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- All Subjects: Nanoscience
- Creators: Tongay, Sefaattin
Description
ABSTRACT The unique structural features of deoxyribonucleic acid (DNA) that are of considerable biological interest also make it a valuable engineering material. Perhaps the most useful property of DNA for molecular engineering is its ability to self-assemble into predictable, double helical secondary structures. These interactions are exploited to design a variety of DNA nanostructures, which can be organized into both discrete and periodic structures. This dissertation focuses on studying the dynamic behavior of DNA nanostructure recognition processes. The thermodynamics and kinetics of nanostructure binding are evaluated, with the intention of improving our ability to understand and control their assembly. Presented here are a series of studies toward this goal. First, multi-helical DNA nanostructures were used to investigate how the valency and arrangement of the connections between DNA nanostructures affect super-structure formation. The study revealed that both the number and the relative position of connections play a significant role in the stability of the final assembly. Next, several DNA nanostructures were designed to gain insight into how small changes to the nanostructure scaffolds, intended to vary their conformational flexibility, would affect their association equilibrium. This approach yielded quantitative information about the roles of enthalpy and entropy in the affinity of polyvalent DNA nanostructure interactions, which exhibit an intriguing compensating effect. Finally, a multi-helical DNA nanostructure was used as a model `chip' for the detection of a single stranded DNA target. The results revealed that the rate constant of hybridization is strongly dominated by a rate-limiting nucleation step.
ContributorsNangreave, Jeanette (Author) / Yan, Hao (Thesis advisor) / Liu, Yan (Thesis advisor) / Chen, Julian J.-L. (Committee member) / Seo, Dong Kyun (Committee member) / Arizona State University (Publisher)
Created2011
Description
As a rapidly evolving field, nucleic acid nanotechnology focuses on creating functional nanostructures or dynamic devices through harnessing the programmbility of nucleic acids including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), enabled by the predictable Watson-Crick base pairing. The precise control over the sequence and structure, along with the development of simulation softwares for the prediction of the experimental implementation provides the base of designing structures or devices with arbitrary topology and operational logic at nanoscale. Over the past 40 years, the thriving field has pushed the boundaries of nucleic acids, from originally biological macromolecules to functional building blocks with applications in biomedicine, molecular diagnostics and imaging, material science, electronics, crystallography, and more have emerged through programming the sequences and generating the various structures or devices. The underlying logic of nucleic acid programming is the base pairing rule, straightforward and robust. While for the complicated design of sequences and quantitative understanding of the programmed results, computational tools will markedly reduced the level of difficulty and even meet the challenge not available with manual effort. With this thesis three individual projects are presented, with all of them interweaving theory/computation and experiments. In a higher level abstraction, this dissertation covers the topic of biophysical understanding of the dynamic reactions, designing and realizing complex self-assembly systems and finally super-resolutional imaging. More specifically, Chapter 2 describes the study of RNA strand displacement kinetics with dedicated model extracting the reaction rates, providing guidelines for the rational design and regulation of the strand displacement reactions and eventually biochemical processes. In chapter 3 the platform for the design of complex symmetry of the self-assembly target and first experimental implementation of the assembly of pyrochlore lattices with DNA origamis are presented, which potentially can be applied to manipulate lights as optical materials. Chapter 4 focuses on the in solution characterization of the periodicity of DNA origami lattices with super-resolutional microscopy, with algorithms in development for three dimensional structural reconstruction.
ContributorsLiu, Hao (Author) / Yan, Hao (Thesis advisor) / Sulc, Petr (Thesis advisor) / Guo, Jia (Committee member) / Heyden, Matthias (Committee member) / Arizona State University (Publisher)
Created2023
Description
Layer structured two dimensional (2D) semiconductors have gained much interest due to their intriguing optical and electronic properties induced by the unique van der Waals bonding between layers. The extraordinary success for graphene and transition metal dichalcogenides (TMDCs) has triggered a constant search for novel 2D semiconductors beyond them. Gallium chalcogenides, belonging to the group III-VI compounds, are a new class of 2D semiconductors that carry a variety of interesting properties including wide spectrum coverage of their bandgaps and thus are promising candidates for next generation electronic and optoelectronic devices. Pushing these materials toward applications requires more controllable synthesis methods and facile routes for engineering their properties on demand.
