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Review Paper

Applied Science and Convergence Technology 2023; 32(6): 134-140

Published online November 30, 2023


Copyright © The Korean Vacuum Society.

Recent Advances in Photonic Polymerase Chain Reaction Processes with Functionalized Nanomaterials

Rochani Manishikaa , b , † , Sung Eun Seoa , c , † , Kyung Ho Kima , d , Moo-Seung Leee , f , * , and Oh Seok Kwona , g , h , *

aInfectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
bDepartment of Bio-molecular Science, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
cDepartment of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
dImmunotherapy Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
eEnvironmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
fBiomolecular Science, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
gSKKU Advanced Institute of Nanotechnology (SAINT), Department of Nano Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
hDepartment of Nano Science and Technology, Sungkyunkwan University, Suwon 16419, Republic of Korea

Correspondence to:msl031000@kribb.re.kr, oskwon79@skku.edu

†These authors contributed equally to this work as first author.

Received: July 28, 2023; Revised: September 25, 2023; Accepted: October 25, 2023

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc-nd/4.0/) which permits non-commercial use, distribution and reproduction in any medium without alteration, provided that the original work is properly cited.

The amplification of genes [deoxyribose nucleic acid (DNA) and ribose nucleic acid] is a vital molecular tool not only in elementary research but also in application-oriented fields, such as industrial quality control, infectious disease diagnosis, clinical medicine development, and gene cloning. Gene amplification is directed by a photonic thermocycler, which is programmed for the alteration of the reaction temperature every few minutes to allow DNA denaturation and synthesis. Photonic polymerase chain reaction (PCR) represents a novel solution for the rapid amplification of genetic materials to achieve the goals of point-of-care diagnosis in a pandemic situation. Some nanoscale materials are able to emit thermal energy after the absorption of radiation with a wide range of frequency. This energy conversion process has been characterized by the surface plasmatic resonance of photothermal nanomaterials highly related to photonic technology. Many photonic PCR systems related to photothermal activity have been proposed while minimizing the thermal cycle time with photonic PCR techniques. The thermal cycle time of the photonic PCR is faster than conventional PCR applications, and this new technique is thought to have potential for the application to clinical and environmental diagnostics, which is the field with a need for rapid diagnosis.

Keywords: Photonic polymerase chain reaction, Nucleic acid amplification, Photothermal activity, Plasma heating

Polymerase chain reaction (PCR) is a scientific method by which deoxyribose nucleic acid (DNA) and ribose nucleic acid (RNA) can be amplified [1]. In recent years, PCR techniques have led to the development of several different types of PCR technology. Traditional PCR amplifies a specific target sequence in a sample and monitors the amplification progress using fluorescent dimerization. The fundamental goal of real-time PCR is to precisely distinguish and obtain specific nucleic acid sequences in a sample even if there is only a very small quantity of the specimen [2]. In the process of the amplification, the rate for the attainment of the fluorescent signal over a threshold level is related to the amount of the target sequence, which thereby enables quantification. The multiplex PCR technique detects more than one pathogen in a single sample and is used to identify exons and sequences in specific genes. However, the design of primers is difficult because they are meant to adhere to specific DNA sequences [3]. In nested-semi nested PCR, two sets of primers are utilized. The first set of primer is an amplified sequence and the second set of primer is complementary to the first sequence which will be shorter than the first amplified product. This method is more specific but has disadvantages such as the ‘primer and dimerization’ cross reaction [3,4].

However, most of these PCR techniques propose one or more of the following limitations: those techniques are time-consuming, nonquantitative, complex, insufficiently sensitive, and suffer from crossreactions and require the use of radioactivity. To shorten the processing time, a novel PCR method called photonic PCR was developed after being proposed by the Luke Lee team (Fig. 1). The photonic thermocycling method begun with a light emitting diode (LED) light source utilizing the photothermal reaction of characteristic nanomaterials such as graphene, gold nanoparticles (AuNPs), carbon dots, and metal NPs presented noncontact energy conversion and gained certain attention [5]. The photothermal reaction of nanomaterials specifically improves the utilization efficiency of incident light. This results in the decrease of heating and cooling rate (ramp rate) in photonic PCR compared with other PCR techniques [4].

