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At least 379 records · Page 21

CRNT4SBML: a Python package for the detection of bistability in biochemical reaction networks

Motivation: Signaling pathways capable of switching between two states are ubiquitous within living organisms. They provide the cells with the means to produce reversible or irreversible decisions. Switchlike behavior of biological systems is realized through biochemical reaction networks capable of having two or more distinct steady states which are dependent on initial conditions. Investigation of whether a certain signaling pathway can confer bistability involves a substantial amount of hypothesis testing. The cost of direct experimental testing can be prohibitive. Therefore, constraining the hypothesis space is highly bene?cial. One such methodology is based on Chemical Reaction Network Theory which uses computational techniques to rule out pathways that are not capable of bistability regardless of kinetic constant values and molecule concentrations. Although useful, these methods are complicated from both pureandcomputationalmathematicsperspectives.Thus,theiradoptionisverylimitedamongstbiologists. Results: We brought Chemical Reaction Network Theory approaches closer to experimental biologists by automating all the necessary steps in CRNT4SMBL. The input is based on SBML format which is the community standard for biological pathway communication. The tool parses SBML and derives C-graph representations of the biological pathway with mass action kinetics. Next steps involve an ef?cient search for potential saddle-node bifurcation points using an optimization technique. This type of bifurcation is important as it has the potential of acting as a switching point between two steady states. Finally, if any bifurcation points are present, numerical continuation analysis extends the equilibria branches for generating the diagram. Presence of an S-shaped bifurcation diagram indicates that the pathway acts as a bistable switch for the given optimization parameters. Availability: CRNT4SBML is available via the Python Package Index. The documentation can be found at https://crnt4sbml.readthedocs.io. CRNT4SBML is licensed under the Apache Software License 2.0. Contact: vladislav.petyuk@pnnl.gov

Reyes, Brandon C.↗

Predicting Wind Loading and Instability in Solar Tracking PV Arrays

Wind loading and the fluctuating pressure loads it creates on PV panel surfaces are associated with multiple degradation mechanisms and failures. Modest wind speeds create reversing loads that can initiate cell cracks and weather cracked cells. Stronger wind speeds and extreme weather events can lead to larger scale forces and the aerodynamic instability known as torsional galloping. All these effects are dependent on the complex coupling between wind speed, panel orientation, and a myriad of other hardware and site-specific factors. In this work, we present the latest developments from our work to build an open-source, high-performance computing (HPC) fluid dynamics solver to predict and mitigate these effects. This simulation package allows users to easily specify different array layouts, solar-tracking angles, panel geometries, and weather conditions before automatically generating a refined computational mesh and solving for the unsteady loading on each panel surface. Small domains (e.g., a single panel row in isolation) can be solved on a modern laptop, while larger domains or very high-fidelity studies can be solved on distributed or HPC resources with minimal modifications to the underlying problem specification. We present preliminary case studies obtained using this simulation package and highlight how increased wind speeds combined with sub-optimal tracking angles can exacerbate degradation drivers.

aerodynamics↗

Thermodynamic modeling of countercurrent chemical looping reverse water gas shift process for redox material screening

The reverse water gas shift (RWGS) reaction is a key pathway for CO 2 utilization, particularly within Power-to-X process chains aimed at sustainable fuel and chemical production. Countercurrent chemical looping (CL-RWGS) using non-stoichiometric oxides can overcome equilibrium limitations of conventional RWGS reactors, enabling significantly higher CO 2 conversions. However, modeling the limiting performance of such systems is challenging due to their multiphase nature and coupled spatial and temporal variation in chemical composition. In this work, we present a discretized batch equilibrium model that simulates CL-RWGS reactors as a series of localized equilibrium exchanges between gas and solid elements. The model is numerically stable, computationally efficient, and free of kinetic source terms, making it well-suited for parametric studies and system-level integration. It is validated against established convection–diffusion models and shown to predict reasonable upper bounds on experimental results. Application of the model to a range of oxygen carrier materials identifies cerium–zirconium solid solutions, particularly Ce 0.80 Zr 0.20 O 2 , as a promising class offering superior oxygen storage characteristics compared to state-of-the-art La 0.6 Sr 0.4 FeO 3 . This framework provides a robust platform for materials screening, reactor sizing, and performance optimization in chemical looping systems. The model implementation is available as open-source software to support further research and development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Evaluating the Structural Response of Amphiphilic Monolayers to Environmental Stimuli

