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DOE OSTI2025

Structural chirality and related properties in periodic inorganic solids: review and perspectives

Abstract Chirality refers to the asymmetry of objects that cannot be superimposed on their mirror image. It is a concept that exists in various scientific fields and has profound consequences. Although these are perhaps most widely recognized within biology, chemistry, and pharmacology, recent advances in chiral phonons, topological systems, crystal enantiomorphic materials, and magneto-chiral materials have brought this topic to the forefront of condensed matter physics research. Our review discusses the symmetry requirements and the features associated with structural chirality in inorganic materials. This allows us to explore the nature of phase transitions in these systems, the coupling between order parameters, and their impact on the material’s physical properties. We highlight essential contributions to the field, particularly recent progress in the study of chiral phonons, altermagnetism, magnetochirality between others. Despite the rarity of naturally occurring inorganic chiral crystals, this review also highlights a significant knowledge gap, presenting challenges and opportunities for structural chirality mostly at the fundamental level, e.g. chiral displacive phase transitions, possibilities of tuning and switching structural chirality by external means (electric, magnetic, or strain fields), whether chirality could be an independent order parameter, and whether structural chirality could be quantified, etc. Beyond simply summarizing this field of research, this review aims to inspire further research in materials science by addressing future challenges, encouraging the exploration of chirality beyond traditional boundaries, and seeking the development of innovative materials with superior or new properties.

Bousquet, Eric (ORCID:0000000292903463)↗

DOE OSTI2022

Bifurcation Analysis Reveals Solution Structures of Phase Field Models

The phase field method is playing an increasingly important role in understanding and predicting morphological evolution in materials and biological systems. Here, in this study, we develop a new analytical approach based on the bifurcation analysis to explore the mathematical solution structure of phase field models. Revealing such solution structures not only is of great mathematical interest but also may provide guidance to experimentally or computationally uncover new morphological evolution phenomena in materials undergoing electronic and structural phase transitions. To elucidate the idea, we apply this analytical approach to three representative phase field equations: the Allen-Cahn equation, the Cahn-Hilliard equation, and the Allen-Cahn-Ohta-Kawasaki system. The solution structures of these three phase field equations are also verified numerically by the homotopy continuation method.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Nanomechanical sampling of material for nanoscale mass spectrometry chemical analysis

The ability to spatially resolve the chemical distribution of compounds on a surface is important in many applications ranging from biological to material science. To this extent, we have recently introduced a hybrid atomic force microscopy (AFM)-mass spectrometry (MS) system for direct thermal desorption and pyrolysis of material with nanoscale chemical resolution. However, spatially resolved direct surface heating using local thermal desorption becomes challenging on material surfaces with low melting points, because the material will undergo a melting phase transition due to heat dissipation prior to onset of thermal desorption. Therefore, here we developed an approach using mechanical sampling and collection of surface materials on an AFM cantilever probe tip for real-time analysis directly from the AFM tip. This approach allows for material to be concentrated directly onto the probe for subsequent MS analysis. We evaluate the performance metrics of the technique and demonstrate localized MS sampling from a candelilla wax matrix containing UV stabilizers avobenzone and oxinoxate from areas down to 250 nm × 250 nm. Overall, this approach removes heat dissipation into the bulk material allowing for a faster desorption and concentration of the gas phase analyte from a single heating pulse enabling higher signal levels from a given amount of material in a single sampling spot.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Decoupling copolymer, lipid and carbon nanotube interactions in hybrid, biomimetic vesicles

