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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 OSTI2023

A Nitrogen Out-of-Plane (NOOP) Mechanism for Imine-Based Light-Driven Molecular Motors

Light-driven molecular motors have generated considerable interest due to their potential applications in material and biological systems. Recently, Greb and Lehn reported a new class of molecular motors, chiral N-alkyl imines, which undergo unidirectional rotation induced by light and heat. The mechanism of unidirectional motion in molecular motors containing a C═N group has been assumed to consist of photoinduced torsion about the double bond. In this work, we present a computational study of the photoisomerization dynamics of a chiral N-alkyl imine motor. We find that the location and energetics of minimal energy conical intersections (MECIs) alone are insufficient to understand the mechanism of the motor. Furthermore, a key part of the mechanism consists of out-of-plane distortions of the N atom (followed by isomerization about the double bond). Dynamic effects and out-of-plane distortions are critical to understand the observed (rather low) quantum yield for photoisomerization. Finally, our results provide hints as to how the photoisomerization quantum yield might be increased, improving the efficiency of this class of molecular motors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Complex and Unusual Excited-State Relaxation Dynamics of 9,9′-Bifluorenylidene Revealed by Comprehensive Time-Resolved Spectroscopy and MRSF-TDDFT Calculations

Design of novel photochemical molecular motors often requires molecular building blocks that exhibit rather unusual photoactivity, for which conventional analyses of spectroscopic data can lead to conflicting interpretations. We here systematically investigated the excited-state relaxation dynamics of one such molecule, 9,9′-bifluorenylidene (BF), through comprehensive and complementary integration of ultrafast transient absorption (TA) and femtosecond stimulated Raman (FSRS) spectroscopies and first-principles mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT). TA and FSRS identified two sequentially formed transients following photoexcitation. The decay kinetics of the two intermediates differ in response to excitation wavelengths and the viscosity/polarity of solvents. MRSF-TDDFT calculations reveal a direct, barrierless internal-conversion pathway from the bright Franck−Condon state to a dark S1 minimum, where the excited-state population is transiently trapped, accounting for the first transient species observed in spectroscopic experiments. Further tracking down along the PES with MRSF-TDDFT mapped out two nonradiative relaxation pathways via conical intersections that connect the dark S 1 state to three configurations in the ground-state manifolds, within which a ring structure with a C8−C8′ bond and the vibrationally excited ground-state BF were identified from spectroscopic and kinetic data. The complexity of relaxation kinetics was attributed to the flexible torsional and twisting motions about the C9−C9′ bridge bond enabled by the diradical character of the S 1 state. These findings clarify unusual photoactive relaxation dynamics stemming from a novel correlation between structural flexibility and shifting electronic characteristics, and they demonstrate the importance of integrating spectroscopic and advanced electronic structure calculation studies for judicious clarification of complex, competing relaxation pathways of excited states.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Spatio-temporal patterning of extensile active stresses in microtubule-based active fluids

Abstract Microtubule-based active fluids exhibit turbulent-like autonomous flows, which are driven by the molecular motor powered motion of filamentous constituents. Controlling active stresses in space and time is an essential prerequisite for controlling the intrinsically chaotic dynamics of extensile active fluids. We design single-headed kinesin molecular motors that exhibit optically enhanced clustering and thus enable precise and repeatable spatial and temporal control of extensile active stresses. Such motors enable rapid, reversible switching between flowing and quiescent states. In turn, spatio-temporal patterning of the active stress controls the evolution of the ubiquitous bend instability of extensile active fluids and determines its critical length dependence. Combining optically controlled clusters with conventional kinesin motors enables one-time switching from contractile to extensile active stresses. These results open a path towards real-time control of the autonomous flows generated by active fluids.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Active liquid crystals powered by force-sensing DNA-motor clusters

Significance Single-molecule techniques have elucidated how isolated molecular motors generate piconewton forces with unprecedented detail. However, in diverse biological and synthetic settings, force-generating proteins collectively power nonequilibrium dynamics, including continuous large-scale rearrangements and persistent fluid flows. Characterizing motor-generated forces in these dense and dynamical environments remains a challenge. We assembled a reversible DNA-based force-sensing probe that, by an optical readout, reveals the molecular arrangements and the force loads experienced by kinesin motors. These probes provide insight into motor-generated forces that collectively power the unique dynamics of microtubule-based active nematics, a noteworthy example of an internally driven active matter system. DNA-based force probes can be extended to study forces and stresses in various synthetic systems as well as diverse cellular environments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
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 OSTI2022

Construction of Photo‐Responsive Pd 2 L 4 ‐Type Nanocages based on Feringa's Second‐Generation Motor and Its Guest Binding Ability for C 60

