Polydimethylsiloxane (PDMS) has been widely used as a surface coating material, which has been reported to possess dynamic omniphobicity to a wide range of both polar and nonpolar solvents due to its high segmental flexibility and mobility. However, such high flexibility and mobility also enable penetration of small molecules into PDMS coatings, which alter the chemical and physical properties of the coating layers. To improve the anti-penetration properties of PDMS, a series of fluorinated alkyl segments are grafted to a diblock copolymer of polystyrene-block-poly(vinyl methyl siloxane) (PS-b-PVMS) using thiol-ene click reactions. This article reports the chemical characterization of these model fluorosilicone block copolymers and uses fluorescence measurements to investigate the dye penetration characteristics of polymer thin films. The introduction of longer fluorinated alkyl chains can gradually increase the anti-penetration properties as the time to reach the maximum fluorescence intensity (tpeak) gradually increases from 11 s of PS-b-PVMS to more than 1000 s of PS-b-P(n-C6F13-VMS). The improvement of anti-penetration properties is attributed to stronger inter-/intrachain interactions, phase segregation of ordered fluorinated side chains, and enhanced hydrophobicity caused by the grafting of fluorinated alkyl chains.

Droplets impacting with surfaces are commonly encountered processes in the field of protective coatings. The behavior of a colliding binary liquid droplet is sensitive to the impact velocity, surface wetting properties, and the droplet composition. Modeling molecular dynamics and classical density functional theory studies of impacting droplets as well as interfacial-surface free energies was reported on. The presence of two components in the liquid drop makes the surface collision a complicated problem. During the collision the kinetic energy of the drop is converted into heat. Thus, the temperature varies during the collision and throughout the droplet. Two extreme situations were captured by performing both adiabatic and isothermal simulations. Molecular dynamics and classical density functional theory were used to explore the effects of the mixing parameter on the phase diagram of the binary AB mixed droplets. The location of liquid-vapor and liquid-liquid phase separation was determined. In addition, the value of the interfacial tensions of all interfaces was computed. These can be used to predict when an A-rich and B-rich droplet will stay attached and when it will detach.

Designing coatings and films that can protect surfaces is important in a wide variety of applications from corrosion prevention to anti-fouling. These systems are challenging from a modeling perspective because they are invariably multicomponent, which quickly leads to an expansive design space. At a minimum, the system has a substrate, a film (often composed of a polymeric material), a ubiquitous carrier solvent, which may be either a vapor or liquid phase, and one or more contaminants. Each component has an impact on the effectiveness of coating. This paper focuses on films that are used as a barrier to surface contamination, but the results also extend to surface coatings that are designed to extract a low density species from the fluid phase as in liquid chromatography. A coarse-grained model is developed using Yukawa potentials that encompasses both repulsive and attractive interactions among the species. Classical density functional theory calculations are presented to show how contaminant adsorption is controlled by the molecular forces in the system. Two specific vectors through the parameter space are considered to address likely experimental manipulations that change either the solvent or the polymer in a system. We find that all the adsorption results can be unified by considering an appropriate combination of molecular parameters. As a result, these calculations provide a link between molecular interactions and film performance and may serve to guide the rational design of films.

We investigate diffusion in fluids near surfaces that may be coated with polymer films. We first consider diffusion in hard sphere fluids near a planar hard wall. We specifically consider color diffusion, where hard spheres are labeled A or B but are otherwise identical in all respects. In this inhomogeneous fluid, we consider a surface reaction-diffusion problem. At the left wall, a particle of species A is converted to one of species B upon a wall collision. At the opposing wall, the reverse reaction takes place: B → A. Using molecular dynamics simulation, we study the steady state of this system. We demonstrate that in the homogeneous region, a diffusing particle is subject to an equilibrium oscillatory force, the solvation force, that arises from the interfacial structuring of the fluid at the wall. For the hard sphere/hard wall system, the solvation force can be determined in various ways. We use the solvation force [the potential of mean force (PMF)] to solve the continuum diffusion equation. This provides an adequate and accurate description of the reaction-diffusion problem. The analysis is then extended to consider both color diffusion in the presence of a slowly varying one-body field such as gravity and a more applied problem of diffusion of free species through a surface film consisting of tethered chains. In both cases, the PMF experienced by the free particles is affected, but the diffusion problem can be treated in the same way as for the simpler hard sphere color diffusion case.

Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.

Quorum sensing (QS) in bacteria has been well studied as a cellular communication phenomenon for decades. In recent years, such systems have been repurposed for the use of biosensors in both cellular and cell-free contexts as well as for inducible protein expression in nontraditional chassis organisms. Such biosensors are particularly intriguing when considering the association between the pathogenesis of some bacteria and their signaling intermediates. Considering this relationship and considering the recent demonstration of the species Lactobacillus plantarum WCFS1 as both a synthetic biology chassis and an organism capable of detecting a pathogen-associated QS molecule, we wanted to develop this organism as a QS sentinel. We used an approach combining techniques from both systems and synthetic biology to identify a number of native QS-response genes and to alter associated promoter activity to tune the output of L. plantarum cultures exposed to N-3-oxododecanoyl homoserine lactone. The resulting engineered QS sentinel reinforces the potential of modified lactic acid bacteria (LAB) for use in human-health-promoting applications and also demonstrates a simple rational workflow to engineer sentinel organisms to respond to any environmental or chemical stimuli.

Covalently attached liquids provide a liquid-liquid surface interaction for contacting contaminants, typically achieved through use of a polydimethylsiloxane linear polymer bound to the surface at one end. The attached dimethylsiloxane polymer chain retains liquid-like mobility through bending and rotational motions, distinguishing the coatings from those formed by crosslinked polydimethylsiloxane or branched polymer chains. Here, covalently attached liquids are reviewed and their potential for application as topcoat treatments is discussed. This review focuses on a new use scenario: prevention of chemical contamination. When allowed to age in place, chemical contaminants tend to penetrate into painted surfaces. Standard decontamination processes can fail to remove the chemicals within the paint layer, resulting in secondary exposure hazards when environmental conditions change. Covalent liquid coatings provide repellency and shedding behaviors. This review highlights the failure of typical wetting evaluations in predicting performance for the new application as well as the potential of the coatings in enhancing chemical resistance for painted surfaces. Potential methods for further improvements are also discussed. Published 2020. This article is a U.S. Government work and is in the public domain in the USA

Marinobacter spp. are opportunitrophs with a broad metabolic range including interactions with metals and electrodes. Marinobacter atlanticus strain CP1 was previously isolated from a cathode biofilm microbial community enriched from a sediment microbial fuel cell. Like other Marinobacter spp., M. atlanticus generates small amounts of electrical current when grown as a biofilm on an electrode, which is enhanced by the addition of redox mediators. However, the molecular mechanism resulting in extracellular electron transfer is unknown. Here, RNA-sequencing was used to determine changes in gene expression in electrode-attached and planktonic cells of M. atlanticus when grown at electrode potentials that enable current production (310 and 510 mV vs. SHE) compared to a potential that enables electron uptake (160 mV). Cells grown at current-producing potentials had increased expression of genes for molybdate transport, regardless of planktonic or attached lifestyle. Electrode-attached cells at current-producing potentials showed increased expression of the major export protein for the type VI secretion system. Growth at 160 mV resulted in an increase in expression of genes related to stress response and DNA repair including both RecBCD and the LexA/RecA regulatory network, as well as genes for copper homeostasis. Changes in expression of proteins with PEP C-terminal extracellular export motifs suggests that M. atlanticus is remodeling the biofilm matrix in response to electrode potential. These results improve our understanding of the physiological adaptations required for M. atlanticus growth on electrodes, and suggest a role for metal acquisition, either as a requirement for metal cofactors of redox proteins or as a possible electron shuttling mechanism.

Bin/Amphiphysin/RVS (BAR) domain proteins belong to a superfamily of coiled-coil proteins influencing membrane curvature in eukaryotes and are associated with vesicle biogenesis, vesicle-mediated protein trafficking, and intracellular signaling. Here, we report a bacterial protein with BAR domain-like activity, BdpA, from Shewanella oneidensis MR-1, known to produce redox-active membrane vesicles and micrometer-scale outer membrane extensions (OMEs). BdpA is required for uniform size distribution of membrane vesicles and influences scaffolding of OMEs into a consistent diameter and curvature. Cryo-TEM reveals that a strain lacking BdpA produces lobed, disordered OMEs rather than membrane tubules or narrow chains produced by the wild-type strain. Overexpression of BdpA promotes OME formation during planktonic growth of S. oneidensis where they are not typically observed. Heterologous expression results in OME production in Marinobacter atlanticus and Escherichia coli. Based on the ability of BdpA to alter membrane architecture in vivo, we propose that BdpA and its homologs comprise a newly identified class of bacterial BAR domain-like proteins.