In this dissertation, vapor phase transport is used to synthesize layer structured gallium chalcogenide nanomaterials with highly controlled structure, morphology and properties, with particular emphasis on GaSe, GaTe and GaSeTe alloys. Multiple routes are used to manipulate the physical properties of these materials including strain engineering, defect engineering and phase engineering. First, 2D GaSe with controlled morphologies is synthesized on Si(111) substrates and the bandgap is significantly reduced from 2 eV to 1.7 eV due to lateral tensile strain. By applying vertical compressive strain using a diamond anvil cell, the band gap can be further reduced to 1.4 eV. Next, pseudo-1D GaTe nanomaterials with a monoclinic structure are synthesized on various substrates. The product exhibits highly anisotropic atomic structure and properties characterized by high-resolution transmission electron microscopy and angle resolved Raman and photoluminescence (PL) spectroscopy. Multiple sharp PL emissions below the bandgap are found due to defects localized at the edges and grain boundaries. Finally, layer structured GaSe1-xTex alloys across the full composition range are synthesized on GaAs(111) substrates. Results show that GaAs(111) substrate plays an essential role in stabilizing the metastable single-phase alloys within the miscibility gaps. A hexagonal to monoclinic phase crossover is observed as the Te content increases. The phase crossover features coexistence of both phases and isotropic to anisotropic structural transition.
Overall, this work provides insights into the controlled synthesis of gallium chalcogenides and opens up new opportunities towards optoelectronic applications that require tunable material properties.
In this dissertation, vapor phase transport is used to synthesize layer structured gallium chalcogenide nanomaterials with highly controlled structure, morphology and properties, with particular emphasis on GaSe, GaTe and GaSeTe alloys. Multiple routes are used to manipulate the physical properties of these materials including strain engineering, defect engineering and phase engineering. First, 2D GaSe with controlled morphologies is synthesized on Si(111) substrates and the bandgap is significantly reduced from 2 eV to 1.7 eV due to lateral tensile strain. By applying vertical compressive strain using a diamond anvil cell, the band gap can be further reduced to 1.4 eV. Next, pseudo-1D GaTe nanomaterials with a monoclinic structure are synthesized on various substrates. The product exhibits highly anisotropic atomic structure and properties characterized by high-resolution transmission electron microscopy and angle resolved Raman and photoluminescence (PL) spectroscopy. Multiple sharp PL emissions below the bandgap are found due to defects localized at the edges and grain boundaries. Finally, layer structured GaSe1-xTex alloys across the full composition range are synthesized on GaAs(111) substrates. Results show that GaAs(111) substrate plays an essential role in stabilizing the metastable single-phase alloys within the miscibility gaps. A hexagonal to monoclinic phase crossover is observed as the Te content increases. The phase crossover features coexistence of both phases and isotropic to anisotropic structural transition.
Overall, this work provides insights into the controlled synthesis of gallium chalcogenides and opens up new opportunities towards optoelectronic applications that require tunable material properties.
ContributorsCai, Hui, Ph.D (Author) / Tongay, Sefaattin (Thesis advisor) / Dwyer, Christian (Committee member) / Zhuang, Houlong (Committee member) / Arizona State University (Publisher)
Created2018
Description
Carbon nanomaterials have caught tremendous attention in the last few decades due to their unique physical and chemical properties. Tremendous effort has been made to develop new synthesis techniques for carbon nanomaterials and investigate their properties for different applications. In this work, carbon nanospheres (CNSs), carbon foams (CF), and single-walled carbon nanotubes (SWNTs) were studied for various applications, including water treatment, energy storage, actuators, and sensors.
A facile spray pyrolysis synthesis technique was developed to synthesize individual CNSs with specific surface area (SSA) up to 1106 m2/g. The hollow CNSs showed adsorption of up to 300 mg rhodamine B dye per gram carbon, which is more than 15 times higher than that observed for conventional carbon black. They were also evaluated as adsorbents for removal of arsenate and selenate from water and displayed good binding to both species, outperforming commercial activated carbons for arsenate removal in pH > 8. When evaluated as supercapacitor electrode materials, specific capacitances of up to 112 F/g at a current density of 0.1 A/g were observed. When used as Li-ion battery anode materials, the CNSs achieved a discharge capacity of 270 mAh/g at a current density of 372 mA/g (1C), which is 4-fold higher than that of commercial graphite anode.
