
unique morphology and porous biosilica walls, diatoms have been applied in nanotechnology
as gratings [2] and in photolithography as masks [3]. The surface of the diatom frustules is
covered with arrays of nano-pores and micro-pores with pore diameters ranging from several
nm up to micron scale. The light weight and strong mechanical strength properties of diatom
frustules are believed to be derived from the tiny pore structures. Sub-micro regular arrays of
holes have been characterized in frustules [4,5]. Gale et al. [6] reported that the antibody-
functionalized diatom biosilica frustules serve as a microscale biosensor platform for selective
and label-free photoluminescence (PL) based detection of immunocomplex formations. The
photonic properties [7] and the light focusing ability [8] of diatoms had also been reported.
In this study, the peanut-shaped marine diatom, Psammodictyon panduriforme (Gregory)
Mann comb. nov. (Bacillariophyta), was analyzed as an amorphous SiO2 structure of the
diatom frustules with mesoporous patterns in the valves [9]. Optical and material properties of
diatom frustules from P. panduriforme are analyzed in detail. Characterization of chemical
and optical properties of diatom frustules is important and interesting because its diverse
shapes, porous/patterned micro-structures, various optical properties such as fluorescence
emission and light focusing ability, and biocompatibility allow these to be utilized in the field
of biophotonics, sensors, microfluidics, and especially optoelectronic devices.
2. Experiments
The photosynthetic peanut-shaped marine diatom Psammodictyon panduriforme (Gregory)
Mann comb. nov. (Bacillariophyta), was grown by controlling at a temperature of 24°C for
14hrs illumination/10hrs darkness cycles in a 100rpm shaker (orbital shaker). Intact biosilica
of P. panduriforme cells were isolated by treating them with a dilute H2SO4 solution. 50ml
aliquots of culture suspension were collected and centrifuged at 2000rpm for 10minutes. The
pellet was re-suspended in 50ml of de-ionized water, centrifuged in the same conditions, and
washed again for five times. The washed diatom cell pellet from P. panduriforme was
resuspended in dilute H2SO4 solution, and reacted in a 60°C water bath for 10minutes. The
liquid in the suspension turned dark green. The treated cell mass from P. panduriforme was

#258450 Received 28 Jan 2016; revised 24 Mar 2016; accepted 24 Mar 2016; published 4 Apr 2016
© 2016 OSA 1 May 2016 | Vol. 6, No. 5 | DOI:10.1364/OME.6.001436 | OPTICAL MATERIALS EXPRESS 1437
washed five times in de-ionized water, and then stored at 4°C. Unstained P. panduriforme
cells and clean diatom frustules (also from P. panduriforme) were placed on a 0.17mm cover
slip and observed using confocal microscopy (Olympus FV1000, Japan). The objective used
was 40 × from Olympus (0.9 N.A.,Olympus, Japan). The samples were excited by using a 405
nm laser diode as an excitation source. Field emission scanning electron microscopy (cold
cathode type, JEOL Ltd., JSM-6700F, Tokyo, Japan) was conducted on an Energy Dispersion
X-ray Spectroscopy (EDS) system (Noran Phage-ID). The SEM micrographs were used to
observe the morphology and microstructure of the diatom Psammodictyon panduriforme
(Gregory) Mann comb. nov. (Bacillariophyta). The surface morphology, micro-structure, and
crystal structures of the diatom P. panduriforme were examined by high resolution
transmission electron microscopy (HRTEM/JEM-2100, Tokyo, Japan) and operated at an
accelerating voltage of 160 kV. A piece of glass with diatoms from P. panduriforme was
scraped and dispersed on a carbon coated copper mesh (200mesh, Agar Scientific Ltd., U.K.).
The crystal structures and the crystal lattices were determined by using selected area electron
diffraction patterns. Elemental analysis was performed by energy dispersion spectroscopy
(EDS, OXFORDEXL 10/T). It analyzed the elements in diatom frustules from P.
panduriforme. The functional groups and chemical bonding of the diatom frustules valve
biosilica from P. panduriforme were directly analyzed by transmission Fourier transform
infrared spectroscopy (FT-IR). The FT-IR spectra were collected by a Spectrum One (Perkin
Elmer, Norwalk, CT, USA). The scan number was eight with a range from 400 to 4000cm−1
with a resolution of 2 cm−1. A HRXRD diffractometry pattern was another type of data used
to characterize the micro-structures and crystal structures of the diatom P. panduriforme.
HRXRD patterns were detected by a Bruker D8 Advance diffractometer (Germany). The
source of HRXRD was Cu Kα (1.542 angstrom) and the diffractometer was operated at 40kV
and 41mA. The scanning rate was 0.05° at 2θ/sec and the range of 2θ was from 5° to 80°. The
micro-photoluminescence (µ-PL) spectra were measured by using a 325nm He–Cd laser
(Kimmon IK3452R-F) and a 355nm Nd-YVO4 pulse laser as the excited sources. Laser beam
was focused to a 10 µm diameter laser spot size with a convex lens. The PL spectra were
collected by using a Jobin Yvon Triax 550 monochromator with a 600lines/mm grating and a
matched liquid nitrogen cooled CCD detector.
3. Results and discussion
500
Live diatom
Diatom frustule
400 670nm
PL intensity (a.u.)

