Publications by authors named "Rodrigo Noriega"

18 Publications

  • Page 1 of 1

Efficient and effective single-step screening of individual samples for SARS-CoV-2 RNA using multi-dimensional pooling and Bayesian inference.

J R Soc Interface 2021 06 16;18(179):20210155. Epub 2021 Jun 16.

Department of Chemistry, University of Utah, Salt Lake City, UT, USA.

Rapid and widespread implementation of infectious disease surveillance is a critical component in the response to novel health threats. Molecular assays are the preferred method to detect a broad range of viral pathogens with high sensitivity and specificity. The implementation of molecular assay testing in a rapidly evolving public health emergency, such as the ongoing COVID-19 pandemic, can be hindered by resource availability or technical constraints. We present a screening strategy that is easily scaled up to support a sustained large volume of testing over long periods of time. This non-adaptive pooled-sample screening protocol employs Bayesian inference to yield a reportable outcome for each individual sample in a single testing step (no confirmation of positive results required). The proposed method is validated using clinical specimens tested using a real-time reverse transcription polymerase chain reaction test for SARS-CoV-2. This screening protocol has substantial advantages for its implementation, including higher sample throughput, faster time to results, no need to retrieve previously screened samples from storage to undergo retesting, and excellent performance of the algorithm's sensitivity and specificity compared with the individual test's metrics.
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http://dx.doi.org/10.1098/rsif.2021.0155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8205536PMC
June 2021

Measuring the Multiscale Dynamics, Structure, and Function of Biomolecules at Interfaces.

Authors:
Rodrigo Noriega

J Phys Chem B 2021 Jun 27;125(22):5667-5675. Epub 2021 May 27.

Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States.

The individual and collective structure and properties of biomolecules can change dramatically when they are localized at an interface. However, the small spatial extent of interfacial regions poses challenges to the detailed characterization of multiscale processes that dictate the structure and function of large biological units such as peptides, proteins, or nucleic acids. This Perspective surveys a broad set of tools that provide new opportunities to probe complex, dynamic interfaces across the vast range of temporal regimes that connect molecular-scale events to macroscopic observables. An emphasis is placed on the integration over multiple time scales, the use of complementary techniques, and the incorporation of external stimuli to control interfacial properties with spatial, temporal, and chemical specificity.
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http://dx.doi.org/10.1021/acs.jpcb.1c01546DOI Listing
June 2021

Transient kinetic studies of the antiviral Dicer-2 reveal roles of ATP in self-nonself discrimination.

Elife 2021 03 31;10. Epub 2021 Mar 31.

Department of Biochemistry, University of Utah, Salt Lake City, United States.

Some RIG-I-like receptors (RLRs) discriminate viral and cellular dsRNA by their termini, and Dicer-2 (dmDcr-2) differentially processes dsRNA with blunt or 2 nucleotide 3'-overhanging termini. We investigated the transient kinetic mechanism of the dmDcr-2 reaction using a rapid reaction stopped-flow technique and time-resolved fluorescence spectroscopy. Indeed, we found that ATP binding to dmDcr-2's helicase domain impacts association and dissociation kinetics of dsRNA in a termini-dependent manner, revealing termini-dependent discrimination of dsRNA on a biologically relevant time scale (seconds). ATP hydrolysis promotes transient unwinding of dsRNA termini followed by slow rewinding, and directional translocation of the enzyme to the cleavage site. Time-resolved fluorescence anisotropy reveals a nucleotide-dependent modulation in conformational fluctuations (nanoseconds) of the helicase and Platform-PAZ domains that is correlated with termini-dependent dsRNA cleavage. Our study offers a kinetic framework for comparison to other Dicers, as well as all members of the RLRs involved in innate immunity.
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http://dx.doi.org/10.7554/eLife.65810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8079148PMC
March 2021

Multimodal spectroscopic investigation of the conformation and local environment of biomolecules at an electrified interface.

J Mater Chem B 2020 08 27;8(31):7024-7030. Epub 2020 Jul 27.

University of Utah, Department of Chemistry, 315 S. 1400 E, Salt Lake City, UT 84112, USA.