Figure 1. Light-to-heat energy transfer process in ultrafast photonic PCR. (a) Basic steps in one PCR cycle - denaturation, annealing, and elongation. (b) Illustration of photonic heating with DNA molecules and nanoparticles (NPs) in PCR mix; Ii: incident light waves, I0: reflected ray. (c) Scheme of the photonic excitation lightto- heat conversion in a NP (energy gap between ground state and excited state).

2.1. Energy conversion process

Light to heat energy transfer

Ultrafast photonic PCR applications can be achieved using several sorts of plasmons related to volume, surface, and localized surface. Plasmons are normally collective oscillations of electromagnetic waves that are present at the bulk and surface of conducting materials and in the neighborhood of conducting particles [6]. Volume plasmons are specifically related to the natural frequency or plasma frequency of the highest response of the bulk metal material to external light or electromagnetic waves [7]. Surface plasmons are the light waves induced at the metal–dielectric interface. Localized surface plasmons can result from the confinement of a surface plasmon in a NP with a size comparable to or smaller than the wavelength of irradiated light utilized for the excitation of the plasmon. These localized surface plasmons are generated on nanostructures, such as NPs, nanopores, nanorods (NRs), nanowires, nanoribbons, nanotubes, and nanoscaffolds. Plasmonic heating of NP induces more coupling of the photon that arises from the complicated size distribution of the gaps, surface area, and networks where hot spots and a large electromagnetic field are occurred.

Photonic heating is able to rapidly and largely escalate the temperature of NPs and is favorable when used as a heat source in certain fields of application, e.g., photonic PCR described in this study. The energy conversion system which is changed from light to heat have gained increasing research interest for several decades due to their high photothermal properties. The photonic applications showed wide range from biomedical applications to solar energy harvesting to mechanical actuators. In the photonic PCR process NPs absorb light rays and release this energy into the surrounding PCR media. This process is called nonvolumetric heating, and it escalates the thermal process. The photons generated from the excitation source reach the surface of the NP, and plasmon-assisted strong light absorption can occur. The photon–photon energy conversion or the resistance of free electron movement, results in a very small region with an ultrahigh temperature in the photonic PCR media [8]. This high temperature field in the nanomaterial reaction zone is called a hot spot and shows the points of light-to-heat energy conversion in photonic PCR systems [8].


Photoexcitation is the process of exciting the atoms or molecules of a substance by radiant energy absorption [9]. The photoexcitation of metal NPs in photonic PCR can lead to very efficient nanosources of heat due to light absorption [10]. The temperature can become uniform throughout the sample although the size of the heat source is nanometric [11].

These NPs are photoexcited in the range of their localized surface plasmon resonance (LSPR) bands, and the plasmon oscillations relax non-radiatively by electron–electron and electron–lattice photon collisions [12]. This fast process (<1 ps) is followed by a relatively slower (~100 ps) photon-photon relaxation, resulting in NP heating and transferring thermal energy to the surrounding medium [13]. The same light to heat conversion mechanism holds in different nanomaterials featuring LSPR. In general, the energy gap between adjacent energy levels increases with decreasing particle size [14].

One recent advancement is the use of aggregated fluorophores that form NPs for photonic PCR processes to achieve efficient heat emission [15]. Moreover, photothermal surfaces have been provided with various geometries of gold (Au) nanomaterials, such as Au nanostars (AuNSs) and Au nanorods (AuNRs) featuring more than one LSPR near-infrared (NIR) absorption which has allowed multichannel irradiation for cumulative photoexcitation, as reported in recently developed photonic PCR processes. Further local photothermal effects of AuNSs were observed under the irradiation of NIR at low laser intensities [16,17].

Photothermal heating efficiency

The efficiency of photothermal heating is an essential parameter to practically realize photonic PCR [5]. Efficiency is highly dependent on various factors, such as the type of NP, fluid type, NP shape, NP size, NP concentration, and PCR medium temperature [18]. In this section, thermophysical factors affecting the photothermal heating efficiency of each type of nanofluids will be briefly demonstrated. The enhancement of the heating efficiency of nanofluids plays a crucial role in increasing their features of convective heat transfer [19].