Amphiphilic monolayers composed of end groups with distinct polar and nonpolar functional groups offer rapid and reversible interfacial adaptation in response to environmental stimuli such as a change in interfacial medium polarity. We have synthesized and characterized a suite of monolayers with functional groups of competing polarity designed to reconfigure their interfacial chemical composition in response to solvent polarity. In these films, the end group is designed to be able to reorient and expose the functional groups that minimize the interfacial free energy between the film and the environment. Using a combination of spectroscopic, computational, and wettability studies, we have investigated the responsive interfacial behavior of different end groups upon exposure to environments with varying polarities. Contact angle measurements across a series of polar and dispersive probe liquids reveal trends that reflect the underlying molecular flexibility and composition. Vibrational sum frequency generation (SFG) spectroscopy and atomistic molecular dynamics (MD) simulations confirm solvent-driven reorientation of the end groups, with restructuring observed at the interface. To quantify these effects, we have developed a surface energy calculation model that incorporates solvent-induced surface rearrangements into the estimations. Our findings reveal a strong dependence of surface energy and switching behavior on the length and flexibility of the functionalities in the end group, which affects the exposure of certain interfacial compositions under different solvents. These results offer new insights into the design of adaptive monolayers and provide a framework for evaluating solvent-responsive surfaces.

functional groups↗

Hybrid Simulations of FRC Merging and Compression

An improved understanding of field-reversed configuration (FRC) merging and stability in high acceleration and compression magnetic fields is needed to speed up the development of the pulsed fusion concept developed at Helion Energy. All previous theoretical and simulation work on FRC merging and compression was performed using two-dimensional (2D) magnetohydrodynamic (MHD) models. The results of novel 2D hybrid simulations (fluid electrons and full-orbit kinetic ions) of FRC merging and compression are presented. Results of kinetic and MHD simulations, computed using the HYM code, are compared and analyzed. In cases without axial magnetic compression, both the MHD and hybrid simulations show a high sensitivity to the initial parameters (i.e. FRC separation, velocity, normalized separatrix radius, and plasma viscosity), showing that FRCs with large elongation and separatrix radius either do not merge or merge partially, forming a doublet FRC. In conclusion, application of a mirror coil field at the FRC ends with increasing strength is shown to lead to fast and complete merging of the FRCs in MHD and kinetic simulations.

FRC↗

A Comprehensive Review on the Development of Solid–State Metal–Air Batteries Operated on Oxide–Ion Chemistry

The recently developed solid oxide metal–air redox battery (SOMARB) operating on oxide-ion chemistry represents an emerging and promising energy storage technology, which is well suited for managing grid stability and efficiently harvesting renewable energy. Compared to widely reported metal–air batteries operating on liquid-phase alkali-ion or alkaline chemistries, the SOMARB uniquely features a direct reduction of the high concentration of O 2 molecules in the gas phase without invoking the detrimental formation of a diffusion-blocking oxide phase on the surface of the oxygen electrode. A typical SOMARB is composed of a reversible solid oxide cell (RSOC) and an energy storage unit (ESU), which is capable of storing a high capacity of energy at high power without safety concerns. In this article, the SOMARB concept birth and development are reviewed and discussed with the fundamental differences separating it from other types of metal–air batteries, along with the challenges and opportunities around commercialization. Particular focus is placed on the functional materials tailored for ESU and RSOC applications, including recent experimental and computational efforts to boost the redox activity of Fe-based ESU materials and the performance of intermediate temperature RSOCs. Lastly, candid opinions are offered on the challenges and opportunities facing the future development of SOMARBs toward large-scale energy storage applications.

