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At least 487 records · Page 27

Tuning gold-based surface functionalization for streptavidin detection: A combined simulative and experimental study

A rationally designed gold-functionalized surface capable of capturing a target protein is presented using the biotin–streptavidin pair as a proof-of-concept. We carried out multiscale simulations to shed light on the binding mechanism of streptavidin on four differently biotinylated surfaces. Brownian Dynamics simulations were used to reveal the preferred initial orientation of streptavidin over the surfaces, whereas classical molecular dynamics was used to refine the binding poses and to investigate the fundamental forces involved in binding, and the binding kinetics. We assessed the binding events and the stability of the streptavidin attachment through a quartz crystal microbalance with dissipation monitoring (QCM-D). The sensing element comprises of biotinylated polyethylene glycol chains grafted on the sensor’s gold surface via thiol-Au chemistry. Finally, we compared the results from experiments and simulations. We found that the confined biotin moieties can specifically capture streptavidin from the liquid phase and provide guidelines on how to exploit the microscopic parameters obtained from simulations to guide the design of further biosensors with enhanced sensitivity.

59 BASIC BIOLOGICAL SCIENCES↗

Microgravity nucleation and particle coagulation experiments support

A hollow sphere model is developed to predict the range of supersaturation ratio values for refractory metal vapors in a proposed experimental nucleation apparatus. Since the experiments are to be carried out in a microgravity environment, the model neglects the effects of convection and assumes that the only transfer of vapors through an inert gas atmosphere is by conduction and molecular diffusion. A consistent set of physical properties data is assembled for the various candidate metals and inert ambient gases expected to be used in the nucleation experiments. Transient partial pressure profiles are computed for the diffusing refractory species for two possible temperature distributions. The supersaturation ratio values from both candidate temperature profiles are compared with previously obtained experimetnal data on a silver-hydrogen system. The model is used to simulate the diffusion of magnesium vapor through argon and other inert gas atmospheres over ranges of initial and boundary conditions. These results identify different combinations of design and operating parameters which are liekly to produce supersaturation ratio values high enough to induce homogeneous nucleation in the apparatus being designed for the microgravity nucleation experiments.

Lilleleht, L. U.↗

Molecular Nanotechnology and Space Settlement

Atomically precise manipulation of matter is becoming increasingly common in laboratories around the world. As this control moves into aerospace systems, huge improvements in computers, high-strength materials, and other systems are expected. For example, studies suggest that it may be possible to build: 10(exp 18) MIPS computers, 10(exp 15) bytes/sq cm write once memory, $153-412/kg-of-cargo single- stage-to-orbit launch vehicles and active materials which sense their environment and react intelligently. All of NASA's enterprises should benefit significantly from molecular nanotechnology. Although the time may be measured in decades and the precise path to molecular nanotechnology is unclear, all paths (diamondoid, fullerene, self-assembly, biomolecular, etc.) will require very substantial computation. This talk will discuss fullerene nanotechnology and early work on hypothetical active materials consisting of large numbers of identical machines. The speaker will also discuss aerospace applications, particularly missions leading to widespread space settlement (e.g., small near-Earth - object retrieval). It is interesting to note that control of the tiny - individual atoms and molecules - may lead to colonization of the huge -first the solar system, then the galaxy.

Globus, Al↗

Tours of High-containment and Pristine Facilities in Support of Mars Sample Return (MSR) Sample Receiving Facility (SRF) Definition Studies