The complex and dynamic interfacial regions between biological samples and electronic components pose many challenges for characterization, including their evolution over multiple temporal and spatial scales. Spectroscopic probes of buried interfaces employing mid-infrared plasmon resonances and time-resolved fluorescence detection in the visible range are used to study the properties of polypeptides adsorbed at the surface of a working electrode. Information from these complementary spectroscopic probes reveals the interplay of solvation, electric fields, and ion concentration on their resulting macromolecular conformations.
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http://dx.doi.org/10.1039/d0tb01158dDOI Listing
August 2020

Role of Polar Protic Solvents in the Dissociation and Reactivity of Photogenerated Radical Ion Pairs.

J Phys Chem B 2020 04 2;124(15):3083-3089. Epub 2020 Apr 2.

Department of Chemistry, University of Utah, 315 S. 1400 E, Salt Lake City, Utah 84112, United States.

The UV photolysis of bimolecular charge transfer complexes is employed to yield reactive radical ions in their solvent-equilibrated electronic ground state. In polar protic media, noncovalent complexes of 1,2,4,5-tetracyanobenzene and toluene undergo efficient, ultrafast dissociation to ion pairs and equilibrate with their solvent environment before the resulting radical ions engage in electron transfer and proton abstraction on subnanosecond time scales. Solvent molecules play a critical role in these reactive pathways and in the dissociation and relaxation processes that precede them. We report a clear separation of time scales for these relaxation and reactive processes, which implies that solvent-solute interactions can be used as a tool for tuning the reaction pathways of equilibrated radical ions in solution.
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http://dx.doi.org/10.1021/acs.jpcb.9b11299DOI Listing
April 2020

Efficient Charge Transport in Disordered Conjugated Polymer Microstructures.

Authors:
Rodrigo Noriega

Macromol Rapid Commun 2018 Jul 22;39(14):e1800096. Epub 2018 Apr 22.

Chemistry Department, University of Utah, 315 S 1400 E, Salt Lake City, UT, 84112, USA.

A new class of conjugated polymers with high charge mobilities exhibits the apparently conflicting morphological features of increased order at the molecular scale while lacking long-range order and crystallinity. To exploit their unique properties, mechanistic insights for charge transport events taking place from the molecular to the device scale must be uncovered. Thus, a central contributor to the continued progress in conjugated optoelectronic materials will be the development of advanced characterization tools, particularly those targeted to measuring the charge-transfer processes in heterogeneous, anisotropic, and hierarchically structured materials. This feature article describes the morphological properties that make partially ordered polymers an intriguing materials system to explore connections between chemical identity, solid-phase microstructure, and hierarchical charge transport. To this end, recent directions in materials development and new opportunities for characterization are discussed.
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http://dx.doi.org/10.1002/marc.201800096DOI Listing
July 2018

Resolving ultrafast exciton migration in organic solids at the nanoscale.

Nat Mater 2017 11 18;16(11):1136-1141. Epub 2017 Sep 18.

Department of Chemistry, University of California, Berkeley, California 94720, USA.

Effectiveness of molecular-based light harvesting relies on transport of excitons to charge-transfer sites. Measuring exciton migration, however, has been challenging because of the mismatch between nanoscale migration lengths and the diffraction limit. Instead of using bulk substrate quenching methods, here we define quenching boundaries all-optically with sub-diffraction resolution, thus characterizing spatiotemporal exciton migration on its native nanometre and picosecond scales. By transforming stimulated emission depletion microscopy into a time-resolved ultrafast approach, we measure a 16-nm migration length in poly(2,5-di(hexyloxy)cyanoterephthalylidene) conjugated polymer films. Combined with Monte Carlo exciton hopping simulations, we show that migration in these films is essentially diffusive because intrinsic chromophore energetic disorder is comparable to chromophore inhomogeneous broadening. Our approach will enable previously unattainable correlation of local material structure to exciton migration character, applicable not only to photovoltaic or display-destined organic semiconductors but also to explaining the quintessential exciton migration exhibited in photosynthesis.
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http://dx.doi.org/10.1038/nmat4975DOI Listing
November 2017

Resolving and Controlling Photoinduced Ultrafast Solvation in the Solid State.

J Phys Chem Lett 2017 Sep 22;8(17):4183-4190. Epub 2017 Aug 22.

Kavli Energy NanoSciences Institute , Berkeley, California 94720, United States.