08 HYDROGEN↗

Superlattice reflection signatures of the insulator–metal transition in V 3 O 5 thin films

Nanoelectronic systems that are inspired by the brain are increasingly looking to insulator–metal transition (IMT) materials as they can mimic the response characteristics of neurons to temperature changes so that these can be used in robotic and computational applications. V 3 O 5 has an insulator–metal transition at ∼430 or ∼80 K higher than VO 2 and provides a unique high-temperature opportunity for these types of applications. Here, in this work, we track the structural evolution of V 3 O 5 thin films across the IMT through conventional selected-area electron diffraction (SAED) and four-dimensional scanning TEM (4D-STEM), correlated with temperature-dependent resistance measurements. SAED patterns show reversible evidence of superlattice reflections associated with the IMT—present below T IMT and absent above it—consistent with the accompanying drop in resistance. At room temperature, nanobeam electron diffraction patterns further reveal three local configurations: (i) type I regions with clean patterns lacking superlattice reflections and spot splitting; (ii) type II regions exhibiting rows of superlattice reflections and split spots indicative of crystallographic variants; and (iii) type III regions with negligible superlattice reflections but larger spot splitting suggestive of overlapping domains of insulating and conducting phases likely driven by local lattice distortions. Upon heating, the superlattice reflections disappear between 413 and 453 K, concurrent with the resistance drop at T IMT , consistent with the emergence of a conducting phase. The overall diffraction geometry remains essentially unchanged up to 573 K, implying that relative domain orientations persist through the transition. These observations reveal nanoscale structural heterogeneity in V 3 O 5 thin films across the IMT and inform operation in regimes where mixed-phase textures are expected. A plausible indexing framework rationalizing the observed geometries is presented in the Discussion section, alongside its limitations and alternative interpretations.

25 ENERGY STORAGE↗

Anisotropic epitaxial stabilization of a low-symmetry ferroelectric with enhanced electromechanical response

Here piezoelectrics interconvert mechanical energy and electric charge and are widely used in actuators and sensors. The best performing materials are ferroelectrics at a morphotropic phase boundary, where several phases coexist. Switching between these phases by electric field produces a large electromechanical response. In ferroelectric BiFeO3, strain can create a morphotropic-phase-boundary-like phase mixture and thus generate large electric-field-dependent strains. However, this enhanced response occurs at localized, randomly positioned regions of the film. Here, we use epitaxial strain and orientation engineering in tandem-anisotropic epitaxy-to craft a low-symmetry phase of BiFeO3 that acts as a structural bridge between the rhombohedral-like and tetragonal-like polymorphs. Interferometric displacement sensor measurements reveal that this phase has an enhanced piezoelectric coefficient of x2.4 compared with typical rhombohedral-like BiFeO3. Band-excitation frequency response measurements and first-principles calculations provide evidence that this phase undergoes a transition to the tetragonal-like polymorph under electric field, generating an enhanced piezoelectric response throughout the film and associated field-induced reversible strains. These results offer a route to engineer thin-film piezoelectrics with improved functionalities, with broader perspectives for other functional oxides.

36 MATERIALS SCIENCE↗

Desalination metamodels and a framework for cross-comparative performance simulations

There is an opportunity to save energy and reduce operational expenses when choosing a suitable desalination method aided by computational modeling. Existing models are not conducive to generalized comparisons between different desalination methods. Therefore, the work in this study developed metamodels for six desalination methods, grouped them into thermal and molecular transport families, and validated their predictive performance within 9% difference from published data. This validated framework allowed comparisons of desalination methods at their prescribed ranges of operational conditions that they were designed for. These conditions specify feed salinity ranges of 1.6 to 2.4 g/kg for Capacitive Deionization and Reverse Osmosis (RO), 2.8 to 4.2 g/kg for Electrodialysis, 28 to 42 g/kg for Thermovapor Compression and Humidification-Dehumidification, and 37 to 55 g/kg for Multi-Effect Distillation (MED). Despite different operational conditions, all models exhibit non-linear, positive correlation between energy consumption and system size in response to feed salinity and production rate. The framework is also employed in a cross-comparative analysis between MED and RO whose results suggest that energy intensity for MED is an order of magnitude greater than RO for the same operational conditions, but actual operational costs are comparable. Overall, the framework is ready for deployment in case studies of actual desalination plants.

