Search NASA⌕ Search

SEARCH · Search NASA

Results for “phase transitions in biological systems”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Stability Analysis of Parameter Varying Genetic Toggle Switches Using Koopman Operators

The genetic toggle switch is a well known model in synthetic biology that represents the dynamic interactions between two genes that repress each other. The mathematical models for the genetic toggle switch that currently exist have been useful in describing circuit dynamics in rapidly dividing cells, assuming fixed or time-invariant kinetic rates. There is a growing interest in being able to model and extend synthetic biological function for growth conditions such as stationary phase or during nutrient starvation. As cells transition from one growth phase to another, kinetic rates become time-varying parameters. In this paper, we propose a novel class of parameter varying nonlinear models that can be used to describe the dynamics of genetic circuits, including the toggle switch, as they transition from different phases of growth. We show that there exists unique solutions for this class of systems, as well as for a class of systems that incorporates the microbial phenomena of quorum sensing. Further, we show that the domain of these systems, which is the positive orthant, is positively invariant. We also showcase a theoretical control strategy for these systems that would grant asymptotic monostability of a desired fixed point. We then take the general form of these systems and analyze their stability properties through the framework of time-varying Koopman operator theory. A necessary condition for asymptotic stability is also provided as well as a sufficient condition for instability. A Koopman control strategy for the system is also proposed, as well as an analogous discrete time-varying Koopman framework for applications with regularly sampled measurements.

Harrison, Jamiree (ORCID:0000000265351579)↗
DOE OSTI2023

Photothermally Activated Artificial Neuromorphic Synapses

Biological nervous systems rely on the coordination of billions of neurons with complex, dynamic connectivity to enable the ability to process information and form memories. In turn, artificial intelligence and neuromorphic computing platforms have sought to mimic biological cognition through software-based neural networks and hardware demonstrations utilizing memristive circuitry with fixed dynamics. Here, to incorporate the advantages of tunable dynamic software implementations of neural networks into hardware, we develop a proof-of-concept artificial synapse with adaptable resistivity. This synapse leverages the photothermally induced local phase transition of VO 2 thin films by temporally modulated laser pulses. Such a process quickly modifies the conductivity of the film site-selectively by a factor of 500 to “activate” these neurons and store “memory” by applying varying bias voltages to induce self-sustained Joule heating between electrodes after activation with a laser. These synapses are demonstrated to undergo a complete heating and cooling cycle in less than 120 ns.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2023

Evolutionary consequences of nascent multicellular life cycles

A key step in the evolutionary transition to multicellularity is the origin of multicellular groups as biological individuals capable of adaptation. Comparative work, supported by theory, suggests clonal development should facilitate this transition, although this hypothesis has never been tested in a single model system. We evolved 20 replicate populations of otherwise isogenic clonally reproducing ‘snowflake’ yeast (Δace2/∆ace2) and aggregative ‘floc’ yeast (GAL1p::FLO1 /GAL1p::FLO1) with daily selection for rapid growth in liquid media, which favors faster cell division, followed by selection for rapid sedimentation, which favors larger multicellular groups. While both genotypes adapted to this regime, growing faster and having higher survival during the group-selection phase, there was a stark difference in evolutionary dynamics. Aggregative floc yeast obtained nearly all their increased fitness from faster growth, not improved group survival; indicating that selection acted primarily at the level of cells. In contrast, clonal snowflake yeast mainly benefited from higher group-dependent fitness, indicating a shift in the level of Darwinian individuality from cells to groups. Through genome sequencing and mathematical modeling, we show that the genetic bottlenecks in a clonal life cycle also drive much higher rates of genetic drift—a result with complex implications for this evolutionary transition. Our results highlight the central role that early multicellular life cycles play in the process of multicellular adaptation.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2020

Buckling-induced interaction between circular inclusions in an infinite thin plate

