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Results for “Biomolecular Materials”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2012

Novel Photonic & Electronic BioMolecular Materials

The overall objective is to create robust artificial protein modules as scaffolds to control both (a) the conformation of novel cofactors incorporated into the modules thereby making the modules possess a desired functionality and (b) the organization of these functional modules into ordered macroscopic ensembles, whose macroscopic materials properties derive from the designed microscopic function of the modules. We focus on two specific types of cofactors for imparting functionality in this project; primarily nonlinear optical (NLO) chromophores designed to exhibit extraordinary molecular hyperpolarizabilities, as well as donor-bridge-acceptor cofactors designed to exhibit highly efficient, 'through-bonds' light-induced electron transfer (LIET) over nano-scale distances. The ensembles range from 2-D to 3-D, designed to possess the degree of orientational and positional order necessary to optimize their macroscopic response, the latter ranging from liquid-crystalline or glass-like to long-range periodic. Computational techniques, firmly based in statistical thermodynamics, are utilized for the design the artificial protein modules, based on robust {alpha}-helical bundle motifs, necessarily incorporating the desired conformation, location, and environment of the cofactor. Importantly, this design approach also includes optimization of the interactions between the modules to promote their organization into ordered macroscopic ensembles in 2-D and 3-D via either directed-assembly or self-assembly. When long-range periodic order is required, the design can be optimized to result a specified lattice symmetry. The structure and functionality of the individual modules are fully characterized at the microscopic level, as well as that of the ensembles at the macroscopic level, employing modern experimental physical-chemical and computational techniques. These include, for example, multi-dimensional NMR, various pump-probe transient spectroscopies to ultrafast time-scales, and hyper-Rayleigh scattering at the microscopic level, and synchrotron radiation-based x-ray scattering and x-ray spectroscopy, cold neutron scattering, molecular dynamics simulation, and optical harmonic generation at the macroscopic level. This overall approach has some distinct advantages, compared to more traditional approaches, for example, those based on organic polymers, biopolymers or undressed cofactors. The resulting functional ensembles thereby have potential for important device applications in the areas of optical communications and photovoltaics. The approach also has an absolute requirement for a tightly coupled collaborative effort necessary to span the rigorous demands for the design, synthesis and characterization of such novel photonic and electronic biomolecular materials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Method for lithograghic patterning of sensitive materials

Methods for patterning highly sensitive materials, such as organic materials, organic semiconductors, biomolecular materials, and the like, with photolithographic resolution are disclosed. In some embodiments, a germanium mask (304) is formed on the surface of the sensitive material (302), thereby protecting it from subsequent processes that employ harsh chemicals that would otherwise destroy the sensitive material (302). A microlithography mask (306) is patterned on the germanium mask layer (304), after which the germanium exposed by the microlithography mask (306) is removed by dissolving it in water. After transferring the pattern of the germanium mask (304) into the sensitive material (302), the germanium and microlithography masks (304, 306) are completely removed by immersing the substrate in water, which dissolves the remaining germanium and lifts off the microlithography mask material. As a result, the only chemical to which the sensitive material (302) is exposed during the patterning process is water, thereby mitigating or avoiding damage to the material (302).

36 MATERIALS SCIENCE↗
DOE OSTI2010

Biomolecular hybrid material and process for preparing same and uses for same

Disclosed is a composition and method for fabricating novel hybrid materials comprised of, e.g., carbon nanotubes (CNTs) and crosslinked enzyme clusters (CECs). In one method, enzyme-CNT hybrids are prepared by precipitation of enzymes which are subsequently crosslinked, yielding crosslinked enzyme clusters (CECs) on the surface of the CNTs. The CEC-enzyme-CNT hybrids exhibit high activity per unit area or mass as well as improved enzyme stability and longevity over hybrid materials known in the art. The CECs in the disclosed materials permit multilayer biocatalytic coatings to be applied to surfaces providing hybrid materials suitable for use in, e.g., biocatalytic applications and devices as described herein.