300 520nm

200 470nm

100 x3

0
400 500 600 700 800
Wavelength (nm)

Fig. 1. The PL spectra of live diatoms and diatom frustules P. panduriforme diatoms were
measured. The PL intensity of diatom frustules was amplified about 3-fold to show the peaks.

The fluorescence emission spectra of live P. panduriforme diatoms and diatom frustules with
the organic matter removed from them were observed with a 405nm diode laser illumination
as shown in Fig. 1. A distinct emission peak wavelength at 670nm (red fluorescence) was
measured that indicated an emission from the chlorophyll[R] in live diatom P. panduriforme

#258450 Received 28 Jan 2016; revised 24 Mar 2016; accepted 24 Mar 2016; published 4 Apr 2016
© 2016 OSA 1 May 2016 | Vol. 6, No. 5 | DOI:10.1364/OME.6.001436 | OPTICAL MATERIALS EXPRESS 1438
cells. After removing the organic material from the diatom P. panduriforme, the peak
wavelengths of the diatom frustules were observed at 470nm and 520nm.
The SEM micrographs and the EDS characterization of frustules of the diatom P.
panduriforme were measured as seen in Fig. 2. In Figs. 2(a) and 2(b), the full view of the
diatom is observed showing that P. panduriforme has peanut-like shaped frustules. The silica
frustule consists of two overlapping valves that are joined by girdle bands. The length of the
frustules ranges from 8 to 15μm and the width from 5 to 8μm. Krögerl et al. [10] reported that
a diatom cell wall consists of two thecae: an epitheca (ET) and a hypotheca (HT) as the valve
structures, with the girdle bands (GB) at the sidewall surface. The isoalted diatom cell wall in
P. panduriforme was observed to have a species-specific pore structure on the valve surface
and on the girdle band sidewall as shown in Fig. 2(a). In Fig. 2(b), the complete diatom
frustules from P. panduriforme with the ET and the HT structures were observed in detail for
structural analysis. In Fig. 2(c), the mesoporous frustule structure of the diatom P.
panduriforme is observed in side view of the girdle band structure. Figures 2(d),(e) show the
magnified surface of the frustules biosilica valve in the diatom P. panduriforme with the
porous structures. The frustules exhibit regular shapes, ranging between 350 and 400nm in
size and are occluded by internal cribra with circular pores of 40–60 nm in diameter. Figure
2(f) is the EDS spectrum of the frustule biosilica from the diatom P. panduriforme. The peaks
of sodium, calcium and magnesium are attributed to tiny amounts of residual sea water salts.
The aluminum signal is correlated to the Al-coated glass substrate. There are two main peaks,
silicon (1.72keV) and oxygen (0.52keV). The molar ratio of Si/O is 1/3.6 which is close to the
1/4 and corresponding to chemical stoichiometric composition of SiO2.

(a) (b) ET (c) ET (epitheca)

HT

GB 2μm HT 2μm 500nm

GB
(d) ET (epitheca) (e) Mesoporous structure (f)

500nm 200nm
KeV

Fig. 2. SEM micrographs and EDS characterization of frustules biosilica from the diatom
Psammodictyon panduriforme: (a)(b) Full views of single diatom frustules. (c) The porous
structure of the sidewall region of P. panduriforme. (d)(e) Magnified micrographs of the valve
structures of P. panduriforme. The mesoporous structure can be observed in the valve
structure. (f) The EDS spectrum of frustules from the diatom P. panduriforme showing the
biosilica composition.