Electroactive bacteria are living catalysts, mediating energy-generating reactions at anodes or energy storage reactions at cathodes via extracellular electron transfer (EET). The Cathode-ANode (CANode) biofilm community was recently shown to facilitate both reactions; however, the identities of the primary constituents and underlying molecular mechanisms remain unknown. Here, we used metagenomics and metatranscriptomics to characterize the CANode biofilm. We show that a previously uncharacterized member of the family Desulfobulbaceae, Desulfobulbaceae-2, which had <1% relative abundance, had the highest relative gene expression and accounted for over 60% of all differentially expressed genes. At the anode potential, differential expression of genes for a conserved flavin oxidoreductase (Flx) and heterodisulfide reductase (Hdr) known to be involved in ethanol oxidation suggests a source of electrons for the energy-generating reaction. Genes for sulfate and carbon dioxide reduction pathways were expressed by Desulfobulbaceae-2 at both potentials and are the proposed energy storage reactions. Reduction reactions may be mediated by direct electron uptake from the electrode or from hydrogen generated at the cathode potential. The Desulfobulbaceae-2 genome is predicted to encode at least 85 multiheme (≥3 hemes) c-type cytochromes, some with as many as 26 heme-binding domains, that could facilitate reversible electron transfer with the electrode. Gene expression in other CANode biofilm species was also affected by the electrode potential, although to a lesser extent, and we cannot rule out their contribution to observed current. Results provide evidence of gene expression linked to energy storage and energy-generating reactions and will enable development of the CANode biofilm as a microbially driven rechargeable battery. IMPORTANCE Microbial electrochemical technologies (METs) rely on electroactive bacteria to catalyze energy-generating and energy storage reactions at electrodes. Known electroactive bacteria are not equally capable of both reactions, and METs are typically configured to be unidirectional. Here, we report on genomic and transcriptomic characterization of a recently described microbial electrode community called the Cathode-ANode (CANode). The CANode community is able to generate or store electrical current based on the electrode potential. During periods where energy is not needed, electrons generated from a renewable source, such as solar power, could be converted into energy storage compounds to later be reversibly oxidized by the same microbial catalyst. Thus, the CANode system can be thought of as a living "rechargeable battery." Results show that a single organism may be responsible for both reactions demonstrating a new paradigm for electroactive bacteria.

New methods for antimicrobial design are critical for combating pathogenic bacteria in the post-antibiotic era. Fortunately, competition within complex communities has led to the natural evolution of antimicrobial peptide (AMP) sequences that have promising bactericidal properties. Unfortunately, the identification, characterization, and production of AMPs can prove complex and time consuming. Here, we report a peptide generation framework, PepVAE, based around variational autoencoder (VAE) and antimicrobial activity prediction models for designing novel AMPs using only sequences and experimental minimum inhibitory concentration (MIC) data as input. Sampling from distinct regions of the learned latent space allows for controllable generation of new AMP sequences with minimal input parameters. Extensive analysis of the PepVAE-generated sequences paired with antimicrobial activity prediction models supports this modular design framework as a promising system for development of novel AMPs, demonstrating controlled production of AMPs with experimental validation of predicted antimicrobial activity.

This review describes an ongoing effort intended to develop wireless sensor networks for real-time monitoring of airborne targets across a broad area. The goal is to apply the spectrophotometric characteristics of porphyrins and metalloporphyrins in a colorimetric array for detection and discrimination of changes in the chemical composition of environmental air samples. The work includes hardware, software, and firmware design as well as development of algorithms for identification of event occurrence and discrimination of targets. Here, we describe the prototype devices and algorithms related to this effort as well as work directed at selection of indicator arrays for use with the system. Finally, we review the field trials completed with the prototype devices and discuss the outlook for further development.