Bilayer vesicles that mimic a real biological cell can be tailored to carry out a specific function by manipulating the molecular composition of the amphiphiles. These bio-inspired and bio-mimetic structures are increasingly being employed for a number of applications from drug delivery to water purification and beyond. Complex hybrid bilayers are the key building blocks for fully synthetic vesicles that can mimic biological cell membranes, which often contain a wide variety of molecular species. While the assembly and morpholgy of pure phospholid bilayer vesicles is well understood, the functionality and structure dramaticlly changes when copolymer and/or carbon nanotube porins (CNTP) are added. The aim of this study is to understand how the collective molecular interactions within hybrid vesicles affect their nanoscale structure and properties. In situ small and wide angle X-ray scattering (SAXS/WAXS) and molecular dynamics simulations (MD) are used to investigate the morphological effect of molecular interactions between polybutadiene polyethylene oxide, lipids and carbon nanotubes (CNT) within the hybrid vesicle bilayer. Within the lipid/copolymer system, the hybrid bilayer morphology transitions from phase separated lipid and compressed copolymer at low copolymer loadings to a mixed bilayer where opposing lipids are mostly separated from the inner region. This transition begins between 60 wt% and 70 wt%, with full homogenization observed by 80 wt% copolymer. The incorporation of CNT into the hybrid vesicles increases the bilayer thickness and enhances the bilayer symmetry. Analysis of the WAXS and MD indicate that the CNT–dioleoyl interactions are much stronger than the CNT–polybutadiene.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2005

Optimal Sampling of a Reaction Coordinate in Molecular Dynamics

Estimating how free energy changes with the state of a system is a central goal in applications of statistical mechanics to problems of chemical or biological interest. From these free energy changes it is possible, for example, to establish which states of the system are stable, what are their probabilities and how the equilibria between these states are influenced by external conditions. Free energies are also of great utility in determining kinetics of transitions between different states. A variety of methods have been developed to compute free energies of condensed phase systems. Here, I will focus on one class of methods - those that allow for calculating free energy changes along one or several generalized coordinates in the system, often called reaction coordinates or order parameters . Considering that in almost all cases of practical interest a significant computational effort is required to determine free energy changes along such coordinates it is hardly surprising that efficiencies of different methods are of great concern. In most cases, the main difficulty is associated with its shape along the reaction coordinate. If the free energy changes markedly along this coordinate Boltzmann sampling of its different values becomes highly non-uniform. This, in turn, may have considerable, detrimental effect on the performance of many methods for calculating free energies.

Pohorille, Andrew↗

DOE OSTI2023

Critical behavior in a chiral molecular model

Understanding the condensed-phase behavior of chiral molecules is important in biology as well as in a range of technological applications, such as the manufacture of pharmaceuticals. Here, we use molecular dynamics simulations to study a chiral four-site molecular model that exhibits a second-order symmetry-breaking phase transition from a supercritical racemic liquid into subcritical D-rich and L-rich liquids. We determine the infinite-size critical temperature using the fourth-order Binder cumulant, and we show that the finite-size scaling behavior of the order parameter is compatible with the 3D Ising universality class. We also study the spontaneous D-rich to L-rich transition at a slightly subcritical temperature of T = 0.985Tc, and our findings indicate that the free energy barrier for this transformation increases with system size as N2/3, where N is the number of molecules, consistent with a surface-dominated phenomenon. The critical behavior observed herein suggests a mechanism for chirality selection in which a liquid of chiral molecules spontaneously forms a phase enriched in one of the two enantiomers as the temperature is lowered below the critical point. Furthermore, the increasing free energy barrier with system size indicates that fluctuations between the L-rich and D-rich phases are suppressed as the size of the system increases, trapping it in one of the two enantiomerically enriched phases. Such a process could provide the basis for an alternative explanation for the origin of biological homochirality. We also conjecture the possibility of observing nucleation at subcritical temperatures under the action of a suitable chiral external field.