Carbon foams were synthesized using direct pyrolysis and had SSA up to 2340 m2/g. When used as supercapacitor electrode materials, a specific capacitance up to 280 F/g was achieved at current density of 0.1 A/g and remained as high as 207 F/g, even at a high current density of 10 A/g.
A printed walking robot was made from common plastic films and coatings of SWNTs. The solid-state thermal bimorph actuators were multifunctional energy transducers powered by heat, light, or electricity. The actuators were also investigated for photo/thermal detection. Electrochemical actuators based on MnO2 were also studied for potential underwater applications.
SWNTs were also used to fabricate printable electrodes for trace Cr(VI) detection, which displayed sensitivity up to 500 nA/ppb for Cr(VI). The limit of detection was shown to be as low as 5 ppb. A flow detection system based on CNT/printed electrodes was also demonstrated.
A facile spray pyrolysis synthesis technique was developed to synthesize individual CNSs with specific surface area (SSA) up to 1106 m2/g. The hollow CNSs showed adsorption of up to 300 mg rhodamine B dye per gram carbon, which is more than 15 times higher than that observed for conventional carbon black. They were also evaluated as adsorbents for removal of arsenate and selenate from water and displayed good binding to both species, outperforming commercial activated carbons for arsenate removal in pH > 8. When evaluated as supercapacitor electrode materials, specific capacitances of up to 112 F/g at a current density of 0.1 A/g were observed. When used as Li-ion battery anode materials, the CNSs achieved a discharge capacity of 270 mAh/g at a current density of 372 mA/g (1C), which is 4-fold higher than that of commercial graphite anode.
Carbon foams were synthesized using direct pyrolysis and had SSA up to 2340 m2/g. When used as supercapacitor electrode materials, a specific capacitance up to 280 F/g was achieved at current density of 0.1 A/g and remained as high as 207 F/g, even at a high current density of 10 A/g.
A printed walking robot was made from common plastic films and coatings of SWNTs. The solid-state thermal bimorph actuators were multifunctional energy transducers powered by heat, light, or electricity. The actuators were also investigated for photo/thermal detection. Electrochemical actuators based on MnO2 were also studied for potential underwater applications.
SWNTs were also used to fabricate printable electrodes for trace Cr(VI) detection, which displayed sensitivity up to 500 nA/ppb for Cr(VI). The limit of detection was shown to be as low as 5 ppb. A flow detection system based on CNT/printed electrodes was also demonstrated.
ContributorsWang, Chengwei, Ph.D (Author) / Chan, Candace K. (Thesis advisor) / Tongay, Sefaattin (Committee member) / Wang, Qing Hua (Committee member) / Seo, Dong (Committee member) / Arizona State University (Publisher)
Created2015
Description
This thesis presents systematic studies on angle dependent Raman and Photoluminescence (PL) of a new class of layered materials, Transition Metal Trichalcogenides (TMTCs), which are made up of layers possessing anisotropic structure within the van-der-Waals plane. The crystal structure of individual layer of MX3 compounds consists of aligned nanowire like 1D chains running along the b-axis direction. The work focuses on the growth of two members of this family - ZrS3 and TiS3 - through Chemical Vapor Transport Method (CVT), with consequent angle dependent Raman and PL studies which highlight their in-plane optically anisotropic properties. Results highlight that the optical properties of few-layer flakes are highly anisotropic as evidenced by large PL intensity variation with polarization direction (in ZrS3) and an intense variation in Raman intensity with variation in polarization direction (in both ZrS3 and TiS3).
Results suggest that light is efficiently absorbed when E-field of the polarized incident excitation laser is polarized along the chain (b-axis). It is greatly attenuated and absorption is reduced when field is polarized perpendicular to the length of 1D-like chains, as wavelength of the exciting light is much longer than the width of each 1D chain. Observed PL variation with respect to the azimuthal flake angle is similar to what has been previously observed in 1D materials like nanowires. However, in TMTCs, since the 1D chains interact with each other, it gives rise to a unique linear dichroism response that falls between 2D and 1D like behavior. These results not only mark the very first demonstration of high PL polarization anisotropy in 2D systems, but also provide a novel insight into how interaction between adjacent 1D-like chains and the 2D nature of each layer influences the overall optical anisotropy of Quasi-1D materials. The presented results are anticipated to have impact in technologies involving polarized detection, near-field imaging, communication systems, and bio-applications relying on the generation and detection of polarized light.