During 2019 and 2020, the NASA Tiger Team RAMA (acronym of the authors) toured several high-containment biosafety laboratories and pristine space-mission facilities worldwide to better understand their practices, capabilities, and lessons-learned to aid in planning a Sample Receiving Facility (SRF) in support of Mars Sample Return (MSR). The team also included tours of a manufacturer of mobile and modular high-containment facilities as well as manufacturers of isolators and gloveboxes. In addition, the team visited the European Space Agency (ESA)ultraclean and sterile ISO 3 / airborne molecular contamination -9 (AMC-9) isolator line to clean and assemble the most critical hardware for ESA’s ExoMars Mars Lander System, and researchers developing a novel double-walled isolator (DWI) and robotic handling techniques in support of an MSR SRF. The RAMA team visits covered several construction modalities for an MSR SRF: (1) a new traditional fixed facility; (2) use of an existing fixed Biosafety Level 4(BSL-4) facility; (3) a novel modular BSL-4 approach; and (4) a hybrid combination of fixed, modular, and existing facilities. A new fixed facility approach can be tailored to MSR’s needs and is the approach used by all U.S. BSL-4 laboratories constructed to date. However, this approach could be the most expensive modality, take the longest to implement (8-12 years), and have significant programmatic risk of delay. The utilization of an existing BSL-4 facility may be possible depending on the final contamination control and science requirements for the MSR SRF. Due to the internal dimensions of the labs visited and facility structural requirements, it is unlikely that any modification can be made to the facility to meet cleanliness requirements. Furthermore, due to possible construction delays, possible capacity issues, and potential cross contamination vectors from in-house select agents, there may also be significant programmatic risks for sharing an existing facility. Another approach is building a contemporary modular facility. This is a novel approach that has recently been used for a BSL-3/3Ag facilities. The modular elements would be installed in a traditional building or shell structure. A modular facility has many advantages over a traditional fixed facility with lower costs, shorter design/construction/ commissioning schedule, and flexibility for easier retrofits and future expansion. Lastly, a hybrid approach of combining the use of either: (1) a modular facility inside a new fixed facility or (2) a modular and/or fixed BSL-4 annex in conjunction with an existing BSL-4 space should be considered. The advantage of a hybrid approach is that the facility could leverage the strengths of other approaches. Beyond facility construction approaches, the RAMA team investigated technologies and techniques for isolating and handling Martian samples in pristine environments. For example, ESA has been studying and developing a DWI breadboard along with other sample-handling technologies. The research and development investment for clean, remote manipulation and robotics at the start of the facility design phase would be beneficial to the SRF. Additionally, under-standing the lessons learned from Thales Alenia Space during the construction and operation of the most advanced state-of-the-art precision cleaning, sterilization, and assembly glovebox isolators ever developed for spacecraft hardware are also critical for the SRF. The RAMA team lays out a summary of the 18 facilities toured, and includes 43 observations,18 findings, and 22 areas of possible follow-up that the RAMA team and others could pursue to enable further findings. The observations and findings illustrate that constructing an MSR SRF would combine the complexity of both high-containment and pristine facilities, and merging these technologies would be challenging, but achievable.

Mars Sample Return↗

Intra- and Intermolecular Self-Assembly of a 20-nm-Wide Supramolecular Hexagonal Grid.

For the past three decades, the coordination-driven self-assembly of three-dimensional structures has undergone rapid progress; however, parallel efforts to create large discrete two-dimensional architectures-as opposed to polymers-have met with limited success. The synthesis of metallo-supramolecular systems with well-defined shapes and sizes in the range of 10-100 nm remains challenging. Here we report the construction of a series of giant supramolecular hexagonal grids, with diameters on the order of 20 nm and molecular weights greater than 65 kDa, through a combination of intra- and intermolecular metal-mediated self-assembly steps. The hexagonal intermediates and the resulting self-assembled grid architectures were imaged at submolecular resolution by scanning tunnelling microscopy. Characterization (including by scanning tunnelling spectroscopy) enabled the unambiguous atomic-scale determination of fourteen hexagonal grid isomers.

Zhang, Zhe↗

Spatiotemporal Studies of Soluble Inorganic Nanostructures with X‐rays and Neutrons

Abstract This Review addresses the use of X‐ray and neutron scattering as well as X‐ray absorption to describe how inorganic nanostructured materials assemble, evolve, and function in solution. We first provide an overview of techniques and instrumentation (both large user facilities and benchtop). We review recent studies of soluble inorganic nanostructure assembly, covering the disciplines of materials synthesis, processes in nature, nuclear materials, and the widely applicable fundamental processes of hydrophobic interactions and ion pairing. Reviewed studies cover size regimes and length scales ranging from sub‐Ångström (coordination chemistry and ion pairing) to several nanometers (molecular clusters, i.e. polyoxometalates, polyoxocations, and metal‐organic polyhedra), to the mesoscale (supramolecular assembly processes). Reviewed studies predominantly exploit 1) SAXS/WAXS/SANS (small‐ and wide‐angle X‐ray or neutron scattering), 2) PDF (pair‐distribution function analysis of X‐ray total scattering), and 3) XANES and EXAFS (X‐ray absorption near‐edge structure and extended X‐ray absorption fine structure, respectively). While the scattering techniques provide structural information, X‐ray absorption yields the oxidation state in addition to the local coordination. Our goal for this Review is to provide information and inspiration for the inorganic/materials science communities that may benefit from elucidating the role of solution speciation in natural and synthetic processes.