42 ENGINEERING↗

Anatomy of information scrambling and decoherence in the integrable Sachdev-Ye-Kitaev model

The growth of information scrambling, captured by out-of-time-order correlation functions (OTOCs), is a central indicator of the nature of many-body quantum dynamics. Here, we compute analytically the complete time dependence of the OTOC for an integrable Sachdev-Ye-Kitaev (SYK) model, 𝑁 Majoranas with random two-body interactions of infinite range, coupled to a Markovian bath at finite temperature. In the limit of no coupling to the bath, the time evolution of scrambling experiences different stages. For 𝑡≲√𝑁, after an initial polynomial growth, the OTOC approaches saturation in a power-law fashion with oscillations superimposed. At 𝑡∼√𝑁, the OTOC reverses trend and starts to decrease linearly in time. The reason for this linear decrease is that, despite being a subleading 1/𝑁 effect, the OTOC in this region is governed by the spectral form factor of the antisymmetric couplings of the SYK model. The linear decrease stops at 𝑡∼2⁢𝑁, the Heisenberg time, where saturation occurs. The effect of the environment is an overall exponential decay of the OTOC for times longer than the inverse of the coupling strength to the bath. Here, the oscillations at 𝑡≲√𝑁 indicate lack of thermalization—a desired feature for better performance of quantum information devices.

Open quantum systems & decoherence↗

Dynamic modeling and simulation of pressure swing adsorption processes using toPSAil

Pressure swing adsorption (PSA) has attracted significant recent interest for chemical process intensification due to its potential for high energy efficiency and amenability to small, modular designs. However, the lack of simulation tools that are readily available, transparent, and trusted, has been identified as a serious impediment to widespread adoption of PSA, as well as to further research on PSA modeling, numerical solution, optimization, and control. This paper presents a complete framework for dynamic modeling and simulation of PSA processes and its implementation in an open-source simulator called toPSAil. Further, the presentation is tutorial and includes many modeling and implementation details often overlooked in existing literature. Novel methods are presented for handling flow reversals and implementing various pressure–flow relationships, along with controlled boundary conditions. Finally, the code contains several innovations designed to improve efficiency and reduce the extensive trial-and-error tuning often required to produce a working PSA cycle.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Correlated nanoelectronics and the second quantum revolution

The growing field of correlated nanoelectronics exists at the intersection of two established fields: correlated oxide electronics and semiconductor nanoelectronics. The development of quantum technologies that exploit quantum coherence and entanglement for the purposes of computation, simulation, and sensing will require complex material properties to be controlled at nanoscale dimensions. Heterostructures and nanostructures formed at the interface between LaAlO 3 and SrTiO 3 exhibit striking behavior that arises from the ability to program the conductive behavior at extreme nanoscale dimensions. The active electronic layer, SrTiO 3 , exhibits a wide range of gate-tunable phenomena such as ferroelectricity, ferroelasticity, magnetism, superconductivity, and spin–orbit coupling, all of which can be controlled at the nanoscale using two reversible methods: conductive atomic force microscope lithography and ultra-low-voltage electron beam lithography. Mesoscopic devices such as single-electron transistors and quasi-one-dimensional electron waveguides can be “sketched” using these techniques, and the properties of these devices differ significantly from those created from traditional semiconductors, such as Si or GaAs. The strongly correlated nature of the SrTiO 3 system is evident from superconducting behavior as well as a state in which electrons are paired outside the superconducting state. A highly exotic phase was discovered in which a degenerate quantum liquid is formed from bound states of n = 2, 3, 4, … electrons. Further development of correlated nanoelectronics based on the LaAlO 3 /SrTiO 3 system can potentially lead to a general platform for quantum simulation as well as a pathway for the development of highly entangled states of multiple photons.