Results suggest that light is efficiently absorbed when E-field of the polarized incident excitation laser is polarized along the chain (b-axis). It is greatly attenuated and absorption is reduced when field is polarized perpendicular to the length of 1D-like chains, as wavelength of the exciting light is much longer than the width of each 1D chain. Observed PL variation with respect to the azimuthal flake angle is similar to what has been previously observed in 1D materials like nanowires. However, in TMTCs, since the 1D chains interact with each other, it gives rise to a unique linear dichroism response that falls between 2D and 1D like behavior. These results not only mark the very first demonstration of high PL polarization anisotropy in 2D systems, but also provide a novel insight into how interaction between adjacent 1D-like chains and the 2D nature of each layer influences the overall optical anisotropy of Quasi-1D materials. The presented results are anticipated to have impact in technologies involving polarized detection, near-field imaging, communication systems, and bio-applications relying on the generation and detection of polarized light.
ContributorsPant, Anupum (Author) / Tongay, Sefaattin (Thesis advisor) / Alford, Terry Lynn (Committee member) / He, Ximin (Committee member) / Arizona State University (Publisher)
Created2016
Description
Proteins and peptides fold into dynamic structures that access a broad functional landscape, however, designing artificial polypeptide systems continues to be a great chal-lenge. Conversely, deoxyribonucleic acid (DNA) engineering is now routinely used to build a wide variety of two dimensional and three dimensional (3D) nanostructures from simple hybridization based rules, and their functional diversity can be significantly ex-panded through site specific incorporation of the appropriate guest molecules. This dis-sertation describes a gentle methodology for using short (8 nucleotide) peptide nucleic acid (PNA) linkers to assemble polypeptides within a 3D DNA nanocage, as a proof of concept for constructing artificial catalytic centers. PNA-polypeptide conjugates were synthesized directly using microwave assisted solid phase synthesis or alternatively PNA linkers were conjugated to biologically expressed proteins using chemical crosslinking. The PNA-polypeptides hybridized to the preassembled DNA nanocage at room tempera-ture or 11 ⁰C and could be assembled in a stepwise fashion. Time resolved fluorescence anisotropy and gel electrophoresis were used to determine that a negatively charged az-urin protein was repelled outside of the negatively charged DNA nanocage, while a posi-tively charged cytochrome c protein was retained inside. Spectroelectrochemistry and an in-gel luminol oxidation assay demonstrated the cytochrome c protein remained active within the DNA nanocage and its redox potential decreased modestly by 10 mV due to the presence of the DNA nanocage. These results demonstrate the benign PNA assembly conditions are ideal for preserving polypeptide structure and function, and will facilitate the polypeptide-based assembly of artificial catalytic centers inside a stable DNA nanocage. A prospective application of assembling multiple cyclic γ-PNA-peptides to mimic the oxygen-evolving complex (OEC) catalytic active site from photosystem II (PSII) is described. In this way, the robust catalytic capacity of PSII could be utilized, without suffering the light-induced damage that occurs by the photoreactions within PSII via triplet state formation, which limits the efficiency of natural photosynthesis. There-fore, this strategy has the potential to revolutionize the process of designing and building robust catalysts by leveraging nature's recipes, and also providing a flexible and con-trolled artificial environment that might even improve them further towards commercial viability.