Solid-state solvation (SSS) is a solid-state analogue of solvent-solute interactions in the liquid state. Although it could enable exceptionally fine control over the energetic properties of solid-state devices, its molecular mechanisms have remained largely unexplored. We use ultrafast transient absorption and optical Kerr effect spectroscopies to independently track and correlate both the excited-state dynamics of an organic emitter and the polarization anisotropy relaxation of a small polar dopant embedded in an amorphous polystyrene matrix. The results demonstrate that the dopants are able to rotationally reorient on ultrafast time scales following light-induced changes in the electronic configuration of the emitter, minimizing the system energy. The solid-state dopant-emitter dynamics are intrinsically analogous to liquid-state solvent-solute interactions. In addition, tuning the dopant/polymer pore ratio offers control over solvation dynamics by exploiting molecular-scale confinement of the dopants by the polymer matrix. Our findings will enable refined strategies for tuning optoelectronic material properties using SSS and offer new strategies to investigate mobility and disorder in heterogeneous solid and glassy materials.
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http://dx.doi.org/10.1021/acs.jpclett.7b01689DOI Listing
September 2017

Uncovering Single-Molecule Photophysical Heterogeneity of Bright, Thermally Activated Delayed Fluorescence Emitters Dispersed in Glassy Hosts.

J Am Chem Soc 2016 Oct 4;138(41):13551-13560. Epub 2016 Oct 4.

Kavli Energy NanoSciences Institute , Berkeley, California 94720, United States.

Recently developed all-organic emitters used in display applications achieve high brightness by harvesting triplet populations via thermally activated delayed fluorescence. The photophysical properties of these emitters therefore involve new inherent complexities and are strongly affected by interactions with their host material in the solid state. Ensemble measurements occlude the molecular details of how host-guest interactions determine fundamental properties such as the essential balance of singlet oscillator strength and triplet harvesting. Therefore, using time-resolved fluorescence spectroscopy, we interrogate these emitters at the single-molecule level and compare their properties in two distinct glassy polymer hosts. We find that nonbonding interactions with aromatic moieties in the host appear to mediate the molecular configurations of the emitters, but also promote nonradiative quenching pathways. We also find substantial heterogeneity in the time-resolved photoluminescence of these emitters, which is dominated by static disorder in the polymer. Finally, since singlet-triplet cycling underpins the mechanism for increased brightness, we present the first room-temperature measurement of singlet-triplet equilibration dynamics in this family of emitters. Our observations present a molecular-scale interrogation of host-guest interactions in a disordered film, with implications for highly efficient organic light-emitting devices. Combining a single-molecule experimental technique with an emitter that is sensitive to triplet dynamics, yet read out via fluorescence, should also provide a complementary approach to performing fundamental studies of glassy materials over a large dynamic range of time scales.
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http://dx.doi.org/10.1021/jacs.6b05488DOI Listing
October 2016

Manipulating Excited-State Dynamics of Individual Light-Harvesting Chromophores through Restricted Motions in a Hydrated Nanoscale Protein Cavity.

J Phys Chem B 2015 Jun 2;119(23):6963-73. Epub 2015 Jun 2.

∇Kavli Energy NanoSciences Institute, Berkeley, California 94720, United States.

Manipulating the photophysical properties of light-absorbing units is a crucial element in the design of biomimetic light-harvesting systems. Using a highly tunable synthetic platform combined with transient absorption and time-resolved fluorescence measurements and molecular dynamics simulations, we interrogate isolated chromophores covalently linked to different positions in the interior of the hydrated nanoscale cavity of a supramolecular protein assembly. We find that, following photoexcitation, the time scales over which these chromophores are solvated, undergo conformational rearrangements, and return to the ground state are highly sensitive to their position within this cavity and are significantly slower than in a bulk aqueous solution. Molecular dynamics simulations reveal the hindered translations and rotations of water molecules within the protein cavity with spatial specificity. The results presented herein show that fully hydrated nanoscale protein cavities are a promising way to mimic the tight protein pockets found in natural light-harvesting complexes. We also show that the interplay between protein, solvent, and chromophores can be used to substantially tune the relaxation processes within artificial light-harvesting assemblies in order to significantly improve the yield of interchromophore energy transfer and extend the range of excitation transport. Our observations have implications for other important, similarly sized bioinspired materials, such as nanoreactors and biocompatible targeted delivery agents.
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http://dx.doi.org/10.1021/acs.jpcb.5b03784DOI Listing
June 2015

Chain conformations dictate multiscale charge transport phenomena in disordered semiconducting polymers.

