Microbial biofilms as living photoconductors due to ultrafast electron transfer in cytochrome OmcS nanowires.

Light-induced microbial electron transfer has potential for efficient production of value-added chemicals, biofuels and biodegradable materials owing to diversified metabolic pathways. However, most microbes lack photoactive proteins and require synthetic photosensitizers that suffer from photocorrosion, photodegradation, cytotoxicity, and generation of photoexcited radicals that are harmful to cells, thus severely limiting the catalytic performance. Therefore, there is a pressing need for biocompatible photoconductive materials for efficient electronic interface between microbes and electrodes. Here we show that living biofilms of Geobacter sulfurreducens use nanowires of cytochrome OmcS as intrinsic photoconductors. Photoconductive atomic force microscopy shows up to 100-fold increase in photocurrent in purified individual nanowires. Photocurrents respond rapidly (<100 ms) to the excitation and persist reversibly for hours. Femtosecond transient absorption spectroscopy and quantum dynamics simulations reveal ultrafast (~200 fs) electron transfer between nanowire hemes upon photoexcitation, enhancing carrier density and mobility. Our work reveals a new class of natural photoconductors for whole-cell catalysis.

A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks.

Although proteins are considered as nonconductors that transfer electrons only up to 1 to 2 nanometers via tunneling, Geobacter sulfurreducens transports respiratory electrons over micrometers, to insoluble acceptors or syntrophic partner cells, via nanowires composed of polymerized cytochrome OmcS. However, the mechanism enabling this long-range conduction is unclear. Here, we demonstrate that individual nanowires exhibit theoretically predicted hopping conductance, at rate (>1010 s-1) comparable to synthetic molecular wires, with negligible carrier loss over micrometers. Unexpectedly, nanowires show a 300-fold increase in their intrinsic conductance upon cooling, which vanishes upon deuteration. Computations show that cooling causes a massive rearrangement of hydrogen bonding networks in nanowires. Cooling makes hemes more planar, as revealed by Raman spectroscopy and simulations, and lowers their reduction potential. We find that the protein surrounding the hemes acts as a temperature-sensitive switch that controls charge transport by sensing environmental perturbations. Rational engineering of heme environments could enable systematic tuning of extracellular respiration.

Protein nanowires with tunable functionality and programmable self-assembly using sequence-controlled synthesis.

Advances in synthetic biology permit the genetic encoding of synthetic chemistries at monomeric precision, enabling the synthesis of programmable proteins with tunable properties. Bacterial pili serve as an attractive biomaterial for the development of engineered protein materials due to their ability to self-assemble into mechanically robust filaments. However, most biomaterials lack electronic functionality and atomic structures of putative conductive proteins are not known. Here, we engineer high electronic conductivity in pili produced by a genomically-recoded E. coli strain. Incorporation of tryptophan into pili increased conductivity of individual filaments >80-fold. Computationally-guided ordering of the pili into nanostructures increased conductivity 5-fold compared to unordered pili networks. Site-specific conjugation of pili with gold nanoparticles, facilitated by incorporating the nonstandard amino acid propargyloxy-phenylalanine, increased filament conductivity ~170-fold. This work demonstrates the sequence-defined production of highly-conductive protein nanowires and hybrid organic-inorganic biomaterials with genetically-programmable electronic functionalities not accessible in nature or through chemical-based synthesis.

Structure of Geobacter pili reveals secretory rather than nanowire behaviour.