Plasmonic-mediated thermocyclers mainly employ NPs such as Au, carbon, TiO2, or thin nanofilms consisted of metal substrates as heaters based on plasmonic photothermal effect to directly increase the temperature of the surrounding solution, which remarkably enhances the efficiency of heating effect and minimizes the consumption of energy [20,21]. Previous studies examined the thermophysical properties of various species of nanofluids in terms of the concentration of NP, media volume, and media temperature. Those concentrations of several nanofluids varying from 0.25 to 2.00 wt% were prepared and utilized in those previous experiments [22]. Those studies revealed that the rise of thermal efficiency is highly affect by NP concentration [23]. Additionally, the light source wavelength affects their photothermal conversion efficiency (Fig. 2) [24,25].

Figure 2. Heat generation by thin Au films by using electromagnetic waves. Calculated electromagnetic field distributions for the (a) 10 nm and (b) 120 nm thick Au films on a PMMA substrate. The wavelength of light was 450 nm with a normal incident angle. Corresponding residual heat distributions for the (c) 10 nm and (d) 120 nm thick Au films on a PMMA substrate. (e) Calculated absorption spectra of the thin Au films with various thicknesses. (f) Light-to-heat conversion efficiency of the thin Au films averaged over the emission wavelength from three different LED sources as a function of Au film thickness. Reproduced with permission from [25], Copyright 2015, Springer Nature.

However, the specific heat of nanofluids declines with increasing NP concentration which is advantageous for improving the absorption and heat transport capacity of nanofluids in PCR. In contact thermocyclers, the loss of thermal energy is induced in the thermal transfer medium or the surroundings before the heat energy reaches the reaction solution [1]. Furthermore, Au nanocrystals incorporated with semiconductor materials that have band gap energies smaller than the illumination light energy is able to enhance the efficiency of photothermal conversion due to the presence of an additional light absorption channel [26,27].

Photothermal heating in photonic PCR

Photonic heating leads to a heating rate that is tens to hundreds of times greater than that of conventional PCR and is able to be obtained by photonic PCR, which complete 30 thermocycles within less than 5 min (Fig. 3) [25,28]. The temperatures during the process of photonic PCR are able to be effortlessly managed by the irradiated light intensity, physical and chemical properties and concentration of metal NPs [5,29]. This characteristic led to the establishment of more convenient photonic PCR applications [5]. Well-dispersed metal NPs in photonic PCR solution occur volumetric heating, obtaining high heating rate and uniform temperature field, leading to fast thermocycles [25,26]. Plasmonic reaction driven heating enables the PCR solution to be isolated with an energy supplier, which conducts noncontact heating [30]. The noncontact heating procedure mainly reduce the energy and time utilized during transfer of thermal energy [4]. Disadvantages of this process are that the laser used in photonic PCR is not cost-effective, and the real-time results of the amplification process is not able to be monitored [31]. Then, scientists presented a comparably rapid plasmonic PCR with (30 cycles within 54 sec) utilizing AuNRs and a NIR laser (808 nm) as a modified version [4,31]. The real-time monitoring of amplification reaction above is available with the detection of the redshift in absorbance or the measurement of the intensity of fluorescence of the PCR solutions [4,32]. The surface plasmon resonance wavelengths of metal NPs overlap with the emission wavelength of organic dyes contained in PCR solution, which restrict the applications of fluorescence-based plasmon-driven ultrafast photonic PCR [33].

Figure 3. Ultrafast photonic PCR thermal cycling and DNA amplification. (a) Diagram of 30 ultrafast photonic PCR thermal cycles from 95 to 55 °C. (b) Heating and cooling rates obtained from ultrafast photonic thermal cycling, which were 12.0 and 6.6 °C s–1, respectively. (c) Agarose gel results presenting the amplicon from the products of photonic PCR and bench-top thermal cycler using a lamda-DNA template. Reproduced with permission from [25], Copyright 2015, Springer Nature.