Introduction This effort seeks to develop chemical and biological sensing capabilities suitable for use in long duration, distributed sensing applications. For this type of application, it is desirable to provide inexpensive devices that can detect a range of targets, both known and unknown, with minimal power requirements. Porphyrins and metalloporphyrins are intensely colored, aromatic molecules with spectrophotometric characteristics that are sensitive to interaction with other chemicals. Porphyrins offer diverse chemical interactions that can be changed through alterations to the molecular structure and the coordinated metal. Through selection of a group of porphyrin indicators, it is possible to generate an array for which the relative responses of the indicator materials can provide target discrimination. The indicators selected for this effort provide reversible responses to chemical targets, offering the potential for long duration deployments and ongoing or repeated use of the indicator arrays [1-5]. Method Hardware. The prototype sensing hardware, our Array Based Environmental Air Monitor (ABEAM), is used with the paper supported porphyrin and porphyrin-antimicrobial peptide indicators. This device comprises a custom housing and control board with commercially available color sensors [4]. Communication with the device is via USB or wireless, with power supplied by DC barrel jack or batteries. Device output is as red, green, and blue (RGB) values versus time either stored in onboard flash memory or reported to a control computer via drip-feed [3-5]. Algorithm. An automated algorithm was developed to process ABEAM output for identification of chemical exposures [1, 3]. Processing by the algorithm is based on the angles between slopes in the device reported RGB color data for each of the color sensors. In general, two windows of data are compared for each color on each device: a baseline window populated by 120 data points and an active window populated by 20 points. The active window includes those points collected in the most recent 10 min with the baseline window including the previous 60 min. The use of these two sliding windows accounts for device drift as well as diurnal changes in environmental conditions. Results and Conclusions Initial work with the ABEAM prototype was completed without the housing or fans [2, 4, 6]. This effort largely focused on identification of indicator materials for use in an array that would allow for discrimination of alcohols (ethanol, methanol, and isopropanol) as model targets to be used in environmental evaluations. Under this work, a standard deviation based algorithm for event identification was developed. When the focus of the effort shifted from rapid on/off target exposures to those completed in an enclosure, to more effectively simulate expected environmental exposures, dramatic differences were noted in the performance of the standard deviation algorithm. The responses of the indicator materials did not occur within a short enough time duration to trigger the algorithm. The slope based algorithm (Section II) was developed as a result. This move from screening experiments to environmental exposures also served to identify shortfalls in instrument parameters. With the short on/off exposures, the use of a 5 s sampling interval with a 100 ms integration time produced data sufficient for characterization. For longer duration autonomous deployments, the 5 s sampling interval produced memory overrun in less than three days. The 30 s sampling interval allowed a run time of seven days in the original device and fourteen days in a follow-on iteration of the prototype. It was also necessary to extend the integration time for the devices under environmental exposure (to 400 ms) to provide sufficient signal to noise ratios for discrimination of events by the slope based algorithm [3-4]. We have demonstrated that the ABEAM provides detection of the alcohol targets in either an indoor or outdoor environment. When parameters are optimized and a negative control is included in the array, a specificity of 0.97 with sensitivity 1.0 can be achieved [3]. Here, we also present the results of recent evaluations of a network of six devices used in an outdoor environment for the detection of methyl salicylate. This is the first demonstration of these devices used with ongoing drip-feed data reporting and real-time analysis via wireless communications and using battery power. References 1. J. S. Erickson; A. P. Malanoski; B. J. White; D. A. Stenger; E. R. Tankard, Practical Implementation of Detection Algorithm for Reflectance-Based, Real-Time Sensing, US Naval Research Laboratory, Washington, DC (2018) MR/6930--18-9812. 2. B. J. Johnson; J. S. Erickson; J. Kim; A. P. Malanoski; I. A. Leska; S. M. Monk; D. J. Edwards; T. N. Young; J. Verbarg; C. Bovais; R. D. Russell; D. A. Stenger, Miniaturized reflectance devices for chemical sensing. Meas. Sci. Technol. 25 (2014) 095101 095101. DOI: 10.1088/0957-0233/25/9/095101 3. B. J. Johnson; A. P. Malanoski; J. S. Erickson; R. Liu; A. R. Remenapp; D. A. Stenger; M. H. Moore, Reflectance-based detection for long term environmental monitoring. Heliyon 3 (2017) e00312 DOI: 10.1016/j.heliyon.2017.e00312 4. A. P. Malanoski; B. J. Johnson; J. S. Erickson; D. A. Stenger, Development of a Detection Algorithm for Use with Reflectance-Based, Real-Time Chemical Sensing. Sensors 16 (2016) 1927. DOI: 10.3390/s16111927 5. B. J. White; J. S. Erickson; A. P. Malanoski; M. H. Moore, Reflectance-Based Sensing: Post-Evaluation Analysis of Sensor Responses, US Naval Research Laboratory, Washington, DC (2019) MR/6930--19-9852. 6. B. J. Johnson; R. Liu; R. C. Neblett; A. P. Malanoski; M. Xu; J. S. Erickson; L. Zang; D. A. Stenger; M. H. Moore, Reflectance-based detection of oxidizers in ambient air. Sens. Actuator B-Chem. 227 (2016) 399-402 DOI: 10.1016/j.snb.2015.12.040 Figure 1