Chemistry↗

NASA NTRS1994

Artificial gravity in space and in medical research

The history of manned space flight has repeatedly documented the fact that prolonged sojourn in space causes physiological deconditioning. Physiological deterioration has raised a legitimate concern about man's ability to adequately perform in the course of long missions and even the possibility of leading to circumstances threatening survival. One of the possible countermeasures of physiological deconditioning, theoretically more complete than others presently used since it affects all bodily systems, is artificial gravity. Space stations and spacecrafts can be equipped with artificial gravity, but is artificial gravity necessary? The term "necessary" must be qualified because a meaningful answer to the question depends entirely on further defining the purpose of space travel. If man intends to stay only temporarily in space, then he must keep himself in good physical condition so as to be able to return to earth or to land on any other planetary surface without undue exposure to major physiological problems resulting from transition through variable gravitational fields. Such a situation makes artificial gravity highly desirable, although perhaps not absolutely necessary in the case of relative short exposure to microgravity, but certainly necessary in interplanetary flight and planetary landings. If the intent is to remain indefinitely in space, to colonize space, then artificial gravity may not be necessary, but in this case the consequences of long term effects of adaptation to weightlessness will have to be weighed against the biological evolutionary outcomes that are to be expected. At the moment, plans for establishing permanent colonies in space seem still remote. More likely, the initial phase of exploration of the uncharted solar system will take place through successive, scope limited, research ventures ending with return to earth. This will require man to be ready to operate in gravitational fields of variable intensity. Equipping spacecrafts or space stations with some means of artificial gravity in this initial phase is, therefore, necessary without question. In a strict sense artificial gravity is conceived as a means of replacing natural gravity in space by the centripetal acceleration generated by some sort of rotating device. Rotating devices create an inertial force which has effects on bodies similar to those caused by terrestrial gravity, but artificial gravity by a rotation device is not the same as terrestrial gravity, as we shall see. Present research in artificial gravity for space exploration is projected in two main directions: artificial gravity for whole space stations and artificial gravity produced by short arm centrifuges designed for human use in space.

Case Reports↗

DOE OSTI2020

Integrative Circuit-Host Modeling of a Genetic Switch in Varying Environments

Synthetic biology is advancing into a new phase where real-world applications are emphasized. There is hence an urgent need for mathematical modeling that can quantitatively describe the behaviors of genetic devices in natural, fluctuating environments. We utilize an integrative circuit-host modeling framework to examine the dynamics of a genetic switch and its host cell in varying environments. For both steady-state and transient cases, we find increasing nutrient reduces the bistability region of the phase space and eventually drives the switch from bistability to monostability. In response, cellular growth and proteome partitioning experience the same transition. Antibiotic perturbations cause the similar circuit and host responses as nutrient variations. However, one difference is the trend of growth rate, which augments with nutrient but declines with antibiotic levels. The framework provides a mechanistic scheme to account for both the dynamic and static characteristics of the circuit-host system upon environmental perturbations, underscoring the intimacy of gene circuits and their hosts and elucidating the complexity of circuit behaviors arising from environmental variations.

59 BASIC BIOLOGICAL SCIENCES↗

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)↗

NASA NTRS2003

Tensegrity II. How structural networks influence cellular information processing networks

The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

Review↗

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↗

NASA NTRS2005

Hydrodynamics of Packed Bed Reactor in Low Gravity

Packed bed reactors are well known for their vast and diverse applications in the chemical industry; from gas absorption, to stripping, to catalytic conversion. Use of this type of reactor in terrestrial applications has been rather extensive because of its simplicity and relative ease of operation. Developing similar reactors for use in microgravity is critical to many space-based advanced life support systems. However, the hydrodynamics of two-phase flow packed bed reactors in this new environment and the effects of one physiochemical process on another has not been adequately assessed. Surface tension or capillary forces play a much greater role which results in a shifting in flow regime transitions and pressure drop. Results from low gravity experiments related to flow regimes and two-phase pressure drop models are presented in this paper along with a description of plans for a flight experiment on the International Space Station (ISS). Understanding the packed bed hydrodynamics and its effects on mass transfer processes in microgravity is crucial for the design of packed bed chemical or biological reactors to be used for water reclamation and other life support processes involving water purification.

Motil, Brian J.↗

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↗

NASA NTRS2000

Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous mixing. A similar difficulty may be encountered in any method relying on global modifications of phase space.

Darve, Eric↗