Yin, Jia‐Fu↗

Design of light- and chemically responsive protein assemblies through host-guest interactions

Host-guest (HG) interactions have been widely used to build responsive materials and molecular machines owing to their inherently dynamic nature, interaction specificity, and responsiveness to diverse stimuli. Here, in this work, we have set out to exploit these advantages of HG chemistry in the design of dynamic protein assemblies, using a C 4 symmetric protein, C98 RhuA, as a building block. We show that a C98 RhuA variant individually modified with β-cyclodextrin (βCD) (host) or azobenzene (guest) functionalities can specifically pair with each other to form highly ordered 1D and 2D assemblies. Association and dissociation of βCD RhuA- azo RhuA assemblies can be controlled by UV and visible light as well as by small-molecule modulators of βCD-azobenzene interactions. Kinetics analyses reveal that βCD RhuA- azo RhuA nanotubes assemble without a nucleation barrier, a highly unusual occurrence for helical supramolecular systems. Taken together, our findings provide a compelling example for achieving complex structural and dynamic outcomes in protein assembly through simple chemical design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure and Shape of Surface-Mediated Assembly of Surfactants

Achieving controls on the self-assembly of cationic and block copolymer micelles has significant implications for advancing novel material systems for energy, environmental, and biological applications and for tuning fluid flow behavior in subsurface geologic environments. While it is known that the aggregation of micelles is influenced by the composition of the surrounding fluid, the influence of a solid interface has been less explored. In this study, we probe the organization of cetyltrimethylammonium bromide (CTAB) micelles in the absence and presence of the Pluronic P123 block copolymer and quartz substrate using transmission and grazing-incidence small-angle X-ray scattering measurements and classical molecular dynamics (MD) simulations. In the absence of the quartz interface, CTAB with and without P123 molecules assemble as ellipsoid core–shell micelles. Densification of the core on adding P123 is noted from the decrease in the core radius from 15.9 to 14.6 Å. Here, the presence of a quartz substrate causes the micelles to elongate, which is noted by the emergence of a power-law slope in the low q region (<0.02 Å –1 ). Moreover, in the presence of both P123 and the quartz substrate, the micelle shape changes from ellipsoid core–shell to cylindrical core–shell, and a significantly higher number of aggregates are formed. The higher number of aggregates, and faster aggregation kinetics are linked to the organization of the solvent structures as noted from the MD simulations. These findings demonstrate the effects of adding a block copolymer and including a quartz substrate on the self-assembly of cationic (CTAB) micelles, which can be used to inform the design of functional material systems that harness surfactant chemistries.

42 ENGINEERING↗

Assessing electrogenetic activation via a network model of biological signal propagation

Introduction: Molecular communication is the transfer of information encoded by molecular structure and activity. We examine molecular communication within bacterial consortia as cells with diverse biosynthetic capabilities can be assembled for enhanced function. Their coordination, both in terms of engineered genetic circuits within individual cells as well as their population-scale functions, is needed to ensure robust performance. We have suggested that “electrogenetics,” the use of electronics to activate specific genetic circuits, is a means by which electronic devices can mediate molecular communication, ultimately enabling programmable control. Methods: Here, we have developed a graphical network model for dynamically assessing electronic and molecular signal propagation schemes wherein nodes represent individual cells, and their edges represent communication channels by which signaling molecules are transferred. We utilize graph properties such as edge dynamics and graph topology to interrogate the signaling dynamics of specific engineered bacterial consortia. Results: We were able to recapitulate previous experimental systems with our model. In addition, we found that networks with more distinct subpopulations (high network modularity) propagated signals more slowly than randomized networks, while strategic arrangement of subpopulations with respect to the inducer source (an electrode) can increase signal output and outperform otherwise homogeneous networks. Discussion: We developed this model to better understand our previous experimental results, but also to enable future designs wherein subpopulation composition, genetic circuits, and spatial configurations can be varied to tune performance. We suggest that this work may provide insight into the signaling which occurs in synthetically assembled systems as well as native microbial communities.