Design of slender artificial materials and morphogenesis of thin biological tissues typically involve stimulation of isolated regions (inclusions) in the growing body. These inclusions apply internal stresses on their surrounding areas that are ultimately relaxed by out-of-plane deformation (buckling). Here, we utilize the Föppl-von Kármán model to analyze the interaction between two circular inclusions in an infinite plate that their centers are separated a distance of 2ℓ. In particular, we investigate a region in phase space where buckling occurs at a narrow transition layer of length ℓ D around the radius of the inclusion, $R (ℓ_D \ll R)$. We show that the latter length scale defines two regions within the system, the close separation region, $ℓ – R \sim ℓ_D$, where the transition layers of the two inclusions approximately coalesce, and the far separation region, $ℓ – R \gg ℓ_D$. While the interaction energy decays exponentially in the latter region, $E_{\text{int}} ∝ e^{– (ℓ – R)/ℓ_D}$, it presents nonmonotonic behavior in the former region. While this exponential decay is predicted by our analytical analysis and agrees with the numerical observations, the close separation region is treated only numerically. In particular, we utilize the numerical investigation to explore two different scenarios within the final configuration: The first where the two inclusions buckle in the same direction (up-up solution) and the second where the two inclusions buckle in opposite directions (up-down solution). We show that the up-down solution is always energetically favorable over the up-up solution. In addition, we point to a curious symmetry breaking within the up-down scenario; we show that this solution becomes asymmetric in the close separation region.

42 ENGINEERING↗
DOE OSTI2022

Tuneable phase behaviour and glass transition via polymerization-induced phase separation in crosslinked step-growth polymers

We report once limited to chain-growth polymerizations, fine control over polymerization-induced phase separation (PIPS) has recently been demonstrated in rubber-toughened thermoset materials formed through step-growth polymerizations. The domain length scales of these thermoset materials can be elegantly tuned by utilizing a binary mixture of curing agents (CAs) that individually yield disparate morphologies. Importantly, varying the composition of the binary mixture affects characteristics of the materials such as glass transition temperature and tensile behavior. Here, we establish a full phase diagram of PIPS in a rubber-toughened epoxy system tuned by a binary CA mixture to provide a robust framework of phase behaviour. X-Ray scattering in situ and post-PIPS is employed to elucidate the PIPS mechanism whereby an initial polymerization-induced compositional fluctuation causes nanoscale phase separation of rubber and epoxy components prior to local chain crosslinking and potential macrophase separation. We further demonstrate the universality of this approach by alternatively employing binary epoxy or binary rubber mixtures to achieve broad variations in morphology and glass transitions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Formation Mechanisms, Crystal Structure, and Interfacial Reactivity of (Mixed) Metal Sulfide Nanoparticles Produced via Biological versus Abiotic Systems

The primary goals of this project were to understand the formation mechanisms and reactivity of mix-metal sulfide nanophases (Cu-Fe, Ni-Fe, Co-Fe sulfides) produced via biological and abiotic pathways that are relevant to low-temperature aqueous environments. These mix-metal sulfide nanophases have been identified in a range of natural and anthropogenic systems and are considered to play key roles in the biogeochemical cycling of elements, biomineralization, environmental remediation, resource recovery, eco-toxicity, and the origin and evolution of life. Using a comparative approach, we aimed to elucidate: (i) if these mix-metal sulfides tend to form nanoscale phases regardless of their formation pathways; (ii) what mechanisms are involved in the biological and abiotic crystallization processes; (iii) what phases form that have been otherwise expected; and (iv) if we can combine the experimental results with what we see and surmise from field studies to facilitate a more comprehensive understanding regarding the origin and biogeochemical roles of these mix-metal sulfides. Along a related pathway of electron transfer in nano-systems, in this case dealing with Fe-oxides instead of Fe-sulfides, we have continued to explore the reactions and solid products of heterogeneous catalytic oxidation of aqueous Mn(II) by dissolved oxygen in the presence of iron oxides (hematite) nanoparticles. The nano-Mn-oxides produced are known to be efficient sorbents of transition metal elements, including Cu, Ni, and Co studied in our sulfide work.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Unraveling the Molecular Origin of Prey-Wrapping Spider Silk's Unique Mechanical Properties and Assembly Process Using NMR

