Thermodynamics of Li+-Crown Ether Interactions in Aqueous Solvent.

Lithium ion-based batteries are ubiquitous in modern technology due to applications in personal electronics and high-capacity storage for electric vehicles. Concerns about lithium supply and battery waste have prompted interest in lithium recycling methods. The crown ether 12-crown-4 has been studied for its abilities to form stable complexes with lithium ions (Li+). In this paper, molecular dynamics simulations are applied to examine the binding properties of a 12-crown-4-Li+ system in aqueous solution. It was found that 12-crown-4 did not form stable complexes with Li+ in aqueous solution due to the binding geometry which was prone to interference by surrounding water molecules. In addition, the binding properties of sodium ions (Na+) to 12-crown-4 are examined for comparison. Subsequently, calculations were performed with the crown ethers 15-crown-5 and 18-crown-6 to study their complexation with Li+ as well as Na+. It was determined that binding was unfavorable for both types of ions for all three crown ethers tested, though 15-crown-5 and 18-crown-6 showed a marginally greater affinity for Li+ than 12-crown-4. Metastable minima present in the potential of mean force for Na+ render binding marginally more likely there. We discuss these results in the context of membrane-based applications of crown ethers for Li+ separations.

MoSDeF Cassandra: A complete Python interface for the Cassandra Monte Carlo software.

We introduce a new Python interface for the Cassandra Monte Carlo software, molecular simulation design framework (MoSDeF) Cassandra. MoSDeF Cassandra provides a simplified user interface, offers broader interoperability with other molecular simulation codes, enables the construction of programmatic and reproducible molecular simulation workflows, and builds the infrastructure necessary for high-throughput Monte Carlo studies. Many of the capabilities of MoSDeF Cassandra are enabled via tight integration with MoSDeF. We discuss the motivation and design of MoSDeF Cassandra and proceed to demonstrate both simple use-cases and more complex workflows, including adsorption in porous media and a combined molecular dynamics - Monte Carlo workflow for computing lateral diffusivity in graphene slit pores. The examples presented herein demonstrate how even relatively complex simulation workflows can be reduced to, at most, a few files of Python code that can be version-controlled and shared with other researchers. We believe this paradigm will enable more rapid research advances and represents the future of molecular simulations.

Machine Learning Directed Optimization of Classical Molecular Modeling Force Fields.

Accurate force fields are necessary for predictive molecular simulations. However, developing force fields that accurately reproduce experimental properties is challenging. Here, we present a machine learning directed, multiobjective optimization workflow for force field parametrization that evaluates millions of prospective force field parameter sets while requiring only a small fraction of them to be tested with molecular simulations. We demonstrate the generality of the approach and identify multiple low-error parameter sets for two distinct test cases: simulations of hydrofluorocarbon (HFC) vapor-liquid equilibrium (VLE) and an ammonium perchlorate (AP) crystal phase. We discuss the challenges and implications of our force field optimization workflow.

Reverse engineering morphogenesis through Bayesian optimization of physics-based models.

Morphogenetic programs coordinate cell signaling and mechanical interactions to shape organs. In systems and synthetic biology, a key challenge is determining optimal cellular interactions for predicting organ shape, size, and function. Physics-based models defining the subcellular force distribution facilitate this, but it is challenging to calibrate parameters in these models from data. To solve this inverse problem, we created a Bayesian optimization framework to determine the optimal cellular force distribution such that the predicted organ shapes match the experimentally observed organ shapes. This integrative framework employs Gaussian Process Regression, a non-parametric kernel-based probabilistic machine learning modeling paradigm, to learn the mapping functions relating to the morphogenetic programs that maintain the final organ shape. We calibrated and tested the method on Drosophila wing imaginal discs to study mechanisms that regulate epithelial processes ranging from development to cancer. The parameter estimation framework successfully infers the underlying changes in core parameters needed to match simulation data with imaging data of wing discs perturbed with collagenase. The computational pipeline identifies distinct parameter sets mimicking wild-type shapes. It enables a global sensitivity analysis to support the regulation of actomyosin contractility and basal ECM stiffness to generate and maintain the curved shape of the wing imaginal disc. The optimization framework, combined with experimental imaging, identified that Piezo, a mechanosensitive ion channel, impacts fold formation by regulating the apical-basal balance of actomyosin contractility and elasticity of ECM. This workflow is extensible toward reverse-engineering morphogenesis across organ systems and for real-time control of complex multicellular systems.

Multiscale Equation-Oriented Optimization Decreases the Carbon Intensity of Shale Gas to Liquid Fuel Processes.

Shale gas is revolutionizing the U.S. energy and chemical commodity landscape and can ease the transition to a sustainable decarbonized economy. This work develops an equation-oriented (EO) multiscale modeling framework using the open-source IDAES-PSE platform that tractably incorporates microkinetic detail in process design via reduced-order kinetic (ROK) models. Using multiobjective optimization with embedded heat integration and life-cycle analysis, we simultaneously minimize the minimum selling price of liquid hydrocarbons (e.g., liquid fuels/additives from shale gas) and process emissions (via a CO2 tax). Optimization reduces greenhouse gas emissions per MJ of fuel produced by over 35% compared to the literature and achieves a carbon efficiency of 87%. The optimizer changes the recycling rate, temperatures, and pressures to mitigate the effect of ROK model-form uncertainty on product portfolio predictions. Moreover, we show that the optimal process design is insensitive to changing CO2 tax rates. Finally, the EO framework enables a fast sensitivity analysis of shale gas composition variability across 12 regions of the Eagle Ford basin. These results highlight the benefits of the open-source EO framework: fast, scalable, customized, and reproducible system analysis and optimization for sustainable energy technologies beyond shale utilization.