Extracellular electron transfer by Geobacter species through surface appendages known as microbial nanowires1 is important in a range of globally important environmental phenomena2, as well as for applications in bio-remediation, bioenergy, biofuels and bioelectronics. Since 2005, these nanowires have been thought to be type 4 pili composed solely of the PilA-N protein1. However, previous structural analyses have demonstrated that, during extracellular electron transfer, cells do not produce pili but rather nanowires made up of the cytochromes OmcS2,3 and OmcZ4. Here we show that Geobacter sulfurreducens binds PilA-N to PilA-C to assemble heterodimeric pili, which remain periplasmic under nanowire-producing conditions that require extracellular electron transfer5. Cryo-electron microscopy revealed that C-terminal residues of PilA-N stabilize its copolymerization with PilA-C (to form PilA-N-C) through electrostatic and hydrophobic interactions that position PilA-C along the outer surface of the filament. PilA-N-C filaments lack π-stacking of aromatic side chains and show a conductivity that is 20,000-fold lower than that of OmcZ nanowires. In contrast with surface-displayed type 4 pili, PilA-N-C filaments show structure, function and localization akin to those of type 2 secretion pseudopili6. The secretion of OmcS and OmcZ nanowires is lost when pilA-N is deleted and restored when PilA-N-C filaments are reconstituted. The substitution of pilA-N with the type 4 pili of other microorganisms also causes a loss of secretion of OmcZ nanowires. As all major phyla of prokaryotes use systems similar to type 4 pili, this nanowire translocation machinery may have a widespread effect in identifying the evolution and prevalence of diverse electron-transferring microorganisms and in determining nanowire assembly architecture for designing synthetic protein nanowires.

Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation.

Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor.

The blind men and the filament: Understanding structures and functions of microbial nanowires.

Extracellular electron transfer via filamentous protein appendages called 'microbial nanowires' has long been studied in Geobacter and other bacteria because of their crucial role in globally-important environmental processes and their applications for bioenergy, biofuels, and bioelectronics. Thousands of papers thought these nanowires as pili without direct evidence. Here, we summarize recent discoveries that could help resolve two decades of confounding observations. Using cryo-electron microscopy with multimodal functional imaging and a suite of electrical, biochemical, and physiological studies, we find that rather than pili, nanowires are composed of cytochromes OmcS and OmcZ that transport electrons via seamless stacking of hemes over micrometers. We discuss the physiological need for two different nanowires and their potential applications for sensing, synthesis, and energy production.

Electric field stimulates production of highly conductive microbial OmcZ nanowires.

Multifunctional living materials are attractive due to their powerful ability to self-repair and replicate. However, most natural materials lack electronic functionality. Here we show that an electric field, applied to electricity-producing Geobacter sulfurreducens biofilms, stimulates production of cytochrome OmcZ nanowires with 1,000-fold higher conductivity (30 S cm-1) and threefold higher stiffness (1.5 GPa) than the cytochrome OmcS nanowires that are important in natural environments. Using chemical imaging-based multimodal nanospectroscopy, we correlate protein structure with function and observe pH-induced conformational switching to ß-sheets in individual nanowires, which increases their stiffness and conductivity by 100-fold due to enhanced π-stacking of heme groups; this was further confirmed by computational modeling and bulk spectroscopic studies. These nanowires can transduce mechanical and chemical stimuli into electrical signals to perform sensing, synthesis and energy production. These findings of biologically produced, highly conductive protein nanowires may help to guide the development of seamless, bidirectional interfaces between biological and electronic systems.

Direct observation of anisotropic growth of water films on minerals driven by defects and surface tension.

Knowledge of the occurrences of water films on minerals is critical for global biogeochemical and atmospheric processes, including element cycling and ice nucleation. The underlying mechanisms controlling water film growth are, however, misunderstood. Using infrared nanospectroscopy, amplitude-modulated atomic force microscopy, and molecular simulations, we show how water films grow from water vapor on hydrophilic mineral nanoparticles. We imaged films with up to four water layers that grow anisotropically over a single face. Growth usually begins from the near edges of a face where defects preferentially capture water vapor. Thicker films produced by condensation cooling completely engulf nanoparticles and form thicker menisci over defects. The high surface tension of water smooths film surfaces and produces films of inhomogeneous thickness. Nanoscale topography and film surface energy thereby control anisotropic distributions and thicknesses of water films on hydrophilic mineral nanoparticles.

Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers.