We have developed the ABEAM-15, a custom-built multiplexed reflectance device for the detection of vapor phase and aerosolized chemical plumes. The instrument incorporates fifteen individual sensing elements, has wireless communications, offers support for a battery pack, and is capable of both live and fully autonomous operation. Two housing options have been fabricated: a compact open housing for indoor use and a larger weather-sealed housing for outdoor use. Previously developed six-plex analysis algorithms are extended to 15-plex format and implemented on a laptop computer. We report the results of recent outdoor field trials with this instrument in Denver, CO in a stadium security scenario. Through software, the wireless modules on each instrument were configured to form a six-instrument, star-point topology, distributed microsensor network with live reporting and real-time data analysis. The network was tested with aerosols of methyl salicylate.

Bin/Amphiphysin/RVS (BAR) domain proteins belong to a superfamily of coiled-coil proteins influencing membrane curvature in eukaryotes and are associated with vesicle biogenesis, vesicle-mediated protein trafficking, and intracellular signaling. Here we report the first prokaryotic BAR domain protein, BdpA, from Shewanella oneidensis MR-1, known to produce redox-active membrane vesicles and micrometer-scale outer membrane extensions (OMEs). BdpA is required for uniform size distribution of membrane vesicles and scaffolding OMEs into a consistent diameter and curvature. Cryogenic transmission electron microscopy reveals a strain lacking BdpA produces lobed, disordered OMEs rather than membrane tubes produced by the wild type strain. Overexpression of BdpA promotes OME formation during conditions where they are less common. Heterologous expression results in OME production in Marinobacter atlanticus and Escherichia coli . Based on the ability of BdpA to alter membrane curvature in vivo , we propose that BdpA and its homologs comprise a newly identified class of prokaryotic BAR (P-BAR) domains. ### Competing Interest Statement The authors have declared no competing interest.

This report describes the hardware for a prototype sensor system and a processing algorithm developed for application with time dependent, reflectance color values obtained using that device. The system utilizes paper supported porphyrin and metalloporphyrin indicators for chemical detection. Here, we explain the event identification algorithm, variations for application of the algorithm in real-time, and potential adjustments to improve sensitivity and selectivity in the output. The described algorithm has been developed with a view toward minimizing the processing power necessary to facilitate its application onboard highly miniaturized sensor devices. The goal is to develop devices that can be utilized as part of a highly distributed chemical sensing network.

Natural living conductive biofilms transport electrons between electrodes and cells, as well as among cells fixed within the film, catalyzing an array of reactions from acetate oxidation to CO_2 reduction. Synthetic biology offers tools to modify or improve electron transport through biofilms, creating a new class of engineered living conductive materials. Engineered living conductive materials could be used in a range of applications for which traditional conducting polymers are not appropriate, including improved catalytic coatings for microbial fuel-cell electrodes, self-powered sensors for austere environments, and next-generation living components of bioelectronic devices that interact with the human microbiome.

Here, we present the complete genome sequence of Leisingera aquamixtae R2C4, isolated from the electroautotrophic microbial consortium biocathode MCL (Marinobacter-Chromatiaceae-Labrenzia). As an isolate of a current-producing system, the genome sequence of L. aquamixtae will yield insights regarding electrode-associated microorganisms and communities. A dark pigment is also observed during cultivation.