ContributorsFlory, Justin David (Author) / Fromme, Petra (Thesis advisor) / Yan, Hao (Committee member) / Buttry, Daniel (Committee member) / Ghirlanda, Giovanna (Committee member) / Arizona State University (Publisher)
Created2014
Description
A new class of layered materials called the transition metal trichalcogenides (TMTCs) exhibit strong anisotropic properties due to their quasi-1D nature. These 2D materials are composed of chain-like structures which are weakly bound to form planar sheets with highly directional properties. The vibrational properties of three materials from the TMTC family, specifically TiS3, ZrS3, and HfS3, are relatively unknown and studies performed in this work elucidates the origin of their Raman characteristics. The crystals were synthesized through chemical vapor transport prior to mechanical exfoliation onto Si/SiO¬2 substrates. XRD, AFM, and Raman spectroscopy were used to determine the crystallinity, thickness, and chemical signature of the exfoliated crystals. Vibrational modes and anisotropic polarization are investigated through density functional theory calculations and angle-resolved Raman spectroscopy. Particular Raman modes are explored in order to correlate select peaks to the b-axis crystalline direction. Mode III vibrations for TiS3, ZrS3, and HfS3 are shared between each material and serves as a unique identifier of the crystalline orientation in MX3 materials. Similar angle-resolved Raman studies were conducted on the novel Nb0.5Ti0.5S3 alloy material grown through chemical vapor transport. Results show that the anisotropy direction is more difficult to determine due to the randomization of quasi-1D chains caused by defects that are common in 2D alloys. This work provides a fundamental understanding of the vibrational properties of various TMTC materials which is needed to realize applications in direction dependent polarization and linear dichroism.
ContributorsKong, Wilson (Author) / Tongay, Sefaattin (Thesis advisor) / Wang, Liping (Committee member) / Green, Matthew (Committee member) / Arizona State University (Publisher)
Created2017
Description
Satisfying the ever-increasing demand for electricity while maintaining sustainability and eco-friendliness has become a key challenge for humanity. Around 70% of energy is rejected as heat from different sectors. Thermoelectric energy harvesting has immense potential to convert this heat into electricity in an environmentally friendly manner. However, low efficiency and high manufacturing costs inhibit the widespread application of thermoelectric devices. In this work, an inexpensive solution processing technique and a nanostructuring approach are utilized to create thermoelectric materials. Specifically, the solution-state and solid-state structure of a lead selenide (PbSe) precursor is characterized by different spectroscopic techniques. This precursor has shown promise for preparing thermoelectric lead selenide telluride (PbSexTe1-x) thin films. The precursor was prepared by reacting lead and diphenyl diselenide in different solvents. The characterization reveals the formation of a solvated lead(II) phenylselenolate complex which deepens the understanding of the formation of these precursors. Further, using slightly different chemistry, a low-temperature tin(II) selenide (SnSe) precursor was synthesized and identified as tin(IV) methylselenolate. The low transformation temperature makes it compatible with colloidal PbSe nanocrystals. The colloidal PbSe nanocrystals were chemically treated with a SnSe precursor and subjected to mild annealing to form conductive nanocomposites. Finally, the room temperature thermoelectric characterization of solution-processed PbSexTe1-x thin films is presented. This is followed by a setup development for temperature-dependent measurements and preliminary temperature-dependent measurements on PbSexTe1-x thin films.
ContributorsVartak, Prathamesh Bhalchandra (Author) / Wang, Robert Y. (Thesis advisor) / Wang, Liping (Committee member) / Trovitch, Ryan J. (Committee member) / Tongay, Sefaattin (Committee member) / Goodnick, Stephen M. (Committee member) / Arizona State University (Publisher)
Created2020
Description
More recently there have been a tremendous advancement in theoretical studies showing remarkable properties that could be exploited from transition metal dichalcogenide (TMDC) Janus crystals through various applications. These Janus crystals are having a proven intrinsic electrical field due to breaking of out-of-plane inversion symmetry in a conventional TMDC when one of the chalcogenides atomic layer is being completely replaced by a layer of different chalcogen element. However, due to lack of accurate processing control at nanometer scales, key for creating a highly crystalline Janus structure has not yet been familiarized. Thus, experimental characterization and implication of these Janus crystals are still in a state of stagnation. This work presents a new advanced methodology that could prove to be highly efficient and effective for selective replacement of top layer atomic sites at room temperature conditions.
This is specifically more focused on proving an easy repeatability for replacement of top atomic layer chalcogenide from a parent structure of already grown TMDC monolayer (via CVD) by a post plasma processing technique. Though this developed technique is not limited to only chalcogen atom replacement but can be extended to any type of surface functionalization requirements.
Basic characterization has been performed on the Janus crystal of SeMoS and SeWS where, creation and characterization of SeWS has been done for the very first time, evidencing a repeatable nature of the developed methodology.
