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

Characterization and Interactions of Ultrafast Surface Plasmon Pulses

Surface Plasmon Polaritons (SPPs) are considered to be attractive components for plasmonics and nanophotonic devices due to their sensitivity to interface changes, and their ability to guide and confine light beyond the diffraction limit. They have been utilized in SPP resonance sensors and near field imaging techniques and, more recently, SPP experiments to monitor and control ultrafast charge carrier and energy relaxation dynamics in thin films. In this thesis, we discuss excitation and propagation properties of ultrafast SPPs on thin extended metal films and SPP waveguide structures. In addition, localized and propagating surface plasmon interactions in functional plasmonic nanostructures will also be addressed. For the excitation studies of ultrafast SPPs, we have done detailed analysis of femtosecond surface plasmon pulse generation under resonant excitation condition using prism coupling technique. Our results show that photon-SPP coupling is a resonant process with a finite spectral bandwidth that causes spectral phase shift and narrowing of the SPP pulse spectrum. Both effects result in temporal pulse broadening and, therefore, set a lower limit on the duration of ultrafast SPP pulses. These findings are necessary for the successful integration of plasmonic components into high-speed SPP circuits and time-resolved SPP sensors. To demonstrate interactions between localized and propagating surface plasmons, we used block-copolymer based self assembly techniques to deposit long range ordered gold nanoparticle arrays onto silver thin films to fabricate composite nanoparticle thin film structures. We demonstrate that these gold nanoparticle arrays interact with SPPs that propagate at the film/nanoparticle interface and therefore, modify the dispersion relation of SPPs and lead to strong field localizations. These results are important and advantageous for plasmonic device applications. For the propagation studies of ultrafast SPPs, we have designed and constructed a home-built femtosecond photon scanning tunneling microscope (fsPSTM) to visualize ultrafast SPPs in photonic devices based on metal nanostructures. Temporal and phase information have been obtained by incorporating the fsPSTM into one arm of a Mach-Zehnder interferometer, allowing heterodyne detection. Understanding plasmon propagation in metal nanostructures is a requirement for implementing such structures into opto-electronic and telecommunication technologies

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

Electrostatic Force Microscopy and Spectral Studies of Electron Attachment to Single Quantum Dots on Indium Tin Oxide Substrates

We report electrostatic force microscopy (EFM) studies combined with wavelength-resolved photoluminescence imaging of electron attachment to individual CdSe/ZnS quantum dots (QDs) coupled to semiconducting tin-doped indium oxide (ITO) substrates. Quantitative EFM measurements show unambiguous signatures of 2–3 excess electrons on individual QDs on ITO, while the distribution of measured recombination energies of QDs coupled to ITO shows ≈ −35 meV red shift (compared to QDs drop-cast on clean glass), the signature of a second-order quantum-confined Stark effect resulting from multiple-electron attachment to the QDs. We also show that the extent of QD charging can be tuned by modulating the ITO bias: EFM measurements show that ≈4 electrons are added to QDs under −2 V applied ITO bias, whereas only ≈2 electrons can be removed from the QDs for +2 V applied bias arising from Fermi level mismatch of ITO with respect to the QDs. Voltage-correlated spectral measurements on ITO coupled QDs showed a spectral modulation in their peak fluorescence energies, which can be attributed to addition or removal of electrons from the QDs

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 <i>E</i>₁₁ 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 <i>E</i>₁₁ 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

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

Long-range (&gt;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

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&nbsp;100-fold increase in photocurrent in purified individual nanowires. Photocurrents respond rapidly (&lt;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

Metallic 1T phase source/drain electrodes for field effect transistors from chemical vapor deposited MoS2

Two dimensional transitionmetal dichalcogenides (2D TMDs) offer promise as optoelectronic materials due to their direct band gap and reasonably good mobility values. However, most metals form high resistance contacts on semiconducting TMDs such as MoS2. The large contact resistance limits the performance of devices. Unlike bulk materials, low contact resistance cannot be stably achieved in 2D materials by doping. Here we build on our previous work in which we demonstrated that it is possible to achieve low contact resistance electrodes by phase transformation. We show that similar to the previously demonstrated mechanically exfoliated samples, it is possible to decrease the contact resistance and enhance the FET performance by locally inducing and patterning the metallic 1T phase of MoS2 on chemically vapor deposited material. The device properties are substantially improved with 1T phase source/drain electrodes