The X-ray diffraction curves of the frustules from the diatom P. panduriforme and the
glass substrate serving as a template were measured and are shown in Fig. 3(a). The material
properties of frustules from the diatom P. panduriforme are identified by a broad peak
indicating that diatom frustules are composed of an amorphous biosilica similar to glass
substrate. Diatom frustules consist of porous and amorphous bio-mineralized architectures.

#258450 Received 28 Jan 2016; revised 24 Mar 2016; accepted 24 Mar 2016; published 4 Apr 2016
© 2016 OSA 1 May 2016 | Vol. 6, No. 5 | DOI:10.1364/OME.6.001436 | OPTICAL MATERIALS EXPRESS 1439
From the EDS and the x-ray diffraction results, the frustules from the diatom P. panduriforme
were analyzed as amorphous silicic acid, SiO2, with a porous wall structure.

(a) (b)
700
Si-H
Diatom frustules 100 Diatom frustules
Si-H 2
600 Glass
80

Reflectance(%)
500

intensity(a.u.)
60 C-H Si-OH
Si-OH H-0-H
400
Glass 40 Si-O-Si
Si-C
300
20
200
Diatom 0
100
-20 Si-O-Si
0
5 10 15 20 25 30 35 40 3600 3000 2400 1800 1200 600
-1
2θ Wavenumber (cm )

Fig. 3. (a) The X-ray diffraction pattern of the biosilica in the diatom Psammodictyon
panduriforme compared to commercial glass. (b) The FT-IR spectrum of the diatom biosilica
in P. panduriforme.

The FT-IR spectrum of the frustules in the diatom P. panduriforme is shown in Fig. 3(b).
The most common peaks of the diatom frustules consisted of the Si-O-Si stretching at 1040-
1095cm−1, the Si-O-Si bending at 797-800cm−1, the Si-O stretching of Si-OH groups at
797cm−1, and O-H stretching of hydroxyl groups at 3435cm−1. The weak signals of 664 and
2200cm−1 represents very tiny amounts of Si-H bands. The peaks of 3740-3780 and 1630-
1640cm−1 were identified as Si-OH bonds. There are also peaks of carboxyl groups, including
C = O stretching at 1735cm−1, C-H stretching at 2850 (CH2) and 2925 (CH3) cm−1. A small C-
H peak at 2917cm−1 and a possible peak at 800 cm−1 covered by the Si-O-Si at the same
location. The source of the carboxyl groups are owed to the residual organic materials in the
diatom P. panduriforme. They correspond to the primary amide of proteins bounded on the
surface of the diatom biosilica.

(a) 5x10
4 (b) 2200
Excited by 325nm HeCd laser Excited at 355nm pulse laser
Measured temperature
4 10K 2000
4x10
PL Intensity (a.u.)

475.2nm
PL Intensity (a.u.)

300K
534nm 1800
4
3x10
1600
4 417nm
2x10
1400

4
1x10 1200

0 1000
300 400 500 600 700 800 440 460 480 500 520
Wavelength (nm) Wavelength (nm)

Fig. 4. The micro-photoluminescence spectra of diatom frustule were measured by (a) 325 CW
laser and (b) 355nm pulse laser acted the excitation laser sources.

The μ-PL spectra of frustules of the diatom P. panduriforme were measured as shown in
Fig. 4(a) excited by a continuous-wavelength 325nm HeCd laser. The two dominant peak
wavelengths and the line-widths of the PL spectra were measured at 417 nm (39nm) and
534nm (121nm). The peak wavelength of the frustules from the diatom P. panduriforme was
measured at 534nm (2.32 eV) similar to what Stefano et al.’s reports [11]. Zhu et al. [12]
reported that three PL bands centered around 1.7, 2.1, and 2.9 eV have been detected from a-
SiOx:H material prepared by dual-plasma chemical vapor deposition. The radiative defect