Chun, Kayla↗

Tunable Mid-Infrared Interband Emission from Tensile-Strained InGaAs Quantum Dots

We demonstrate the ability to tailor self-assembled growth of In 0.5 Ga 0.5 As quantum dots (QDs) on GaSb(111)A surfaces by molecular beam epitaxy. Spontaneous formation via the Volmer–Weber growth mode produces QDs with excellent structural and optical quality. By harnessing tensile strain to reduce their band gap energy, these QDs are characterized by light emission that extends into the midwave infrared wavelength range of 3.2–3.9 μm (0.318–0.388 eV). As we increase QD size, we can tune the band alignment from type-III to type-II, where light emission occurs due to interband recombination between quantum confined electrons in the InGaAs QDs and holes in the GaSb barriers. Of particular interest is an unusual blue-shift in emission wavelength with increasing QD size, which we attribute to the incorporation of Sb into the InGaAs QDs from the GaSb barriers. By expanding this approach to produce tensile-strained QDs from other narrow band gap semiconductors, we anticipate the development of a range of highly tunable mid-infrared light sources.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polymer Coatings on Virus-like Particle Nanoreactors at Low Ionic Strength—Charge Reversal and Substrate Access

Virus-like particles (VLPs) are a class of biomaterials which serve as platforms for achieving the desired functionality through interior and exterior modifications. Through ionic strength-mediated electrostatic interactions, VLPs have been assembled into hierarchically ordered materials. This work builds on predictive models to prepare polymer-coated VLP dusters at very low ionic strength. Zeta potential measurements showed that the clusters carried a strongly positive charge, a complete charge reversal from the VLP building block. SAXS analysis confirmed polymer adsorption onto the VLP exterior. Furthermore, we then studied the activity of an encapsulated enzyme toward small molecular and macromolecular substrates to determine the effect of each component of the hierarchically assembled material. We found that while encapsulation and polymer coating did not have a large effect on access to the enzyme by its native, small molecular substrate, substrate modification with a macromolecule caused the polymer coating and encapsulation to affect the access to the enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

Improving Energy Transfer within Metal–Organic Frameworks by Aligning Linker Transition Dipoles along the Framework Axis

Crystalline metal-organic frameworks (MOFs) can assemble chromophoric molecules into a wide range of spatial arrangements, which are controlled by the MOF topology. Like natural light-harvesting complexes (LHCs), the precise arrangement modulates interchromophoric interactions, in turn determining excitonic behavior and migration dynamics. To unveil the key factors that control efficient exciton displacements within MOFs, we first developed linkers with low electronic symmetry (as defined by large transition dipoles) and then assembled them into MOFs. These linkers possess extended conjugation along one molecular axis, engendering low optical bandgaps and improved oscillator strength for their lowest-energy transition (S 0 → S 1 ). This enhances absorption-emission spectral overlap and boosts the efficiency of Forster resonance energy transfer, which was observed experimentally by a sizable decrease in emission quantum yield (QY), accompanied by a faster population decay profile. We find that MOFs that orient these elongated linkers along their asymmetric pore channel, e.g., the hexagonal pores in an xly network, manifested >50% decrease in their emission QY with faster decay profiles relative to their corresponding solution dissolved linkers. This is due to an efficient migration of photogenerated excitons at the crystallite peripheral sites to internal sites, which was facilitated by polarized absorption-emission overlap among the parallelly aligned linkers. In contrast, symmetric MOFs, such as those with sqc-a topological net, orient elongated linkers along two perpendicular crystal axes, which hinders efficient exciton migration. This study underscores that MOFs are promising to develop artificial LHCs, but that to achieve an efficient exciton displacement, appropriate topology-guided assembly is required to fully realize the true potential of linkers with low electronic symmetry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC

The Multidisciplinary Observatory for Study of the Arctic Climate (MOSAiC) expedition consisted of a year-long drifting survey of the Central Arctic Ocean. The ecosystems component of MOSAiC included the sampling of molecular data, with metagenomes collected from a diverse range of environments. The generation of metagenome-assembled-genomes (MAGs) from metagenomes are a starting point for genome-resolved analyses. This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. The metagenomic samples are from the surface ocean, chlorophyll maximum, mesopelagic and bathypelagic, within leads and under-ice ocean, as well as melt ponds, ice ridges, and first- and second-year sea ice. This set of MAGs can be used to benchmark microbial biodiversity in the Central Arctic Ocean, compare individual strains across space and time, and to study changes in Arctic microbial communities from the winter to summer, at a genomic level.