36 MATERIALS SCIENCE↗

Toward Discord : Code for Simulating Continuous Spin Systems

A new computational tool to simulate classical spin systems with frustrated crystal structures is presented. Complementary single- and cluster-spin flip algorithms are implemented to calculate the diffuse scattering patterns, spin-pair correlations, and thermodynamic quantities. Test cases of geometrically frustrated kagome, pyrochlore, and cubic systems are detailed. Two recent scientific cases are also shown here. This new method, together with recent developments of the rmc-discord package (https://github.com/zjmorgan/rmc-discord), represent integrated and strategic step in a complete forward and reverse Monte Carlo framework discord.

36 MATERIALS SCIENCE↗

Catalytic N–H Bond Formation Promoted by a Ruthenium Hydride Complex Bearing a Redox-Active Pyrimidine-Imine Ligand

The synthesis of a piano-stool ruthenium hydride, [(η 5 -C 5 Me 5 )Ru(PmIm)H] (PmIm = (N-(1,3,5-trimethylphenyl)-1-(pyrimidin-2-yl)ethan-1-imine) for the dual purpose of catalytic dihydrogen activation and subsequent hydrogen atom transfer for the formation of weak chemical bonds is described. Introduction of a neutral, potentially redox-active PmIm supporting ligand was designed to eliminate the possibility of deleterious C(sp 2 )–H reductive coupling and elimination that has been identified as a deactivation pathway with related rhodium and iridium catalysts. Treatment of [(η 5 -C 5 Me 5 )RuCl 2 ] n with one equivalent PmIm ligand in the presence of zinc and sodium methoxide resulted in isolation of the diruthenium complex, [(η 5 -C 5 Me 5 )Ru(PmIm)] 2 , arising from C–C bond formation between two PmIm chelates. Addition of H 2 to the ruthenium dimer under both thermal and blue light irradiation conditions furnished the targeted hydride, [(η 5 -C 5 Me 5 )Ru(PmIm)H] which has a relatively weak DFT-calculated Ru–H bond dissociation free energy (BDFE) of 47.9 kcal/mol. Addition of TEMPO to [(η 5 -C 5 Me 5 )Ru(PmIm)H] generated the 17-electron metalloradical, [(η 5 -C 5 Me 5 )Ru(PmIm)], which was characterized by EPR spectroscopy. The C–C bond forming process was reversible as irradiation of [(η 5 -C 5 Me 5 )Ru(PmIm)] 2 generated [(η 5 -C 5 Me 5 )Ru(PmIm)H] and a piano-stool ruthenium complex containing an enamide ligand derived from H-atom ab-straction from the PmIm chelate. Equilibration studies were used to establish an experimental estimate of the effective Ru–H BDFE and a value of 50.8 kcal/mol was obtained, in agreement with the observed loss of H 2 and the DFT-computed value. Here, the ruthenium hydride was an effective catalyst for the thermal catalytic hydrogenation of TEMPO, acridine and a cobalt-imido complex and for the selective reduction of azobenzene to diphenylhydrazine using H 2 as the terminal reductant, highlighting the role of this complex is catalytic weak bond formation using H 2 as the stoichiometric reductant.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Reversible Cl/Cl - redox in a spinel Mn 3 O 4 electrode

A unique prospect of using halides as charge carriers is the possibility of the halides undergoing anodic redox behaviors when serving as charge carriers for the charge-neutrality compensation of electrodes. However, the anodic conversion of halides to neutral halogen species has often been irreversible at room temperature due to the emergence of diatomic halogen gaseous products. Here, we report that chloride ions can be reversibly converted to near-neutral atomic chlorine species in the Mn 3 O 4 electrode at room temperature in a highly concentrated chloride-based aqueous electrolyte. Notably, the Zn 2+ cations inserted in the first discharge and trapped in the Mn 3 O 4 structure create an environment to stabilize the converted chlorine atoms within the structure. Characterization results suggest that the Cl/Cl - redox is responsible for the observed large capacity, as the oxidation state of Mn barely changes upon charging. Computation results corroborate that the converted chlorine species exist as polychloride monoanions, e.g., [Cl 3 ] - and [Cl 5 ] - , inside the Zn 2+ -trapped Mn 3 O 4 , and the presence of polychloride species is confirmed experimentally. Our results point to the halogen plating inside electrode lattices as a new charge-storage mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing the self-ionization of liquid water with ab initio deep potential molecular dynamics