Abstract We present the construction of a M 2 L 4 ‐type metal‐organic nanocage featuring four endohedral Feringa's motor motifs and its adaptive encapsulation towards a C 60 guest molecule. The structure of the cage, though complicated on the 1 H NMR spectrum due to the adoption of mixed ligands, was unambiguously characterized with a combination of ESI‐MS, 2D DOSY, 13 C NMR and particularly the SAXS technique. The molecular motor within the cage demonstrated similar photophysical properties to the uncoordinated one, indicating the motor's function was not compromised when it was anchored in such a confined nanospace. Furthermore, the nanocage showed good guest encapsulation ability towards C 60 , and a guest induced‐fit behavior of the cage was revealed based on the extensive SAXS analysis and molecular dynamics simulation. The adaptive motorized nanocage reported here represents one of the very few examples of integrating individual motors into a discrete nanoconfined system and offers prospects to achieve its non‐equilibrium functions.

Chemistry↗
DOE OSTI2020

Cryo-EM structures provide insight into how E. coli F 1 F o ATP synthase accommodates symmetry mismatch

F 1 F o ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the F o motor generates rotation of the central stalk, inducing conformational changes in the F 1 motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1–3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of F o associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F 1 and F o motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the F o motor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Revealing a Hidden Intermediate of Rotatory Catalysis with X-ray Crystallography and Molecular Simulations

The mechanism of rotatory catalysis in ATPhydrolyzing molecular motors remains an unresolved puzzle in biological energy transfer. Notwithstanding the wealth of available biochemical and structural information inferred from years of experiments, knowledge on how the coupling between the chemical and mechanical steps within motors enforces directional rotatory movements remains fragmentary. Even more contentious is to pinpoint the rate-limiting step of a multistep rotation process. Here, using vacuolar or V 1 -type hexameric ATPase as an exemplary rotational motor, we present a model of the complete 4-step conformational cycle involved in rotatory catalysis. First, using Xray crystallography, a new intermediate or “dwell” is identified, which enables the release of an inorganic phosphate (or P i ) after ATP hydrolysis. Using molecular dynamics simulations, this new dwell is placed in a sequence with three other crystal structures to derive a putative cyclic rotation path. Free-energy simulations are employed to estimate the rate of the hexameric protein transformations and delineate allosteric effects that allow new reactant ATP entry only after hydrolysis product exit. An analysis of transfer entropy brings to light how the side-chain-level interactions transcend into larger-scale reorganizations, highlighting the role of the ubiquitous arginine-finger residues in coupling chemical and mechanical information. An inspection of all known rates encompassing the 4-step rotation mechanism implicates the overcoming of the ADP interactions with V 1 -ATPase to be the rate-limiting step of motor action.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Multiscale Microtubule Dynamics in Active Nematics

In microtubule-based active nematics, motor-driven extensile motion of microtubule bundles powers chaotic large-scale dynamics. We quantify the interfilament sliding motion both in isolated bundles and in a dense active nematic. The extension speed of an isolated microtubule pair is comparable to the molecular motor stepping speed. In contrast, the net extension in dense 2D active nematics is significantly slower; the interfilament sliding speeds are widely distributed about the average and the filaments exhibit both contractile and extensile relative motion. These measurements highlight the challenge of connecting the extension rate of isolated bundles to the multimotor and multifilament interactions present in a dense 2D active nematic. Furthermore, they also provide quantitative data that is essential for building multiscale models.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

The molecular mechanism of load adaptation by branched actin networks

Branched actin networks are self-assembling molecular motors that move biological membranes and drive many important cellular processes, including phagocytosis, endocytosis, and pseudopod protrusion. When confronted with opposing forces, the growth rate of these networks slows and their density increases, but the stoichiometry of key components does not change. The molecular mechanisms governing this force response are not well understood, so we used single-molecule imaging and AFM cantilever deflection to measure how applied forces affect each step in branched actin network assembly. Although load forces are observed to increase the density of growing filaments, we find that they actually decrease the rate of filament nucleation due to inhibitory interactions between actin filament ends and nucleation promoting factors. The force-induced increase in network density turns out to result from an exponential drop in the rate constant that governs filament capping. The force dependence of filament capping matches that of filament elongation and can be explained by expanding Brownian Ratchet theory to cover both processes. We tested a key prediction of this expanded theory by measuring the force-dependent activity of engineered capping protein variants and found that increasing the size of the capping protein increases its sensitivity to applied forces. In summary, we find that Brownian Ratchets underlie not only the ability of growing actin filaments to generate force but also the ability of branched actin networks to adapt their architecture to changing loads.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Synthetic active liquid crystals powered by acoustic waves.