Proc Natl Acad Sci U S A 2013 Oct 23;110(41):16315-20. Epub 2013 Sep 23.

Departments of Applied Physics, Materials Science and Engineering, and Chemical Engineering, Stanford University, Stanford, CA 94305.

Existing models for the electronic properties of conjugated polymers do not capture the spatial arrangement of the disordered macromolecular chains over which charge transport occurs. Here, we present an analytical and computational description in which the morphology of individual polymer chains is dictated by well-known statistical models and the electronic coupling between units is determined using Marcus theory. The multiscale transport of charges in these materials (high mobility at short length scales, low mobility at long length scales) is naturally described with our framework. Additionally, the dependence of mobility with electric field and temperature is explained in terms of conformational variability and spatial correlation. Our model offers a predictive approach to connecting processing conditions with transport behavior.
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http://dx.doi.org/10.1073/pnas.1307158110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799354PMC
October 2013

A general relationship between disorder, aggregation and charge transport in conjugated polymers.

Nat Mater 2013 Nov 4;12(11):1038-44. Epub 2013 Aug 4.

1] Department of Applied Physics, Stanford University, Stanford, California 94305, USA [2] [3].

Conjugated polymer chains have many degrees of conformational freedom and interact weakly with each other, resulting in complex microstructures in the solid state. Understanding charge transport in such systems, which have amorphous and ordered phases exhibiting varying degrees of order, has proved difficult owing to the contribution of electronic processes at various length scales. The growing technological appeal of these semiconductors makes such fundamental knowledge extremely important for materials and process design. We propose a unified model of how charge carriers travel in conjugated polymer films. We show that in high-molecular-weight semiconducting polymers the limiting charge transport step is trapping caused by lattice disorder, and that short-range intermolecular aggregation is sufficient for efficient long-range charge transport. This generalization explains the seemingly contradicting high performance of recently reported, poorly ordered polymers and suggests molecular design strategies to further improve the performance of future generations of organic electronic materials.
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http://dx.doi.org/10.1038/nmat3722DOI Listing
November 2013

Low-temperature processed Ga-doped ZnO coatings from colloidal inks.

J Am Chem Soc 2013 Mar 21;135(9):3439-48. Epub 2013 Feb 21.

Dipartimento di Ingegneria Industriale, Università di Padova, Via Marzolo, 9, 35131 Padova, Italy.

We present a new colloidal synthesis of gallium-doped zinc oxide nanocrystals that are transparent in the visible and absorb in the near-infrared. Thermal decomposition of zinc stearate and gallium nitrate after hot injection of the precursors in a mixture of organic amines leads to nanocrystals with tunable properties according to gallium amount. Substitutional Ga(3+) ions trigger a plasmonic resonance in the infrared region resulting from an increase in the free electrons concentration. These nanocrystals can be deposited by spin coating, drop casting, and spray coating resulting in homogeneous and high-quality thin films. The optical transmission of the Ga-ZnO nanoparticle assemblies in the visible is greater than 90%, and at the same time, the near-infrared absorption of the nanocrystals is maintained in the films as well. Several strategies to improve the films electrical and optical properties have been presented, such as UV treatments to remove the organic compounds responsible for the observed interparticle resistance and reducing atmosphere treatments on both colloidal solutions and thin films to increase the free carriers concentration, enhancing electrical conductivity and infrared absorption. The electrical resistance of the nanoparticle assemblies is about 30 kΩ/sq for the as-deposited, UV-exposed films, and it drops down to 300 Ω/sq after annealing in forming gas at 450 °C, comparable with state of the art tin-doped indium oxide coatings deposited from nanocrystal inks.
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http://dx.doi.org/10.1021/ja307960zDOI Listing
March 2013

Controlled conjugated backbone twisting for an increased open-circuit voltage while having a high short-circuit current in poly(hexylthiophene) derivatives.

J Am Chem Soc 2012 Mar 2;134(11):5222-32. Epub 2012 Mar 2.