Prey wrapping spider silk's unique mechanical properties are investigated confirming the silk's high degree of extensibility and superior toughness compared to other types of spider silk. For the first time, the pre-spinning dope phase is studied in isotope-enriched intact aciniform (AC) silk glands using solution NMR that reveals a combination of α-helical domains linked by disordered random coil chains consistent with previously proposed “beads-on-a-string” models. The model is further refined through the AlphaFold2 protein structure prediction tool. Finally, extensive magic angle spinning (MAS) solid-state (SS) NMR data for isotopically-enriched fibers is used to refine the structural model for AC silk from two species, A. aurantia and A. argentata. The SSNMR data shows that the AC silk fibers are highly α-helical, coiled-coil in structure but, also exhibit significant β-sheet components that can be traced back to the Gly-rich disordered linker regions in the pre-spinning dope phase that are converted to β-sheet structures during fiber formation. This combination of mechanical and structural characterization enhances the understanding of AC silk's liquid-to-solid transition and structure-mechanics relationship. In conclusion, these prey wrap silk results and models will provide the basis for the design of biomimetic materials inspired by the AC spider silk system.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Revealing Hot and Long-Lived Metastable Spin States in the Photoinduced Switching of Solvated Metallogrid Complexes with Femtosecond Optical and X-ray Spectroscopies

An atomistic understanding of the photoinduced spin-state switching (PSS) within polynuclear systems of d 4 –d 7 transition metal ion complexes is required for their rational integration into light-driven reactions of chemical and biological interest. However, in contrast to mononuclear systems, the multidimensional dynamics of the PSS in solvated molecular arrays have not yet been elucidated due to the expected complications associated with the connectivity between the metal centers and the strong interactions with the surroundings. Herein, the PSS in a solvated triiron(II) metallogrid complex is characterized using transient optical absorption and X-ray emission spectroscopies on the femtosecond time scale. The complementary measurements reveal the photoinduced creation of energy-rich (hot) and long-lived quintet states, whose dynamics differ critically from their mononuclear congeners. We report this finding opens major prospects for developing novel schemes in solution-phase spin chemistry that are driven by the dynamic PSS process in compact oligometallic arrays.

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

Future directions for active matter on ordered substrates

Active matter is a term encompassing particle-based assemblies with some form of self-propulsion, including certain biological systems as well as synthetic systems such as artificial colloidal swimmers, all of which can exhibit a remarkable variety of new kinds of nonequilibrium phenomena. A wealth of non-active condensed matter systems can be described in terms of a collection of particles coupled to periodic substrates, leading to the emergence of commensurate-incommensurate effects, Mott phases, tribology effects, and pattern formation. It is natural to ask how such phases are modified when the system is active. Here we provide an overview and future directions for studying individual and collectively interacting active matter particles coupled to periodic substrates, where new types of commensuration effects, directional locking, and active phases can occur. Importantly, further directions for exploration include directional locking effects, the realization of active solitons or active defects in incommensurate phases, active Mott phases, active artificial spin ice, active doping transitions, active floating phases, active surface physics, active matter time crystals, and active tribology.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Optical super-resolution microscopy in polymer science

The advent of optical super-resolution microscopy (OSRM) over two decades ago has transformed light-mediated interrogation of systems down to the nanoscale. This innovative set of approaches to optics breaks the so-called diffraction limit of light (~200 nm), allowing for the first time to use optics in the far field to visualize behavior on nanoscopic length scales. While these visualization tools have rapidly found widespread use in biology and related fields, their implementation in materials and, more specifically, in polymer science has been far slower. To overcome possible barriers and highlight possible future directions, we present in this paper an introduction to OSRM for polymer scientists, beginning with an overview of relevant techniques and existing optical probes. We then show and examine the first examples of OSRM adaptation across major areas of polymer science, including: polymerization and structural characterization, self-assembly and solution behavior, bulk structure and behavior, crystallization, gel structure and behavior, phase transitions, and biofunctionality. We hope and anticipate that the discussions provided in this review will draw the attention of the polymer community to the capacities of these hitherto underexplored optical visualization techniques to further transform polymer science.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Metal Chalcogenides for Neuromorphic Computing: Emerging Materials and Mechanisms

The approaching end of Moore's Law scaling has significantly accelerated multiple fields of research including neuromorphic-, quantum-, and photonic computing, each of which possesses unique benefits unobtained through conventional binary computers. One of the most compelling arguments for neuromorphic computing systems is power consumption, noting that computations made in the human brain are approximately 106 times more efficient than conventional CMOS logic. This review article focuses on the materials science and physical mechanisms found in metal chalcogenides that are currently being explored for use in neuromorphic applications. We begin by reviewing the key biological signal generation and transduction mechanisms within neuronal components of mammalian brains and subsequently compare with observed experimental measurements in chalcogenides. With robustness and energy efficiency in mind, we will focus on short-range mechanisms such as structural phase changes and correlated electron systems that can be driven by low-energy stimuli, such as temperature or electric field. We aim to highlight fundamental materials research and existing gaps that need to be overcome to enable further integration or advancement of metal chalcogenides for neuromorphic systems.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Scale up, Field testing, and Optimization of Nontoxic, Durable, Economical Coatings for Control of Biofouling and Corrosion (Abstract Only)