Kim, Jungbae↗
DOE OSTI2019

Discovery of Stable and Selective Antibody Mimetics from Combinatorial Libraries of Polyvalent, Loop-Functionalized Peptoid Nanosheets

The ability of antibodies to bind a wide variety of analytes with high specificity and high affinity makes them ideal candidates for therapeutic and diagnostic applications. However, the poor stability and high production cost of antibodies have prompted exploration of a variety of synthetic materials capable of specific molecular recognition. Unfortunately, it remains a fundamental challenge to create a chemically diverse population of protein-like, folded synthetic nanostructures with defined molecular conformations in water. Here we report the synthesis and screening of combinatorial libraries of sequence-defined peptoid polymers engineered to fold into ordered, supramolecular nanosheets displaying a high spatial density of diverse, conformationally constrained peptoid loops on their surface. These polyvalent, loop-functionalized nanosheets were screened using a homogeneous Förster resonance energy transfer (FRET) assay for binding to a variety of protein targets. Peptoid sequences were identified that bound to the heptameric protein, anthrax protective antigen, with high avidity and selectivity. These nanosheets were shown to be resistant to proteolytic degradation, and the binding was shown to be dependent on the loop display density. This work demonstrates that key aspects of antibody structure and function-the creation of multivalent, combinatorial chemical diversity within a well-defined folded structure-can be realized with completely synthetic materials. This approach enables the rapid discovery of biomimetic affinity reagents that combine the durability of synthetic materials with the specificity of biomolecular materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Probing Light Atoms at Subnanometer Resolution: Realization of Scanning Transmission Electron Microscope Holography

Atomic resolution imaging of light elements in electron-transparent materials has long been a challenge. Biomolecular materials, for example, are rapidly altered by incident electrons. We demonstrate a scanning transmission electron microscopy (STEM) technique, called STEM holography, capable of efficient structural analysis of beam-sensitive nanomaterials. STEM holography measures the absolute phase and amplitude of electrons passed through a specimen via interference with a vacuum reference wave. We use an amplitude-dividing nanofabricated grating to prepare multiple beams focused at the sample. We configure the postspecimen microscope imaging system to overlap the beams, forming an interference pattern. We record and analyze the pattern at each 2D-raster-scan-position, reconstructing the complex object wave. As a demonstration, we image gold nanoparticles on an amorphous carbon substrate at 2.4 Å resolution. In conclusion STEM holography offers higher contrast of the carbon while maintaining gold atomic lattice resolution compared to high angle annular dark field STEM.

4D-STEM↗
DOE OSTI2018

Final report for Assembling Microorganisms into Energy Converting Materials

The goal of this project was to integrate microorganisms capable of reversible energy transduction in response to changing relative humidity with non-biological materials to create hybrid energy conversion systems. While plants and many other biological organisms have developed structures that are extraordinarily effective in converting changes in relative humidity into mechanical energy, engineered energy transduction systems rarely take advantage of this powerful phenomenon. Rather than developing synthetic materials that can convert changes in relative humidity in to mechanical energy, we developed approaches to assemble bacterial spores into larger materials. These materials can convert energy from evaporation of water in dry atmospheric conditions, which we demonstrated by building energy harvesters from these materials. We have also developed experiments to investigate the interaction of water with the spore material, and to determine how this interaction imposes limits on energy conversion. In addition, we carried out theoretical calculations to investigate the limits imposed by the environmental conditions to the power available in the energy harvesting process. These calculations took into account heat and water vapor transfer in the atmosphere surrounding the spore based materials. Overall, our results suggest that biomolecular materials are promising candidates to convert energy from evaporation.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Miniaturized Hybrid Materials Inspired by Nature (Final Technical Report)

The objective of our research program is to develop a fundamental scientific understanding of assembly in biomolecular materials mediated by mechanisms that mimic complex events in the cellular environment. The building blocks that we study include globular, disordered, and filamentous proteins, lipids, and nucleic acids. Notably, the nanoscale assemblies may either be similar to, or highly distinct from, those occurring in vivo, owing to the complex nature of the systems. Novel assemblies may further result due to controlled shape changes in building blocks.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Efficient Cytosolic Delivery Using Crystalline Nanoflowers Assembled from Fluorinated Peptoids