Department of Chemistry, Stanford University, Stanford, California 94305, United States.

Conjugated polymers with nearly planar backbones have been the most commonly investigated materials for organic-based electronic devices. More twisted polymer backbones have been shown to achieve larger open-circuit voltages in solar cells, though with decreased short-circuit current densities. We systematically impose twists within a family of poly(hexylthiophene)s and examine their influence on the performance of polymer:fullerene bulk heterojunction (BHJ) solar cells. A simple chemical modification concerning the number and placement of alkyl side chains along the conjugated backbone is used to control the degree of backbone twisting. Density functional theory calculations were carried out on a series of oligothiophene structures to provide insights on how the sterically induced twisting influences the geometric, electronic, and optical properties. Grazing incidence X-ray scattering measurements were performed to investigate how the thin-film packing structure was affected. The open-circuit voltage and charge-transfer state energy of the polymer:fullerene BHJ solar cells increased substantially with the degree of twist induced within the conjugated backbone--due to an increase in the polymer ionization potential--while the short-circuit current decreased as a result of a larger optical gap and lower hole mobility. A controlled, moderate degree of twist along the poly(3,4-dihexyl-2,2':5',2''-terthiophene) (PDHTT) conjugated backbone led to a 19% enhancement in the open-circuit voltage (0.735 V) vs poly(3-hexylthiophene)-based devices, while similar short-circuit current densities, fill factors, and hole-carrier mobilities were maintained. These factors resulted in a power conversion efficiency of 4.2% for a PDHTT:[6,6]-phenyl-C(71)-butyric acid methyl ester (PC(71)BM) blend solar cell without thermal annealing. This simple approach reveals a molecular design avenue to increase open-circuit voltage while retaining the short-circuit current.
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http://dx.doi.org/10.1021/ja210954rDOI Listing
March 2012

Light trapping in thin-film silicon solar cells with submicron surface texture.

Opt Express 2009 Dec;17(25):23058-65

School of Engineering and Science, Electronic Devices and Nanophotonics Laboratory, Jacobs University Bremen, 28759 Bremen, Germany.

The influence of nano textured front contacts on the optical wave propagation within microcrystalline thin-film silicon solar cell was investigated. Periodic triangular gratings were integrated in solar cells and the influence of the profile dimensions on the quantum efficiency and the short circuit current was studied. A Finite Difference Time Domain approach was used to rigorously solve the Maxwell's equations in two dimensions. By studying the influence of the period and height of the triangular profile, the design of the structures were optimized to achieve higher short circuit currents and quantum efficiencies. Enhancement of the short circuit current in the blue part of the spectrum is achieved for small triangular periods (P<200 nm), whereas the short circuit current in the red and infrared part of the spectrum is increased for triangular periods (P = 900nm) comparable to the optical wavelength. The influence of the surface texture on the solar cell performance will be discussed.
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http://dx.doi.org/10.1364/OE.17.023058DOI Listing
December 2009

Large modulation of carrier transport by grain-boundary molecular packing and microstructure in organic thin films.

Nat Mater 2009 Dec 8;8(12):952-8. Epub 2009 Nov 8.

Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, USA.

Solution-processable organic semiconductors are central to developing viable printed electronics, and performance comparable to that of amorphous silicon has been reported for films grown from soluble semiconductors. However, the seemingly desirable formation of large crystalline domains introduces grain boundaries, resulting in substantial device-to-device performance variations. Indeed, for films where the grain-boundary structure is random, a few unfavourable grain boundaries may dominate device performance. Here we isolate the effects of molecular-level structure at grain boundaries by engineering the microstructure of the high-performance n-type perylenediimide semiconductor PDI8-CN2 and analyse their consequences for charge transport. A combination of advanced X-ray scattering, first-principles computation and transistor characterization applied to PDI8-CN2 films reveals that grain-boundary orientation modulates carrier mobility by approximately two orders of magnitude. For PDI8-CN2 we show that the molecular packing motif (that is, herringbone versus slip-stacked) plays a decisive part in grain-boundary-induced transport anisotropy. The results of this study provide important guidelines for designing device-optimized molecular semiconductors.
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http://dx.doi.org/10.1038/nmat2570DOI Listing
December 2009