This is specifically more focused on proving an easy repeatability for replacement of top atomic layer chalcogenide from a parent structure of already grown TMDC monolayer (via CVD) by a post plasma processing technique. Though this developed technique is not limited to only chalcogen atom replacement but can be extended to any type of surface functionalization requirements.
Basic characterization has been performed on the Janus crystal of SeMoS and SeWS where, creation and characterization of SeWS has been done for the very first time, evidencing a repeatable nature of the developed methodology.
ContributorsTrivedi, Dipesh (Author) / Tongay, Sefaattin (Thesis advisor) / Green, Matthew (Committee member) / Zhuang, Houlong (Committee member) / Arizona State University (Publisher)
Created2019
Description
Vibrational spectroscopy is a ubiquitous characterization tool in elucidating atomic structure at the bulk and nanoscale. The ability to perform high spatial resolution vibrational spectroscopy in a scanning transmission electron microscope (STEM) with electron energy-loss spectroscopy (EELS) has the potential to affect a variety of materials science problems. Since 2014, instrumentation development has pushed for incremental improvements in energy resolution, with the current best being 4.2 meV. Although this is poor in comparison to what is common in photon or neutron vibrational spectroscopies, the spatial resolution offered by vibrational EELS is equal to or better than the best of these other techniques.
The major objective of this research program is to investigate the spatial resolution of the monochromated energy-loss signal in the transmission-beam mode and correlate it to the excitation mechanism of the associated vibrational mode. The spatial variation of dipole vibrational signals in SiO2 is investigated as the electron probe is scanned across an atomically abrupt SiO2/Si interface. The Si-O bond stretch signal has a spatial resolution of 2 – 20 nm, depending on whether the interface, bulk, or surface contribution is chosen. For typical TEM specimen thicknesses, coupled surface modes contribute strongly to the spectrum. These coupled surface modes are phonon polaritons, whose intensity and spectral positions are strongly specimen geometry dependent. In a SiO2 thin-film patterned with a 2x2 array, dielectric theory simulations predict the simultaneous excitation of parallel and uncoupled surface polaritons and a very weak excitation of the orthogonal polariton.
It is demonstrated that atomic resolution can be achieved with impact vibrational signals from optical and acoustic phonons in a covalently bonded material like Si. Sub-nanometer resolution mapping of the Si-O symmetric bond stretch impact signal can also be performed in an ionic material like SiO2. The visibility of impact energy-loss signals from excitation of Brillouin zone boundary vibrational modes in hexagonal BN is seen to be a strong function of probe convergence, but not as strong a function of spectrometer collection angles. Some preliminary measurements to detect adsorbates on catalyst nanoparticle surfaces with minimum radiation damage in the aloof-beam mode are also presented.
The major objective of this research program is to investigate the spatial resolution of the monochromated energy-loss signal in the transmission-beam mode and correlate it to the excitation mechanism of the associated vibrational mode. The spatial variation of dipole vibrational signals in SiO2 is investigated as the electron probe is scanned across an atomically abrupt SiO2/Si interface. The Si-O bond stretch signal has a spatial resolution of 2 – 20 nm, depending on whether the interface, bulk, or surface contribution is chosen. For typical TEM specimen thicknesses, coupled surface modes contribute strongly to the spectrum. These coupled surface modes are phonon polaritons, whose intensity and spectral positions are strongly specimen geometry dependent. In a SiO2 thin-film patterned with a 2x2 array, dielectric theory simulations predict the simultaneous excitation of parallel and uncoupled surface polaritons and a very weak excitation of the orthogonal polariton.
It is demonstrated that atomic resolution can be achieved with impact vibrational signals from optical and acoustic phonons in a covalently bonded material like Si. Sub-nanometer resolution mapping of the Si-O symmetric bond stretch impact signal can also be performed in an ionic material like SiO2. The visibility of impact energy-loss signals from excitation of Brillouin zone boundary vibrational modes in hexagonal BN is seen to be a strong function of probe convergence, but not as strong a function of spectrometer collection angles. Some preliminary measurements to detect adsorbates on catalyst nanoparticle surfaces with minimum radiation damage in the aloof-beam mode are also presented.
ContributorsVenkatraman, Kartik (Author) / Crozier, Peter (Thesis advisor) / Rez, Peter (Committee member) / Wang, Robert (Committee member) / Tongay, Sefaattin (Committee member) / Arizona State University (Publisher)
Created2020