2.2. Nanomaterial-based photonic PCR

Introduction to nanomaterials

NPs require the capability to control unique characteristics at the nanoscale (10−9 m), and the development of a variety of methodologies have been progressed recently to achieve this [34]. NPs are able to be synthesized naturally, be created as the byproducts of combustion reactions, or be produced purposefully through engineering to conduct specific functions [34,35]. These nanomaterials have diverse physical and chemical properties [34]. There are four major categories of nanomaterials such as carbon-based nanomaterials, inorganic-based nanomaterials, organic-based nanomaterials, and composite-based nanomaterials [25,36,37]. Nanoscale materials offer unique opportunities for the improvement of our fundamental knowledge and provision of new high-performance technological appliances (photonic devices) that improve our life more concise and subsequently better by releasing human resources from physically demanding laborious tasks [5,38].

This section mainly describes recent advancements in ultrafast photonic PCR based on the photothermal nanomaterial and presents instructions for further progresses. NPs generally perform the conversion process from photon to phonon by absorbing irradiated light for the achievement of an excited singlet states and then return to the ground state via photon emission or nonradiative relaxation [5]. Nonradiative relaxation releases thermal energy, and photon emission generates fluorescence [4,5]. Remarkable advances in the field of photonic PCR have been based on two species of metallic NPs: Au nanofilms and AuNPs with a high thermocycling rate [25,34]. Moreover, some other nanomaterials (magnetic, metal, and carbon) with photon-phonon energy conversion reaction have also been reported in recently advanced photonic PCR (Fig. 4) [5,39].

Figure 4. Photothermal NPs for photonic PCR process (graphene, fullerene, TiO2 NPs, polymer NPs, quantum dots, silica NPs, CNTs, AuNSs, AuNRs, graphene lithium-based nanomaterials, carbon-silver-based hybrid NPs, and SiO2-coated AuNPs). Reproduced with permission from [39], Copyright 2014, Royal Society of Chemistry.
Types of nanomaterial-functionalized PCR

AuNP-based photonic PCR

The advancement of photonic PCR technology is based on dispersion of AuNPs into the PCR system [5]. The light source heats the AuNPs in short pulses, thus maintaining a stable bulk reaction temperature during the nucleic acid amplification process [40,41]. Additionally, recent advancements have shown that AuNPs decrease the synthesis of nonspecific impurities during target amplification process at highly low temperatures, with hypothesized mechanisms as well as the adsorption reaction of DNA and heat-transfer improvement [42]. Moreover, Au nanospheres, Au bipyramid NPs, and AuNRs were tested in a photonic PCR system for further application advancements.

Metal NP-related photonic PCR technology is based on the light assisted PCR technology depending on the strong absorption of irradiated light in the range of infrared by water to produce thermal energy [5,29]. Prior investigations highlighted the latest optimization of PCR efficiency that is performed by adjusting the concentration of the NPs, where the condition of 1.5 µL of 10 ng mL−1 bovine serum albumin containing of 6.6 pM of AuNSs was determined as the optimal condition for a 25 µL PCR system, with a heating and cooling rate of 7.62 and 3.33 °C s–1, respectively, under excitation with a 532 nm laser [29]. Later, it was recommended that AuNRs be substituted with AuNSs for the conduction of photonic PCR owing to their relatively higher photothermal conversion efficiency [5]. In addition, previous studies have indicated the photon-phonon energy conversion process of AuNRs is to not only perform PCR, but also occur cell lysis and extract genomic samples [43]. In a past work, 30 PCR thermocycles were performed from 72 to 95 °C in < 5 min. Plasmonic photothermal colorimetric PCR was performed by using a home-built LED device, and the entire assay process was completed within 20 min due to the photonic effect. Additionally, various effects on DNA quality were observed during the amplification time [21].