#258450 Received 28 Jan 2016; revised 24 Mar 2016; accepted 24 Mar 2016; published 4 Apr 2016
© 2016 OSA 1 May 2016 | Vol. 6, No. 5 | DOI:10.1364/OME.6.001436 | OPTICAL MATERIALS EXPRESS 1440
luminescence mechanisms are attributed to Si–OH groups (2.9 eV) or to oxygen-vacancy
defects (2.1 eV) [13–15]. The biosilica composition and the radiative recombination from
oxygen vacancy of the frustules of the diatom P. panduriforme were analyzed through FTIR
analysis and the PL spectra, respectively. By reducing the measurement temperature from
300K to 10K in the vacuum chamber, the PL emission intensities of the diatom frustules was
slightly increased at 10K indicating that the thermal quench phenomenon was not clearly
observed in the diatom frustules. The radiative defect luminescence was confined by the
mesoporous [16] structure in the frustules of P. panduriforme. In Fig. 4(b), the PL spectrum
of the frustules of the diatom P. panduriforme was measured when excited by a 355nm Nd-
YVO4 pulse laser at 300K. The peak wavelength and the line width of the diatom frustules
were measured at 475.2 nm and 9.3nm, respectively. The broadened PL emission linewidth
was measured through a 325nm CW HeCd laser, and a quasi-regular pore structure was
observed in the diatom frustules. Under a pulsing 355nm laser excitation, the PL emission
linewidth was reduced which could have been caused by the resonance cavity effect in the
quasi-regular pore structure. This linewidth reducing phenomenon is similar to the photonic
crystal structure in Si- and GaAs-based optoelectronic devices with a regular sub-micro air
holes pattern [17,18].
High resolution TEM micrographs of frustule microstructure from the diatom
Psammodictyon panduriforme are shown in Figs. 5. Full view of the single peanut-shaped
diatom frustules measured 11μm in length and 5μm in width, respectively (Fig. 5a). The
surface morphology of frustules from the diatom P. panduriforme consisted of the biosilica
valve and the pore pattern structures shown in Figs. 5(b),(c). The pore array is periodic with
regular nanostructures on the frustules biosilica valve of P. panduriforme. In Fig. 5(d), the
edge of the girdle band of the diatom frustules is filled with mesoporous structures. There are
two to four mesoporous in a micro-grain structure. The fine structure of the pore array on
frustules valves from the diatom P. panduriforme was observed in Fig. 5(e). The diameter of
the pore size measured in average, 50nm. In Fig. 5(f), the ring diffraction pattern of the
frustules from the diatom P. panduriforme was observed demonstrating its amorphous
biosilica structure.
To analyze the light extraction properties, P. panduriforme frustules were spreaded on an
InGaN-based light emitting diodes epitaxial wafer. Wang et al. [19] reported a self-assembly
of nanostructured diatom microshells into patterned arrays. During the coating process, the
diatom frustules were dispersed in an IPA solvent and spin coated onto the ITO layer which
acted as a transparent conductive layer for the fabricated InGaN LED wafer. The thickness
was from a 1 to a 2-layer diatom layer. The LED structure consisted of a low-temperature
grown 30nm-thick GaN buffer layer, a 4μm-thick n-type GaN:Si layer, 0.2μm-thick
InGaN/GaN multiple quantum wells active layers, and a 0.2μm-thick magnesium-doped p-
type GaN:Mg layer that grown on the sapphire substrate through a metalorganic chemical
vapor deposition system [20,21]. The PL spectra were analyzed through an angle-resolved
photoluminescence measurement [22] with a 405nm excitation laser illuminated from the
backside sapphire substrate to excite the InGaN active layer. The PL emission light from the
InGaN active layer transmitted through the diatom frustules layer and detected at the normal
direction by varying the detected angles. The PL emission intensity of the InGaN active layer
was larger than the PL emission intensity of P. panduriforme frustules. The PL emission
spectra were measured by a multi-channel CCD detector with a 550mm focal length
monochromator. The PL spectra was detected at the front-side of the flat LED wafer without
and with the P. panduriforme frustules structure shown in Figs. 6(a),(b). The wavelength-
resolved angular far-field patterns of the P. panduriforme PL spectra were measured. In Fig.
6(a), the Fabry–Pérot (FP) interference line-patterns were observed in the LED wafer that
indicated the smooth InGaN epitaxial layer at top air/GaN surface. In Fig. 6(b), the FP
interference line-patterns were not observed in the LED wafer with the P. panduriforme

#258450 Received 28 Jan 2016; revised 24 Mar 2016; accepted 24 Mar 2016; published 4 Apr 2016
© 2016 OSA 1 May 2016 | Vol. 6, No. 5 | DOI:10.1364/OME.6.001436 | OPTICAL MATERIALS EXPRESS 1441
frustules layer. This is the results of the PL emission light scattered by P. panduriforme
frustules with micro- and meso-pore structure on the LED wafer.