The design and synthesis of biocompatible nanomaterials as cargoes for the intracellular delivery of therapeutic proteins or genes have attracted intense attention because of their promise for use in therapeutics. Despite the advances in this area, very few nanomaterials can be efficiently delivered to the cytosol. To address these challenges, we designed and synthesized crystalline nanoflower-like particles from fluorinated sequence-defined peptoids; the crystallinity and fluorination of these particles enabled highly efficient cytosolic delivery with minimal cytotoxicity. We delivered these particles, 80% appear to diffuse in the cytosol. Furthermore, these nanocrystals can carry mRNA for instance and effectively delivered into cytosol for gene transfection, demonstrating the generality of our nanocrystals. Our results indicate that self-assembly of crystalline nanomaterials from fluorinated peptoids paves a new way toward development of nanocargoes with efficient cytosol gene delivery. Y. Song and M. Wang contributed equally to this work. This work was supported by start-up funds from Washington State University. Peptoid synthesis work was supported by the Materials Synthesis and Simulation Across Scales (MS3) Initiative through the LDRD fund at Pacific Northwest National Laboratory (PNNL). Assembly of peptoid particles and their structural characterizations were supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Biomolecular Materials Program at PNNL. XRD work was conducted at the Advanced Light Source with support from the Molecular Foundry, at Lawrence Berkeley National Laboratory, both of which are supported by the Office of Science, under Contrast No. DE-AC02-05CH11231. PNNL is multi-program national laboratory operated for Department of Energy by Battelle under Contract No. DE-AC05-76RL01830.

peptoids, nanocrystal, cytosol delivery, endosome ↗
DOE OSTI2018

Peptoid Backbone Flexibilility Dictates Its Interaction with Water and Surfaces: A Molecular Dynamics Investigation

Peptoids are peptide-mimetic biopolymers that are easy-to-synthesize and adaptable for use in drugs, chemical scaffolds, and coatings. However, there is insufficient information about their structural preferences and interactions with the environment in various applications. We conducted a study to understand the fundamental differences between peptides and peptoids using molecular dynamics simulations with semi-empirical (PM6) and empirical (AMBER) potentials, in conjunction with metadynamics enhanced sampling. From studies of single molecules in water and on surfaces, we found that sarcosine (model peptoid) is much more flexible than alanine (model peptide) in different environments. However, the sarcosine and alanine interact similarly with a hydrophobic or a hydrophilic. Finally, this study highlights the conformational landscape of peptoids and the dominant interactions that drive peptoids towards these conformations. ACKNOWLEDGMENT: MD simulations and manuscript preparation were supported by the MS3 (Materials Synthesis and Simulation Across Scales) Initiative at Pacific Northwest National Laboratory (PNNL), a multi-program national laboratory operated by Battelle for the U.S. Department of Energy. CJM was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by the US Department of Energy, Office of Basic Energy Sciences, Biomolecular Materials Program at PNNL. Computing resources were generously allocated by University of Washington's IT department and PNNL's Institutional Computing program. The authors greatly acknowledge conversations with Dr. Kayla Sprenger, Josh Smith, and Dr. Yeneneh Yimer.

alanine↗
DOE OSTI2026

Computationally designed coiled coil ‘bundlemers’ as model colloidal nanoparticles for solution assembly and materials design (Final Report)