Titanium nanomaterial-based photonic PCR

Studies have tended to focus on highly efficient target amplification and the impact of addition titanium dioxide (TiO2). NPs have been examined in photonic PCR benefiting from the heating by plasmonic photothermal reaction [22]. Previous studies have demonstrated that TiO2 NPs have the potential to be stable both physically and chemically. Moreover, a literature review proposed that there are significant elements that highly contribute to the enhancement of thermal conductivity in PCR reaction mixtures such as volume fraction, shape, and size of the particle [22,44]. Previous studies have indicated the successful improved utilization of TiO2 NPs with a diameter of 25 nm in the reaction solution. The majority of respondents felt that with 0.4 nM NPs, the amplification efficiency of the PCR product is able to be raised, which can be attributed to the enhancement of the conduction for thermal energy of the sample [44]. A recent development showed photonic PCR with average rates for heating and cooling of 4.44 and 2.65 °C s–1, respectively. This platform enjoys higher ramping rates compared to conventional PCR platforms with lower consumption of energy [45]. This system presents adequate stability and accuracy of the temperature with negligible deviation from the designated values [22]. Furthermore, the TiO2 photonic PCR platform is available for the simultaneous amplification of eight gene samples, which allows it applicable choice for point-of-care diagnostics. However, titanium nitride (TiN) has recently been considered a photothermal nanomaterial to enhance the activity of the PCR cycle. Furthermore, TiN has been revealed to be superior in photothermal applications because of its strong and broad optical absorption [5,22].

Ti NP-assisted PCR system is highly practical for the reduction of the overall PCR period and the amplification enhancement of DNA targets obtained from various samples [5,22,44]. TiO2 NPs are dependent on the polymorphic phases of the TiO2 molecules. Moreover, rutile NPs increased the PCR yield at concentrations of 0.4 and 0.8 nM. Rutile NPs were effective in the enhancement of the PCR amplification, including the high (60.1 %) and long (1,035 bp) guanine-cytosine (GC) content human Hspa1a promoter as well as the low (51.9 %) and short (364 bp) GC content mouse 3-hydroxy-3-methylglutaryl-CoA reductase exon 11 PCR products [46].

Magnetic nanomaterial-based photonic PCR

Engineered magnetic NPs (MNPs) represent a cutting-edge tool in diagnostics because they can be simultaneously functionalized. MNPs possess specific chemical and physical properties that can enhance the efficiency of the photothermal cycle in photonic PCR [47]. Magnetic fields organize colloidal particles rapidly into dynamic photonic structures. Magnetic particles in photonic mixtures efficiently perform nonvolumetric heating.

Few studies have been released about applications of photonic PCR. Initially, in previous studies, NP sizes were verified to evaluate photonic efficiency. The efficiency of photothermal conversion showed indistinguishable difference among NPs in the range of 60−310 nm [48]. In previous studies, individual magnetic Fe3O4 NPs under NIR irradiation were investigated, and clustered Fe3O4 NP treatment showed higher efficiency in terms of photothermal effects [5,49]. Additionally, another study showed that a water colloidal dispersion of MNPs has great potential for use as a heat-mediator agent, and efforts in this field have led to photonic studies [50]. In addition, a gold-coated MNP (composite) was investigated, and this study highlighted the potential to use this nanocomposite particle in photonic applications [51]. A study demonstrated that magnetic materials with a maximum selfheating temperature are highly advantageous in terms of core size and as a coating material [50,52]. Additionally, clustered magnetic particles showed a significant increase in the absorption of NIR in comparison to nonaggregate MNPs. Clustered NPs showed potential for use as efficient photothermal nanomaterials in photonic PCR [53,54]. Integrated ions with metalla-aromatic compounds (aromatic rings in which elements such as oxygen, carbon, oxygen, nitrogen or sulfur are replaced with transition metal atoms) were synthesized and those compounds were loaded them inside a micellar carrier [55,56]. The resulting nanocomposite showed a significant efficiency of photothermal transduction (26.6 %). The integration of photodynamic and photothermal properties obtained a synergistic impact leading to efficient photonic applications (Fig. 5) [56,57].

Figure 5. Photothermal characteristics of the synthesized Fe@Fe3O4 NPs in terms of (a, b) time and laser power, (c, d) time and concentration, and (e) cycle test (10 mg mL–1). Reproduced with permission from [57], Copyright 2020, Springer Nature.