The chemical equilibrium between self-ionized and molecular water dictates the acid–base chemistry in aqueous solutions, yet understanding the microscopic mechanisms of water self-ionization remains experimentally and computationally challenging. Herein, Density Functional Theory (DFT)–based deep neural network (DNN) potentials are combined with enhanced sampling techniques and a global acid–base collective variable to perform extensive atomistic simulations of water self-ionization for model systems of increasing size. The explicit inclusion of long-range electrostatic interactions in the DNN potential is found to be crucial to accurately reproduce the DFT free energy profile of solvated water ion pairs in small (64 and 128 H 2 O) cells. The reversible work to separate the hydroxide and hydronium to a distance S is found to converge for simulation cells containing more than 500 H 2 O, and a distance of ∼ 8 Å is the threshold beyond which the work to further separate the two ions becomes approximately zero. The slow convergence of the potential of mean force with system size is related to a restructuring of water and an increase of the local order around the water ions. Calculation of the dissociation equilibrium constant illustrates the key role of long-range electrostatics and entropic effects in the water autoionization process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

REBOUND: Reverse Engineering Bidirectional Outflow Under Non-Equilibrium Diffusion

Rare-earth elements (REEs) are essential for electronics, renewable energy, and defense technologies. However, the current supply of REEs relies on mining concentrated in a few countries and energy-intensive separations. DOE’s Basic Energy Sciences (BES) program has launched a grand challenge which aims to ensure a sustainable supply of critical REEs by developing innovative and environmentally friendly separation methods. As an alternative to costly and harmful traditional methods, the Non-Equilibrium Transport Driven Separations (NETS) initiative has created a microfluidic Y-channel co-flow method that applies external fields to exploit magneto- and electrohydrodynamic effects for separating dilute REE ions from complex feedstocks. Computational fluid dynamics (CFD) studies have identified a few operating conditions with promising ion selectivity and separation efficiency. However, challenges remain regarding Y-channel versatility across feedstocks and accurate incorporation of physical phenomena into CFD models. In this work, we develop a multi-fidelity modelling approach which integrates experimental results with CFD simulation to build a surrogate model for the dependence of separation efficiency to variation of design parameters. The surrogate model enables a reinforcement learning (RL) method to adaptively launch CFD and experimental runs, improving model fidelity around optimal Y-channel parameters.

36 MATERIALS SCIENCE↗

A light-induced phononic symmetry switch and giant dissipationless topological photocurrent in ZrTe 5

Dissipationless currents from topologically protected states are promising for disorder-tolerant electronics and quantum computation. In this work, we photogenerate giant anisotropic terahertz nonlinear currents with vanishing scattering, driven by laser-induced coherent phonons of broken inversion symmetry in a centrosymmetric Dirac material ZrTe 5 . Our work suggests that this phononic terahertz symmetry switching leads to formation of Weyl points, whose chirality manifests in a transverse, helicity-dependent current, orthogonal to the dynamical inversion symmetry breaking axis, via circular photogalvanic effect. The temperature-dependent topological photocurrent exhibits several distinct features: Berry curvature dominance, particle–hole reversal near conical points and chirality protection that is responsible for an exceptional ballistic transport length of ~10 μm. These results, together with first-principles modelling, indicate two pairs of Weyl points dynamically created by B 1u phonons of broken inversion symmetry. Such phononic terahertz control breaks ground for coherent manipulation of Weyl nodes and robust quantum transport without application of static electric or magnetic fields.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