As a collaborative team at the University of Delaware and the University of Pennsylvania, Kloxin, Pochan and Saven designed new biomimetic nanomaterials de novo, leveraging a variety of complementary areas of expertise: computational design of biopolymers (Saven at the University of Pennsylvania), and synthesis and characterization (Kloxin and Pochan at the University of Delaware). Overall activities included: sequence-specific peptide synthesis; covalent crosslinking; noncovalent assembly; site-specific functionalization; and nanostructural characterization using electron microscopy and solution-phase (x-ray and neutron) scattering. Using natural and non-natural amino acids, the team created modular, functional peptide building blocks for elaboration of new nanostructured materials. Ultimately, the development of robust peptide-based, building blocks provides tools for researchers to readily produce complex nanomaterial structures in a wide range of applications. The project had three, interconnecting goals in an effort to provide the broader scientific community with a new peptide-based paradigm for materials design and characterization. First, we further developed the coiled-coil bundle-based toolbox (otherwise known as the ‘bundlemer’ toolbox) via computational design with experimental bundle assembly verification. Second, we developed new uses of covalent interactions, in addition to desired physical (noncovalent) interactions, to assemble bundlemers into 1-D polymer chains with targeted chain rigidity, length, and dispersity. Thirds, we used the above designs to experimentally realize (physical or covalent) polymers to target the creation of liquid crystals or to realize interparticle assembly into nanoporous lattices. The close integration of the three groups was instrumental in success of the biomolecular materials design, formation, and understanding for future designs.

36 MATERIALS SCIENCE↗
DOE OSTI2025

The Anisotropic Adsorption of De Novo Allosteric Two‐Component Protein Fibers on Mica Surfaces

Protein adsorption at solid–liquid interfaces underlies many biomedical and materials applications, yet the mechanisms governing adsorption of proteins and their assemblies remain poorly understood. Here we investigate de novo–designed proteins that self-assemble into three fibrillar morphologies — small (S), large (L), and helical (H)—on muscovite mica. S-fibers are metastable, forming first but diminishing as L- and H-fibers develop and deposit. Adsorption of both fibers and monomers depends on fiber morphology and solvent environment, which is modulated by the substrate. The anisotropic surface features of the fiber types—long axis of S- and L-fibers and helical grooves of H-fibers—correlate with specific crystallographic directions on mica (001). S- and L-fibers align along the unique lattice axis, while the substrate-facing groove of H-fibers preferentially aligns along the remaining symmetry-related directions. Increasing potassium chloride (KCl) concentrations to molar levels alters adsorption, decreasing monomer coverage relative to fibers. These observations, interpreted through the effect of interfacial interface, indicate that ion-mediated modulation of hydration layers governs electrostatic interactions and alignment. This study reveals how coupling between protein topography, substrate crystallography, and hydration structure dictates selective adsorption and orientation of protein assemblies, offering insights for rational biomolecular material design.

AFM↗
DOE OSTI2026

New principles of self‐organization created through the interplay of DNA condensates, microtubules, and motors

Bioinspired design—which holds great promise for a new generation of materials that are robust to defects, scalable under green manufacture, environmentally responsive, and programmably reconfigurable—requires mastery over molecular self-organization. Yet, from its specific mechanisms to most general architectures, the principles governing self-organization remain poorly understood and not even fully enumerated. For living systems, one obvious architectural principle is the modular reuse of a few simple molecular components in myriad combinations to achieve more complex phenomena. For example, the mechanical tasks of a cell are driven by the nonequilibrium dynamics of cytoskeletal filaments and molecular motors—the same filaments and motors, reprogrammed by a variety of modulators, perform tasks ranging from cell movement to division. Similarly, many compartmentalization tasks are performed by liquid-like condensates of simple components, which act as membraneless organelles to localize particular molecules in space and time (e.g. for gene regulation or RNA processing). In a few cases, condensates combine and interact with the cytoskeleton to create still more complex phenomena, e.g. the nucleation of microtubule asters from the centrosome (a protein condensate) to form the mitotic spindle during cell division. Very little is known about the fundamental mechanisms of such filament-plus-condensate phenomena. Despite few examples, the landscape of behaviors that can be achieved through the combination of condensates, filaments, and motors appears vast. However, exploration has been hindered by a lack of systems that have sufficiently programmable and dynamically tunable interactions between component condensates, filaments, and motors. We proposed to combine programmable DNA condensates, filamentous microtubules, and light-controlled motors into self-organizing systems whose principles go beyond those that have been observed in nature. In one limit, our systems will use microtubules and motors to create the molecular analog of a network of roads, which will organize droplets of DNA condensates capable of carrying molecular cargo. DNA condensates coupled to motors will flow from one microtubule aster hub to another, with their direction and timing controlled by DNA circuits. In another limit, microtubules will swim through bulk DNA condensates and exhibit strong interactions with boundaries between different types of condensates. Microtubule swimmers will reflect, get trapped, or refract at boundaries, under a mechanical analog of the classical optical index of refraction. DNA condensates having different mechanical indexes of refraction will be used to construct the analog of optical lenses, so that microtubule swimmers can be manipulated like light—collimated, diffracted, focused, and sorted based on properties analogous to wavelength. These two limits define two new architectures, within which multiple new mechanistic principles for self-organization will be discovered and explored. To explore these architectures, the motor-based coupling between DNA condensates and filaments will be controlled in time and space through the use of opto-proteins that create reversible links between DNA condensates and motors upon illumination. For each principle of interest, patterns of light will create virtual experiments by defining patterns of activity where DNA condensates walk along filaments, or filaments swim through condensates, and patterns of inactivity which will serve either as controls, or as boundary conditions vital to create the desired phenomena. This research serves the goals of Basic Energy Sciences Biomolecular Material Program by elucidating the principles by which the emergent, nonequilibrium behavior of collections of DNA condensates, motors, and microtubules can be programmed by environmental light patterns to create complex motion and materials transport. Because DNA condensates can be readily coupled to virtually any high performance nanomaterial, from carbon nanotubes, to metal nanoparticles, to light harvesting systems, this work provides a path to the construction, self-maintenance and reconfiguration of materials relevant to the Department of Energy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Spontaneous Reorganization of DNA-Based Polymers in Higher Ordered Structures Fueled by RNA