Active nematic materials combine orientational order with activity at the microscopic level. Current experimental realizations of active nematics include vibrating elongated particles, cell layers, suspensions of elongated bacteria, and a mixture of bio-filaments with molecular motors. The majority of active nematics are of biological origin. The realization of a fully synthetic active liquid crystal comprised of a lyotropic chromonic liquid crystal energized by ultrasonic waves, is reported. This synthetic active liquid crystal is free from biological degradation and variability, exhibits phenomenology associated with active nematics, and enables precise and rapid activity control over a significantly extended range. It is demonstrated that the energy of the acoustic field is converted into microscopic extensile stresses disrupting long-range nematic order and giving rise to an undulation instability and proliferation of topological defects. The emergence of unconventional free-standing persistent vortices in the nematic director field at high activity levels is revealed. The results provide a foundation for the design of externally energized active liquid crystals with stable material properties and tunable topological defect dynamics crucial for the realization of reconfigurable microfluidic systems.

active matter↗
DOE OSTI2021

Single-Crystal Optical Actuation Generated by 100% SO 2 Linkage Photoisomerization in a Ruthenium-Based Coordination Complex

Single-crystal optical actuators are emerging as a new field of materials chemistry because of their wide-ranging potential applications, from light-induced molecular motors to photosensing technologies. Ruthenium-based coordination complexes that contain sulfur dioxide linkage photoisomers have shown particular promise as optical actuators, given that they may exhibit either optical switching or nano-optomechanical transduction in their single-crystal form. The type of single-crystal optical actuation observed in a specific compound within this family of complexes depends upon the nature of the ligand that lies trans to this SO 2 linkage photoisomer, since this governs the type and extent of photoisomer (η 2 -(OS)O or η 1 -OSO) that will form upon the application of light. We report the discovery of a new complex, trans-[Ru(SO 2 )(NH 3 ) 4 (3-iodopyridine)]tosylate 2 (1), which forms an η 1 -OSO photoisomer with 100% photoconversion upon the application of 505 nm light. The photoisomerization process in the ruthenium-based cation of 1 stimulates rotation and translation of the toluenic constituent of its neighboring anion, thereby affording nano-optomechnical transduction. We show that this η 1 -OSO photoisomer transitions to its more thermally stable η 2 -(OS)O photoisomer with an activation energy, E a , of 11(2) kJ/mol using thermally activated single-crystal optical absorption spectroscopy. The application of external light with different wavelengths to 1 is also shown to cause a variation in its optical absorption spectral characteristics. Here, this suggests that the photophysical properties of 1 may be tunable with light.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The nanocaterpillar's random walk: diffusion with ligand–receptor contacts

Particles with ligand–receptor contacts bind and unbind fluctuating “legs” to surfaces, whose fluctuations cause the particle to diffuse. Quantifying the diffusion of such “nanoscale caterpillars” is a challenge, since binding events often occur on very short time and length scales. Here, in this work, we derive an analytical formula, validated by simulations, for the long time translational diffusion coefficient of an overdamped nanocaterpillar, under a range of modeling assumptions. We demonstrate that the effective diffusion coefficient, which depends on the microscopic parameters governing the legs, can be orders of magnitude smaller than the background diffusion coefficient. Furthermore it varies rapidly with temperature, and reproduces the striking variations seen in existing data and our own measurements of the diffusion of DNA-coated colloids. Our model gives insight into the mechanism of motion, and allows us to ask: when does a nanocaterpillar prefer to move by sliding, where one leg is always linked to the surface, and when does it prefer to move by hopping, which requires all legs to unbind simultaneously? We compare a range of systems (viruses, molecular motors, white blood cells, protein cargos in the nuclear pore complex, bacteria such as Escherichia coli, and DNA-coated colloids) and present guidelines to control the mode of motion for materials design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Range and strength of mechanical interactions of force dipoles in elastic fiber networks

Mechanical forces generated by myosin II molecular motors drive diverse cellular processes, most notably shape change, division and locomotion. These forces may be transmitted over long range through the cytoskeletal medium – a disordered, viscoelastic network of biopolymers. The resulting cell size scale force chains can in principle mediate mechanical interactions between distant actomyosin units, leading to self-organized structural order in the cell cytoskeleton. Inspired by such force transmission through elastic structures in the cytoskeleton, we consider a percolated fiber lattice network, where fibers are represented as linear elastic elements that can both bend and stretch, and the contractile activity of myosin motors is represented by force dipoles. Then, by using a variety of metrics, we show how two such contractile force dipoles interact with each other through their mutual mechanical deformations of the elastic fiber network. As a prelude to two-dipole interactions, we quantify how forces propagate through the network from a single anisotropic force dipole by analyzing clusters of nodes connected by highly strained bonds, as well as through the decay rate of strain energy with distance from a force dipole. We show that predominant fiber bending screens out force propagation, resulting in reduced and strongly network configuration-dependent dipole interactions. On the other hand, stretching-dominated networks support longer-ranged inter-dipole interactions that recapitulate the predictions of linear elasticity theory. By characterizing the differences between tensile and compressive force propagation in the fiber network, we show how inter-dipole interaction depends on the dipoles’ mutual separation and orientation. The resulting elastic interaction energy may mediate a force between multiple distant dipoles, leading to their self-organization into ordered configurations. In conclusion, this provides a potential pathway for active mechanical force-driven structural order in elastic biopolymer networks.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Generating forces in confinement via polymerization