Long-range (>10 µm) transport of electrons along networks of Geobacter sulfurreducens protein filaments, known as microbial nanowires, has been invoked to explain a wide range of globally important redox phenomena. These nanowires were previously thought to be type IV pili composed of PilA protein. Here, we report a 3.7 Å resolution cryoelectron microscopy structure, which surprisingly reveals that, rather than PilA, G. sulfurreducens nanowires are assembled by micrometer-long polymerization of the hexaheme cytochrome OmcS, with hemes packed within ∼3.5-6 Å of each other. The inter-subunit interfaces show unique structural elements such as inter-subunit parallel-stacked hemes and axial coordination of heme by histidines from neighboring subunits. Wild-type OmcS filaments show 100-fold greater conductivity than other filaments from a ΔomcS strain, highlighting the importance of OmcS to conductivity in these nanowires. This structure explains the remarkable capacity of soil bacteria to transport electrons to remote electron acceptors for respiration and energy sharing.

Photoluminescence imaging of solitary dopant sites in covalently doped single-wall carbon nanotubes.

Covalent dopants in semiconducting single wall carbon nanotubes (SWCNTs) are becoming important as routes for introducing new photoluminescent emitting states with potential for enhanced quantum yields, new functionality, and as species capable of near-IR room-temperature single photon emission. The origin and behavior of the dopant-induced emission is thus important to understand as a key requirement for successful room-T photonics and optoelectronics applications. Here, we use direct correlated two-color photoluminescence imaging to probe how the interplay between the SWCNT bright E(11) exciton and solitary dopant sites yields the dopant-induced emission for three different dopant species: oxygen, 4-methoxybenzene, and 4-bromobenzene. We introduce a route to control dopant functionalization to a low level as a means for introducing spatially well-separated solitary dopant sites. Resolution of emission from solitary dopant sites and correlation to their impact on E(11) emission allows confirmation of dopants as trapping sites for localization of E(11) excitons following their diffusive transport to the dopant site. Imaging of the dopant emission also reveals photoluminescence intermittency (blinking), with blinking dynamics being dependent on the specific dopant. Density functional theory calculations were performed to evaluate the stability of dopants and delineate the possible mechanisms of blinking. Theoretical modeling suggests that the trapping of free charges in the potential well created by permanent dipoles introduced by dopant atoms/groups is likely responsible for the blinking, with the strongest effects being predicted and observed for oxygen-doped SWCNTs.

Direct imaging of charge transport in progressively reduced graphene oxide using electrostatic force microscopy.

Graphene oxide (GO) has emerged as a multifunctional material that can be synthesized in bulk quantities and can be solution processed to form large-area atomic layered photoactive, flexible thin films for optoelectronic devices. This is largely due to the potential ability to tune electrical and optical properties of GO using functional groups. For the successful application of GO, it is key to understand the evolution of its optoelectronic properties as the GO undergoes a phase transition from its insulating and optically active state to the electrically conducting state with progressive reduction. In this paper, we use a combination of electrostatic force microscopy (EFM) and optical spectroscopy to monitor the emergence of the optoelectronic properties of GO with progressive reduction. EFM measurements enable, for the first time, direct visualization of charge propagation along the conducting pathways that emerge on progressively reduced graphene oxide (rGO) and demonstrate that with the increasing degree of reduction, injected charges can rapidly migrate over a distance of several micrometers, irrespective of their polarities. Direct imaging reveals the presence of an insurmountable potential barrier between reduced GO (rGO) and GO, which plays the decisive role in the charge transport. We complement charge imaging with theoretical modeling using quantum chemistry calculations that further demonstrate that the role of barrier in regulating the charge transport. Furthermore, by correlating the EFM measurements with photoluminescence imaging and electrical conductivity studies, we identify a bifunctional state in GO, where the optical properties are preserved along with good electrical conductivity, providing design principles for the development of GO-based, low-cost, thin-film optoelectronic applications.

Visualization of charge propagation along individual pili proteins using ambient electrostatic force microscopy.

The nanoscale imaging of charge flow in proteins is crucial to understanding several life processes, including respiration, metabolism and photosynthesis. However, existing imaging methods are only effective under non-physiological conditions or are limited to photosynthetic proteins. Here, we show that electrostatic force microscopy can be used to directly visualize charge propagation along pili of Geobacter sulfurreducens with nanometre resolution and under ambient conditions. Charges injected at a single point into individual, untreated pili, which are still attached to cells, propagated over the entire filament. The mobile charge density in the pili, as well as the temperature and pH dependence of the charge density, were similar to those of carbon nanotubes and other organic conductors. These findings, coupled with a lack of charge propagation in mutated pili that were missing key aromatic amino acids, suggest that the pili of G. sulfurreducens function as molecular wires with transport via delocalized charges, rather than the hopping mechanism that is typical of biological electron transport.