The objective of this project is the technical maturation and demonstration of a durable, economical, and nontoxic coating, Superhydrophobic Lubricant Infused Composite (SLIC), that will prevent fouling organisms from growing on marine and hydrokinetic (MHK) structures and prevent invasive mussels from growing on hydropower structures. SLIC technology was developed and patented by PNNL. It combines multiple antifouling mechanisms to provide excellent antifouling performance, durability, and low hydrodynamic drag without using toxic materials. Advanced proof-of-concept testing and demonstrations completed during a Phase 1 TCF project attracted industry interest and partnerships for this Phase 2 effort focused on maturation of a commercial product. Specific tasks and tests will shift the development emphasis to optimizing formulations, validating antifouling performance to address specific application needs, explore compatibility with other paint systems, develop a product with useful shelf life (in can), and determine curing times and effective applications methodology. Phase 2 efforts will focus upon technology transfer and commercialization of the technology with the industrial team. Industrial partners now include a coatings development specialist (Lorama), hydrophobic material manufacturer and paint developer (Dry Surface Technologies), nontoxic biodegradable lubricants manufacturer (BioBlend), and aquatic applications specialists (Prometheus Innovations, River Connectivity Systems). Engagement with the MHK device developers, the PNNL Marine and Coastal Research Laboratory (MCRL) test site in Sequim WA, Bureau of Reclamation, and Taylor Shellfish throughout the project will provide topical expertise and field test sites that will deliver crucial real-world performance data. Through this Phase 2 effort, SLIC will transition from a Technical Readiness Level (TRL) 5 to TRL 6 and long-term performance data will be acquired through demonstrations. The field test data will allow optimization of SLIC formulation to enhance performance (e.g., durability) and packaging, which are key de-risking activities for technology transfer and ultimately to the production of a viable commercial product.

13 HYDRO ENERGY↗
DOE OSTI2026

Size dependent lattice pseudosymmetry for frustrated decahedral nanoparticles

Geometric frustration—where geometry prevents simultaneous satisfaction of local interactions—generates pseudosymmetry and emergent behaviors across physical and biological systems. At the nanoscale, pseudosymmetric features in crystalline materials manifest as local strain and distortion, but how they depend on particle size and control structural stability remains unclear. Here, we report the first study of a size-dependent crossover in pseudosymmetry in multi-twinned gold nanoparticles (NPs), combining four-dimensional scanning transmission electron microscopy with nanoscale strain mapping grounded in continuum solid mechanics. Analysis of more than 20 decahedral NPs (20–55 nm) reveals pronounced heterogeneity in multiple modes of in-plane strain and displacement field in small NPs as five tetrahedral grains close the geometric gap, without extended defects. With increasing particle size, strain fields homogenize across grains and local phases shift from predominantly low-symmetry body-centered tetragonal motifs at small sizes to face-centered cubic character approaching the bulk limit. We identify a crossover particle size of ~35 nm, well below bulk, correlating with a transition from modified-Wulff shapes to pentagonal bipyramids, consistent with finite element predictions. This quantitative framework for mapping size-dependent strain and pseudosymmetry enables precise design and control of functional crystalline solids and phase transformation for catalysis, photonics, electronics, and energy storage.

Lin, Oliver [University of Illinois at Urbana-Cham↗
DOE OSTI2021

Mono- and bilayer smectic liquid crystal ordering in dense solutions of “gapped” DNA duplexes

Significance Liquid crystalline behavior of DNA has been studied for decades, yet only recently has one of the most fundamental liquid crystal phases—the smectic phase in which rod-like objects assemble into stacks of fluid layers—been demonstrated in this system. Here, we describe distinct bilayer and monolayer smectic phases in solutions of “gapped” DNA (GDNA), consisting of two DNA duplexes connected by a single strand. The smectic order is amphotropic (sensitive to temperature as well as concentration), and the layer structure is stable against significant perturbations of the GDNA construct (e.g., “gap” length variation and asymmetry in duplex lengths). The temperature sensitivity may provide a means to compare end-to-end interaction strengths between DNA duplexes at biologically relevant concentrations.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network

Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida KT2440, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida KT2440 and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.