We demonstrate a strategy that allows for the spontaneous reconfiguration of self-assembled DNA polymers exploiting RNA as chemical fuel. To do this, we have rationally designed orthogonally addressable DNA building blocks that can be transiently deactivated by RNA fuels and subtracted temporarily from participation in the self-assembly process. Through a fine modulation of the rate at which the building blocks are reactivated we can carefully control the final composition of the polymer and convert a disordered polymer in a higher order polymer, which is disfavored from a thermodynamic point of view. We measure the dynamic reconfiguration via fluorescent signals and confocal microscopy, and we derive a kinetic model that captures the experimental results. Our approach suggests a novel route toward the development of biomolecular materials in which engineered chemical reactions support the autonomous spatial reorganization of multiple components.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Molecular-level origin of the carboxylate head group response to divalent metal ion complexation at the air-water interface

We exploit gas-phase cluster ion techniques to provide insight into the local interactions underlying divalent metal ion-driven changes in the spectra of carboxylic acids at the air-water interface. This information is used to clarify the experimental findings of surface sensitive spectroscopies that the CO stretching bands of long chain acids appear at very similar energies when the head group is deprotonated by high sub-phase pH or is exposed to relatively high concentrations of Ca2+ divalent metal ions (e.g., Ca2+ and Mg2+). To this end, we report the evolution of the vibrational spectra of size-selected [Ca2+·RCO2¯]+·(H2O)n=0-14 and RCO2¯·(H2O)n=0-14 cluster ions obtained using infrared photofragmentation mass spectrometry toward the features observed at the air-water interface. The carboxylate with R = -CD2CD3 was chosen in order to capture the longer chain behavior and to suppress band congestion that complicates the spectra of the light isotopologue. Surprisingly, not only does stepwise hydration of the RCO2¯ anion and the [Ca2+·RCO2¯]+ contact ion pair yield solvatochromic responses in opposite directions, but in both cases the responses of the two CO bands (?_s^COO and ?_as^COO) to hydration are opposite to each other! The result is that the two CO bands evolve toward their interfacial and bulk asymptotes from opposite directions. Theoretical simulations of the [Ca2+·RCO2¯]+·(H2O)n clusters indicate that the metal ion remains directly bound to the head group in a contact ion pair motif as the asymmetric CO stretch converges at the bulk value by n = 12, establishing that direct metal complexation can account for the interfacial and bulk behavior. We discuss these effects in the context of a qualitative model that invokes the water network-dependent local electric field along the C-C bond connecting the head group to the tail as the key parameter driving the observed trends. M.A.J. and H.C.A. thank the National Science Foundation through the NSF Center for Aerosol Impacts on Chemistry of the Environment (NSF-CAICE), CHE-1305427 for supporting this work. M.A.J. thanks the Air Force Office of Scientific Research for the cryogenic spectrometer used in the gas phase experiments. K.D.J. thanks the Department of Energy under grant no. DE-FG02-00ER15066. C.J. Mundy and S.M. Kathmann are supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. M.D. Baer was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Biomolecular Materials Program at PNNL. PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under Contract No. DE-AC05- 76RL01830. Computing resources for the calculation of harmonic spectra were allocated by PNNL’s Institutional Computing program.