4μm 200nm

0.4μm 0.4μm

0.02 1/nm
100nm

Fig. 5. HR-TEM images and diffraction ring of frustule biosilica in the diatom Psammodictyon
panduriforme. (a) The HRTEM micrographs of full view of single diatom frustules from P.
panduriforme, (b) and (c) the surface of diatom frustule biosilica valve from P. panduriforme
with the pore structures, (d) The edge of the girdle band of frustules from the diatom P.
panduriforme with plenty of mesoporous, (e) The fine structure of pore array on the valve
frustules from the diatom P. panduriforme. (f) The ring diffraction pattern of diatom frustules
biosilica in P. panduriforme.

The far-field radiation patterns of both LED samples were measured through angle-
resolved PL measurements shown in Fig. 6(c). The divergent angles of the LEDs are
identified as the angle of the half-maximum PL emission intensity. The divergent angles of
the LED wafer with and without diatom frustule layer were measured. The divergent angles of
the LED wafer without and with P. panduriforme frustule layer were calculated at 147° and
136°, respectively. The PL emission light can be extracted through the ITO layer and coupled

#258450 Received 28 Jan 2016; revised 24 Mar 2016; accepted 24 Mar 2016; published 4 Apr 2016
© 2016 OSA 1 May 2016 | Vol. 6, No. 5 | DOI:10.1364/OME.6.001436 | OPTICAL MATERIALS EXPRESS 1442
with the diatom frustules. For the far-field radiation pattern, the interference lines pattern were
observed in the ST-LED due to the light reflectance at the top of the air/GaN and at the
bottom of the GaN/sapphire flat interfaces. No interference and narrowing divergent angles
were observed in the InGaN LED with the top diatom frustule layer. The light extraction
efficiency in the InGaN LED can be increased through a low light refractive index diatom
frustule layer above the ITO conductive layer. The divergent angle is slightly reduced due to
the light coupling into the diatom frustules and the light has been redirected in the normal
direction of the LED chips. The slightly narrow divergent angle of LED wafer with P.
panduriforme frustule layer was caused by the PL emission light coupled with the pore
structure of the diatom frustule to improve the light extraction efficiency.
490 490
22000
(a) LED wafer 21120 (b) Diatom on LED wafer
480
19360 480
17600
15840
470 470
14080

Wavelength(nm)
Wavelength(nm)

12320
460 460
10560
8800.0
450 450
7040.0
5280.0
440 3520.0 440

1760.0
430 0.0000 430
0 30 60 90 120 150 180 0 30 60 90 120 150 180

Angle(degree) Angle(degree)

(c) Diatom on LED wafer

90 LED wafer
25000
120 60
20000

15000
150 30
10000

5000

0 180 0

Fig. 6. The wavelength-resolved angular far-field patterns of the PL spectra of the LED wafer
(a) without Psammodictyon panduriforme frustule layer and (b) with Psammodictyon
panduriforme frustule layer. (c) The far-field radiation patterns of the LED wafer without and
with the frustule layer from the diatom Psammodictyon panduriforme were measured through
angle-resolved PL measurements.

4. Conclusion
The frustules of the peanut-shaped marine diatom Psammodictyon panduriforme (Gregory)
Mann comb. nov. (Bacillariophyta) were analyzed as the amorphous silica structure with
mesoporous structure. The two dominant PL emission peaks were observed at 417nm and
534nm and were attributed to the radiative-defect luminescence from the oxygen-vacancy
defects on the diatom frustules from P. panduriforme. Under pulse laser illumination, the
narrow PL spectrum of the diatom frustules from P. Panduriforme was observed to be caused
by the quantum confinement effect on the mesoporous structure in the diatom frustules. The
diatom frustules in P. panduriforme consisted of periodic nano-scale biosilica valves that can
be utilized in optoelectronic devices with mesoporous structures.
Acknowledgment
The authors gratefully acknowledge the financial support for this research by the Ministry of
Science and Technology of Taiwan under grant No. 102-2218-E-005-010-MY3 and 104-
2221-E-005-014-MY2. Chia-Feng Lin, Su-Yuan Lai, and Min-Ying Wang contributed
equally to this work.

#258450 Received 28 Jan 2016; revised 24 Mar 2016; accepted 24 Mar 2016; published 4 Apr 2016
© 2016 OSA 1 May 2016 | Vol. 6, No. 5 | DOI:10.1364/OME.6.001436 | OPTICAL MATERIALS EXPRESS 1443