59 BASIC BIOLOGICAL SCIENCES↗

Investigation of the Self-Assembly Behavior of Statistical Bottlebrush Copolymers via Self-Consistent Field Theory Simulations

Bottlebrush copolymers, a class of high-density side-chain-grafted copolymers with high molecular weights, have recently attracted extensive research attention due to the dramatic reduction of chain entanglement in these copolymers, unique self-assembly behaviors, and distinctive physical properties. In this study, we employ self-consistent field theory simulations to systemically investigate the phase behavior of statistical bottlebrush copolymers A-stat-B, an intriguing subclass of bottlebrush copolymers with random or alternating sequences of A and B side chains. We find that a broader variety of ordered mesophases can be stabilized in the melts of these copolymers relative to the more extensively studied bottlebrush block copolymers. In particular, we observe that these statistical copolymers can stabilize sphere phases over a larger range of species volume fractions than their diblock and tetrablock counterparts but require much higher segregation strength to achieve this. The sphere and hexagonally packed cylinder phases formed by conformationally symmetric statistical bottlebrush copolymers possess interesting discrete core–shell structures with the backbone and lower volume fraction side-chain species forming shells and cores, respectively. Moreover, we uncover a new strategy of stabilizing the Frank–Kasper phase A15 by introducing conformational asymmetry through different side-chain lengths and also observe deflection of order–order phase boundaries and significant mixing between the backbones and short side chains as conformational asymmetry is introduced.

36 MATERIALS SCIENCE↗

Developing planetary protection technology- microbial diversity of the Mars Orbiter Odyssey and the spacecraft assembly and encapsulation facility II

A study in which several surface samples, retrieved from both the Mars Odyssey Spacecraft and the Kennedy Space Center (KSC) Spacecraft Assembly and Encapsulation Facility II (SAEF-II), were prcesed and evaluated by both molecular and traditional culture-based methods for the microbial diversity.

Odyssey spacecraft microbial assembly facility↗

Advanced Methodology and Preliminary Measurements of Molecular and Mechanical Properties of Heart Valves under Dynamic Strain

Mammalian heart valves are soft tissue assemblies with multi-scale material properties. This is because they are constructs comprising both muscle and non-contractile extracellular matrix proteins (such as collagens and proteoglycans) and transition regions where one form of tissue structure becomes another, significantly different form. The leaflets of the mitral and tricuspid valves are connected to chordae tendinae which, in turn, bind through papillary muscles to the cardiac wall of the ventricle. The transition regions between these tissue subsets are complex and diffuse. Their material composition and mechanical properties have not been previously described with both micro and nanoscopic data recorded simultaneously, as reported here. Annotating the mechanical characteristics of these tissue transitions will be of great value in developing novel implants, improving the state of the surgical simulators and advancing robot-assisted surgery. We present here developments in multi-scale methodology that produce data that can relate mechanical properties to molecular structure using scanning X-ray diffraction. We correlate these data to corresponding tissue level (macro and microscopic) stress and strain, with particular emphasis on the transition regions and present analyses to indicate points of possible failure in these tissues.

valve failure↗

Assembly and Analysis of Cell-Scale Membrane Envelopes

The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms-a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NOCI-F Electronic Couplings in Assemblies of Indolonaphthyridine Molecules: From Dimers to the Full Stack

Key electronic processes related to molecular excitonic states of finite stacks of indolonaphthyridine molecules are analyzed via the non-orthogonal configuration interaction with fragments (NOCI-F) method. Indolonaphthyridine is an organic chromophore that can undergo several electronic photoexcitation-related intermolecular processes, such as exciton and electron transfer. The structures studied here are noncrystalline arrangements built as either ordered stacks of indolonaphthyridine or stacks extracted from molecular dynamics simulations including thermal disorder. Taking dimers or trimers from either model, we performed CASSCF and NOCI-F calculations to quantify the intermolecular electronic couplings governing singlet fission, excited singlet and triplet diffusion, and hole and electron diffusion processes. Also, comparing the results for the different models, we studied the effect of structural disorder and distortion on these couplings. Finally, we present a newly developed, advanced postanalysis tool. It takes the NOCI-F data as input to carry out a multifragment full Hamiltonian procedure that involves the complete stack, providing physical information not available from the dimer/trimer models, hence giving access to additional insight into the material’s properties.

coupling reactions↗