09 BIOMASS FUELS↗
DOE OSTI2023

Revealing core-valence interactions in solution with femtosecond X-ray pump X-ray probe spectroscopy

Abstract Femtosecond pump-probe spectroscopy using ultrafast optical and infrared pulses has become an essential tool to discover and understand complex electronic and structural dynamics in solvated molecular, biological, and material systems. Here we report the experimental realization of an ultrafast two-color X-ray pump X-ray probe transient absorption experiment performed in solution. A 10 fs X-ray pump pulse creates a localized excitation by removing a 1 s electron from an Fe atom in solvated ferro- and ferricyanide complexes. Following the ensuing Auger–Meitner cascade, the second X-ray pulse probes the Fe 1 s → 3 p transitions in resultant novel core-excited electronic states. Careful comparison of the experimental spectra with theory, extracts +2 eV shifts in transition energies per valence hole, providing insight into correlated interactions of valence 3 d with 3 p and deeper-lying electrons. Such information is essential for accurate modeling and predictive synthesis of transition metal complexes relevant for applications ranging from catalysis to information storage technology. This study demonstrates the experimental realization of the scientific opportunities possible with the continued development of multicolor multi-pulse X-ray spectroscopy to study electronic correlations in complex condensed phase systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

A Deep Learning-Driven Sampling Technique to Explore the Phase Space of an RNA Stem-Loop

The folding and unfolding of RNA stem-loops are critical biological processes; however, their computational studies are often hampered by the ruggedness of their folding landscape, necessitating long simulation times at the atomistic scale. Here, we adapted DeepDriveMD (DDMD), an advanced deep learning-driven sampling technique originally developed for protein folding, to address the challenges of RNA stem-loop folding. Although tempering- and order parameter-based techniques are commonly used for similar rare-event problems, the computational costs or the need for a priori knowledge about the system often present a challenge in their effective use. DDMD overcomes these challenges by adaptively learning from an ensemble of running MD simulations using generic contact maps as the raw input. DeepDriveMD enables on-the-fly learning of a low-dimensional latent representation and guides the simulation toward the undersampled regions while optimizing the resources to explore the relevant parts of the phase space. We showed that DDMD estimates the free energy landscape of the RNA stem-loop reasonably well at room temperature. Our simulation framework runs at a constant temperature without external biasing potential, hence preserving the information on transition rates, with a computational cost much lower than that of the simulations performed with external biasing potentials. Here, we also introduced a reweighting strategy for obtaining unbiased free energy surfaces and presented a qualitative analysis of the latent space. This analysis showed that the latent space captures the relevant slow degrees of freedom for the RNA folding problem of interest. Finally, throughout the manuscript, we outlined how different parameters are selected and optimized to adapt DDMD for this system. We believe this compendium of decision-making processes will help new users adapt this technique for the rare-event sampling problems of their interest.

Gupta, Ayush↗
DOE OSTI2025

Slow Electron Spin Relaxation at Ambient Temperatures with Copper Coordinated by a Rigid Macrocyclic Ligand

Paramagnetic transition metal complexes can serve as quantum bits, storing phase information through unpaired electrons. Despite their promise, these systems often require low temperatures and tend to rapidly decohere. Recent efforts have sought to improve longitudinal relaxation (T 1 ), which provides an upper limit for phase coherence (T m ), by investigating existing literature compounds with reduced vibrational coupling and orbital angular momentum. However, synthetic strategies for improving T 1 through novel ligand design have remained scant. Here, we disclose the synthesis of a new modular macrocyclic ligand framework with four nitrogen donors (N 4 ) derived from phenanthroline that supports room-temperature coherent Cu(II) spin centers. The optimized complex more than doubles the T 1 over the next best Cu(II)-N 4 compound and exhibits a room temperature coherence time (T m ) of 0.28 μs, close to previously reported values. This performance enhancement arises from a tight binding site with short Cu–N distances, resulting in a stronger ligand field and reduced thermal accessibility of symmetric vibrational modes. This work demonstrates a practical approach to enabling spin coherence at room temperature, a factor critical to accessing relevant quantum bits and biological sensors, through a designer macrocyclic ligand platform.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