Denton, Joanna↗
DOE OSTI2020

Programmable Dynamic Self-Assembly of DNA Nanostructures (Final Technical Report)

This technical report summarizes our research toward the synthesis of active biomolecular materials that take advantage of the biological properties of DNA and RNA, but can operate in non-biological contexts. Our approach takes inspiration from the dynamic assembly and disassembly of cytoskeletal filaments inside cells, and focuses on the generation of artificial filaments with comparable adaptation and responsiveness. We report the construction of DNA nanotube systems that assemble and disassemble reversibly in response to a variety of molecular stimuli including other nucleic acids (DNA and RNA), enzymes, and pH, as well as our progress on developing a reaction network framework to regulate self-assembly. Our DNA polymers are active in that they rely on the programmable energetics of hybridization and on the kinetics of enzymatic reactions to perform assembly and disassembly. Results include experiments and computational models. The research described here was performed between June 15, 2016 and June 15, 2019 at the University of California at Riverside with the support of the collaborative award DE-SC0010595 to PI Elisa Franco at UC Riverside and PI Rebecca Schulman at Johns Hopkins. The report focuses on the research performed by the team of PI Franco. The report also details work performed during a no-cost extension (June 15, 2019 - December 15, 2019) awarded to PI Guillermo Aguilar and PI Franco.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Propulsion of synthetic protocells and coacervates driven by biochemical catalysis

An important area in the design of biomolecular materials is the mimicry of cellular function through the assembly of molecular components into synthetic cells, or protocells. Through compartmentalization and subsequent evolution, biological cells have achieved the goals of specificity, amplification, and response. By assembling cell-like structures that mimic the organization and size of a natural cell but that incorporate novel components and respond to synthetic triggers, we can extend their capabilities beyond what is currently achievable in biology. For applications in energy, these include the ability to convert chemical to mechanical energy, and to enable the response of sensors and responders once a threshold has been reached. This technical report summarizes progress made on this project as of Dec 31, 2023.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Rotational Dynamics and Transition Mechanisms of Surface-Adsorbed Proteins

Assembly of biomolecules at solid-water interfaces requires molecules to traverse complex orientation-dependent energy landscapes through processes that are poorly understood, largely due to the dearth of in-situ single molecule measurements and statistical analyses of the rotational dynamics that define directional selection. Emerging capabilities in high-speed atomic force microscopy and machine learning have allowed us to directly determine the orientational energy landscape and observe and quantify the rotational dynamics for protein nanorods on the surface of muscovite mica under a variety of conditions. Comparisons with kinetic Monte Carlo simulations show that the transition rates between adjacent orientation-specific energetic minima can largely be understood through traditional models of in-plane Brownian rotation across a biased energy landscape, with resulting transition rates that are exponential in the energy-barriers between states. However, transitions between more distant angular states are decoupled from barrier height, with jump-size distributions showing a power-law decay that is characteristic of a non-classical Levy-flight random walk, indicating that large jumps are enabled by alternative modes of motion via activated states. The findings provide new insights into the dynamics of biomolecules at solid-liquid interfaces that lead to self-assembly, epitaxial matching and other orientationally anisotropic outcomes and define a general procedure for exploring such dynamics with implications for hybrid biomolecular-inorganic materials design.

Orientational energy landscapes, Rotational dynami↗