Electronic structure and chemical nature of oxygen dopant states in carbon nanotubes.

We performed low temperature photoluminescence (PL) studies on individual oxygen-doped single-walled carbon nanotubes (SWCNTs) and correlated our observations to electronic structure simulations. Our experiment reveals multiple sharp asymmetric emission peaks at energies 50-300 meV red-shifted from that of the E11 bright exciton peak. Our simulation suggests an association of these peaks with deep trap states tied to different specific chemical adducts. In addition, oxygen doping is also observed to split the E11 exciton into two or more states with an energy splitting <40 meV. We attribute these states to dark states that are brightened through defect-induced symmetry breaking. While the wave functions of these brightened states are delocalized, those of the deep-trap states are strongly localized and pinned to the dopants. These findings are consistent with our experimental observation of asymmetric broadening of the deep trap emission peaks, which can result from interaction between pinned excitons and one-dimensional phonons. Exciton pinning also increases the sensitivity of the deep traps to the local dielectric environment, leading to a large inhomogeneous broadening. Observations of multiple spectral features on single nanotubes indicate the possibility of different chemical adducts coexisting on a given nanotube.

Phase-engineered low-resistance contacts for ultrathin MoS2 transistors.

Ultrathin molybdenum disulphide (MoS2) has emerged as an interesting layered semiconductor because of its finite energy bandgap and the absence of dangling bonds. However, metals deposited on the semiconducting 2H phase usually form high-resistance (0.7 kΩ µm-10 kΩ µm) contacts, leading to Schottky-limited transport. In this study, we demonstrate that the metallic 1T phase of MoS2 can be locally induced on semiconducting 2H phase nanosheets, thus decreasing contact resistances to 200-300 Ω µm at zero gate bias. Field-effect transistors (FETs) with 1T phase electrodes fabricated and tested in air exhibit mobility values of ~50 cm(2) V(-1) s(-1), subthreshold swing values below 100 mV per decade, on/off ratios of >10(7), drive currents approaching ~100 µA µm(-1), and excellent current saturation. The deposition of different metals has limited influence on the FET performance, suggesting that the 1T/2H interface controls carrier injection into the channel. An increased reproducibility of the electrical characteristics is also obtained with our strategy based on phase engineering of MoS2.

Spectral properties of multiply charged semiconductor quantum dots.

Spectrally resolved fluorescence imaging of single CdSe/ZnS quantum dots (QDs), charged by electrospray deposition under negative bias has revealed a surprising net blue shift (∼60 meV peak-to-peak) in the distribution of center frequencies in QD band-edge luminescence. Electrostatic force microscopy (EFM) on the electrospray QD samples showed a subpopulation of charged QDs with 4.7 ± 0.7 excess electrons, as well as a significant fraction of uncharged QDs as evidenced by the distinct cantilever response under bias. We show that the blue-shifted peak recombination energy can be understood as a first-order electronic perturbation that affects the band-edge electron- and hole-states differently. These studies provide new insight into the role of electronic perturbations of QD luminescence by excess charges.

Block-copolymer-based plasmonic nanostructures.

We report on the fabrication and optical characterization of dense and ordered arrays of metal nanoparticles. The metal arrays are produced by reducing metal salts in block copolymer (BCP) templates made by solvent annealing of poly(styrene-b-4-vinylpyridine) (PS-b-P4VP) or poly(styrene-b-ethylene oxide) (PS-b-PEO) diblock copolymer thin films in mixed solvents. The gold and gold/silver composite nanoparticle arrays show characteristic surface plasmon resonances in the visible wavelength range. The patterning can be applied over large areas onto various substrates. We demonstrate that these metal nanoparticle arrays on metal thin films interact with surface plasmon polaritons (SPPs) that propagate at the film/nanoparticle interface and, therefore, modify the dispersion relation of the SPPs.