Understanding how to produce forces using biomolecular building blocks is essential for the development of adaptive synthetic cells and living materials. Here we ask whether a dynamic polymer system can generate deformation forces in soft shells by pure self-assembly, motivated by the fact that biological polymer networks like the cytoskeleton can exert forces, move objects, and deform membranes by simply growing, even in the absence of molecular motors. We address this question by investigating polymer force generation by varying the release rate, the structure, and the interactions of self-assembling monomers. First, we develop a toy computational model of polymerization in a soft elastic shell that reveals the emergence of spontaneous bundling which enhances shell deformation. We then extend our model to account more explicitly for monomer binding dynamics. We find that the rate at which monomers are released into the interior of the shell is a crucial parameter for achieving deformation through polymer growth. Lastly, we demonstrate that the introduction of multivalent particles that can join polymers can either improve or impede polymer performance, depending on the amount and on the structure of the multivalent particles. Our results provide guidance for the experimental realization of polymer systems that can perform work at the nanoscale, for example through rationally designed self-assembling proteins or nucleic acids.

Osmanović, Dino [University of California at Los A↗
DOE OSTI2025

Modeling active nematics via the nematic locking principle

Active nematic systems consist of rod-like internally driven subunits that interact with one another to form large-scale coherent flows. They are important examples of far-from-equilibrium fluids, which exhibit a wealth of nonlinear behavior. This includes active turbulence, in which topological defects in the nematic order braid around one another in a chaotic fashion. One of the most studied examples of active nematics consists of a dense two-dimensional layer of microtubules, crosslinked by kinesin molecular motors that inject extensile deformations into the fluid. Though numerous theoretical studies have modeled microtubule-based active nematics, no consensus has emerged on how to fully and quantitatively capture the features of the experimental system. Here, to better understand the theoretical foundations for modeling this system, we propose a fundamental principle we call the nematic locking principle—individual microtubules cannot rotate without all neighboring microtubules also rotating. Physically, this is justified by the high density of the microtubules, their elongated nature, and their corresponding steric interactions. We assert that the nematic locking principle holds throughout the majority of the material, but breaks down in the neighborhood of topological defects and other regions of low density. We derive the most general nematic transport equation consistent with this principle and also derive the most general term that violates it, introducing fracturing into the material. We then examine the standard Beris–Edwards approach, commonly used to model this system, and show that it violates the nematic locking principle throughout the majority of the material due to fracturing. We then propose a modification to the Beris–Edwards model that enforces nematic locking nearly everywhere. This modification shuts off fracturing except in regions where the order parameter (a proxy for density) is reduced. In these regions fracturing is turned on. The resulting simulations in turn show strong nematic locking throughout the bulk of the material, with narrow bands of fracturing, consistent with experimental observation. One additional advantage of enforcing nematic locking is that nontrivial stationary state solutions, common in Beris–Edwards simulations but not seen in experiments, are eliminated.

Mitchell, Kevin A. [Univ. of California, Merced, C↗
DOE OSTI2026

Cooperative effect of local active stresses on the macroscopic contractility of elastic fiber networks

The collective action of actively contractile units embedded in elastic biopolymer networks plays a crucial role in regulating the network's macroscopic mechanical response. Here, in this study, we investigate how the macroscopic boundary stress in model elastic fiber networks depends on the number and nature of embedded contractile units, each exerting an isotropic force dipole, as well as on the bending stiffness of fibers. We find that the macroscopic stress increases nonlinearly with the number of dipoles due to mutual stiffening of initially soft, bending-dominated networks. Using effective medium theory, we relate this enhanced contractility to an increase in the effective average network coordination number due to constraints imposed by the force dipoles. By comparing three distinct force dipole models that differ in their local structures, we demonstrate that the specific manner in which an active unit constrains the network strongly influences the onset and nature of the stiffening transition. Our results highlight that not only the quantity but also the local geometry of force-generating units critically determines the macroscopic mechanical behavior. This framework provides a physical basis for understanding how biological systems—such as molecular motors in the cytoskeleton, or adherent cells in the extracellular matrix—can modulate network-scale nonlinear elastic properties through local tuning of active force-generating units.

Biological and medical sciences↗