Carbon nanomaterial-based photonic PCR

Carbon nanomaterials, such as fullerene, carbon nanotubes (CNTs), and graphene, with applications in engineering and medical fields, are highlighted [5]. Previous articles have proven the exceptional thermal and mechanical properties of carbon NPs; however, the insufficiency of information on the carbon nanomaterial effect of these parameters in photonic PCR still exists [58,59]. Prior research has reported that the thermal conductivity of single-walled CNTs (SWCNTs) which shows the diameter of 9.8 nm surpasses 2,000 W mK–1 (measured at room temperature) and increases as their size decreases [60]. As the thermal conductivity of CNT is higher than pure water, it has been presented that CNT-containing PCR suspensions possess a higher thermal conductivity and provide advantages such as better thermal transfer and heat equilibrium in PCR tubes [61].

The first investigations of CNTs in PCR were reported with the introduction of SWCNTs as PCR enhancers [62]. Shang and coworkers described that a 0.4 mM C60(OH)20 fullerene derivative completely inhibited the activity of Taq polymerase in PCR [61].

Another experiment tracked the primer-template-polymerasegraphene oxide interactions included in PCR process utilizing a capillary electrophoresis/laser-induced fluorescence polarization assay [56,61]. The results presented that the introduction of graphene oxide induced the synthesis of a matched primer-template complex, but precluded the formation of a mismatched primer-template complex for photonic PCR process, suggesting that the interactions between the primers and graphene oxide play an essential role (Table I) [63].

Table 1 . Photothermal heating efficiency of different photothermal nanomaterials..

Photothermal nanomaterialDiameter (nm)Wave length (nm)Photothermal conversion efficiency (%)Heating rate (°C min–1)Cooling rate (°C min–1)Average PCR volume (µL)Ref.
TiO2 NPs50–8035040.8036.511.820[22]
Graphene oxide1–580859.0043.815.02–10[6466]
Fe3O4 nanoclusters4–670038.007.14.810[62]
Graphene oxide20–3080044.007.56.92-10[64]

2.3. Emerging directions in photonic PCR

Considering potential future needs, several promising developments in photonic PCR are emerging. First, portable genetics analysis instruments with photonic heating with sample in–answer-out capability are needed for the on-site efficient identification of human genes or detection of pathogens. This type of application is well-timed and effective because biothreats are of increasing concern for civilian populations. Second, integrated DNA sequencing systems that can reduce the total cost of de novo sequencing by composite nanomaterials will yield great benefits to all genome-related research. Furthermore, 2D photonic nanocrystals incorporated in the sample tube wall will allow for novel high-efficiency high-temperature light-to-heat conversion schemes for application with different sample dispersion tubes [56]. Additionally, surface modifying of NPs by chemical treatments (such as the absorption of silane coupling agents) will be a useful method to improve the dispersion stability of NPs in various PCR liquid media [61]. Moreover, scientists can work with composite nanomaterials to reduce the photonic PCR cycle time. Silver carbon-based PCR, conductive films, and hybrid nanomaterials with two NPs (e.g., iron oxide and MNPs) are also potential materials that can be used in future photonic PCR processes. As the existing PCR device setup is based on the structure of single reaction area, the advanced investigations will concentrate on the integration of increase of the number of wells and an LED array to engage high-throughput multiplexed amplification, as well as optimizing the condition of PCR reaction area with nanomaterials to achieve uniform heating efficiency in PCR media.

Photonic PCR offers a wealth of possibilities for efficiency in many fields of medicine. The progress made over the last decade has been phenomenal and has resulted in the development of an extremely efficient and versatile laboratory technique for PCR. Nanomaterials in photonic PCR possess unique physical and chemical properties and can provide amazing outcomes for the diagnostic world. The direct addition of nanomaterials into the photonic PCR helps to reduce the thermocycling time and improve the efficiency of the total process.

Many photonic PCR applications are proof-of-concept types. Future attempts in photonic PCR should consider new compositions, combinations, and mechanical structures. Industrial and clinical applications should be encouraged to utilize multidisciplinary participation to have a real societal impact on the up-conversion of photonic diagnostic technology. In conclusion, future directions should be to fabricate an all-in-one combined photonic PCR device related to photothermal nanomaterials consisting of gene extraction, synthesis of amplicon, and detection ability. Moreover, conjugated nanomaterialbased photonic PCR applications have the potential to be used in future devices. All these possibilities can help to accelerate the development of diagnostics in terms of gene-related causes.

This research was supported by the Defense Acquisition Program Administration (ADD-911255202).

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