Critical Mineral Separations: Opportunities for Membrane Materials and Processes to Advance Sustainable Economies and Secure Supplies.

Sustainable energy solutions and electrification are driving increased demand for critical minerals. Unfortunately, current mineral processing techniques are resource intensive, use large quantities of hazardous chemicals, and occur at centralized facilities to realize economies of scale. These aspects of existing technologies are at odds with the sustainability goals driving increased demand for critical minerals. Here, we argue that the small footprint and modular nature of membrane technologies position them well to address declining concentrations in ores and brines, the variable feed concentrations encountered in recycling, and the environmental issues associated with current separation processes; thus, membrane technologies provide new sustainable pathways to strengthening resilient critical mineral supply chains. The success of creating circular economies hinges on overcoming diverse barriers across the molecular to infrastructure scales. As such, solving these challenges requires the convergence of research across disciplines rather than isolated innovations.

Optimization of Reactive Ink Formulation for Controlled Additive Manufacturing of Copolymer Membrane Functionalization.

Multifunctional, nanostructured membranes hold immense promise for overcoming permeability-selectivity trade-offs and enhancing membrane durability in challenging molecule separations. Following the fabrication of copolymer membranes, additive manufacturing technologies can introduce reactive inks onto substrates to modify pore wall chemistries. However, large-scale implementation is hindered by a lack of systematic optimization. This study addresses this challenge by elucidating the membrane functionalization mechanisms and optimal manufacturing conditions using a copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) "click" reaction. Leveraging a data science toolkit (e.g., nonlinear regression, uncertainty quantification, identifiability analyses, model selection, and design of experiments), we developed two mathematical models: (1) algebraic equations to predict equilibrium concentrations after preparing reactive inks by mixing copper sulfate, ascorbic acid (AA), and an alkynyl-terminated reactant; and (2) reaction-diffusion partial differential equations (PDEs) to describe the functionalization process. The ink preparation chemistry with side reactions was validated through pH and UV-vis measurements, while the diffusion and kinetic parameters in the PDE model were calibrated using time-series conversion of the azide moieties inferred from Fourier-transform infrared spectroscopy. This modeling framework avoids redundant experimental efforts and offers a functionalization protocol for scaling up designs. Ink optimization problems were proposed to reduce the use of expensive and environmentally insulting ink materials, i.e., Cu(II), while ensuring the desired chemical distributions. With optimal ink formulation Cu(II)/AA/alkyne = 1:1:2 identified, we uncovered trade-offs between Cu(II) usage and functionalization time; for example, in continuous roll-to-roll manufacturing with a conserved functionalization bath setup, our optimal operational conditions to achieve ≥90% functionalization enable at least a 20% reduction in total copper investment compared to previous experimental results. The data science-enabled ink optimization framework is extendable for on-demand multifunctional membranes in numerous future applications such as metal recovery from wastewater and brine.

Bayesian Optimization of Low-Temperature Nonthermal Plasma Jet Sintering of Nanoinks.

In response to the escalating demand for flexible devices in applications such as wearables, sensors, and touch panels, there is a need for innovative fabrication approaches for devices made from nanomaterial-based inks. Subsequent to ink deposition, a pivotal stage in device manufacturing typically involves high-temperature sintering, posing challenges for heat-sensitive substrates. Nonthermal plasma jet sintering utilizing an atmospheric pressure dielectric barrier discharge (DBD) plasma jet enables sintering at room temperature and standard pressure, facilitating the sintering of printed nanoparticle films without compromising substrate or film surface integrity. However, determining optimal plasma jet sintering conditions can be challenging due to multiple processing variables with intricate interrelationships. This work employed Bayesian optimization (BO) and machine learning (ML) to identify optimal values for seven primary plasma jet sintering variables. Optimization yielded a 99.2% increase in the measured electrical conductivity for plasma jet-sintered indium tin oxide (ITO) films after five rounds of experiments. Moreover, the optimal sintering conditions achieved an electrical conductivity that was 81.4% of conventional furnace sintering at 300 °C, but was three times faster and with a peak substrate temperature below 47 °C. This result demonstrates the prospect of applying BO to optimize processing techniques for emerging low-temperature requirements.

Reverse engineering morphogenesis through Bayesian optimization of physics-based models.

Morphogenetic programs direct the cell signaling and nonlinear mechanical interactions between multiple cell types and tissue layers to define organ shape and size. A key challenge for systems and synthetic biology is determining optimal combinations of intra- and inter-cellular interactions to predict an organ's shape, size, and function. Physics-based mechanistic models that define the subcellular force distribution facilitate this, but it is extremely challenging to calibrate parameters in these models from data. To solve this inverse problem, we created a Bayesian optimization framework to determine the optimal cellular force distribution such that the predicted organ shapes match the desired organ shapes observed within the experimental imaging data. This integrative framework employs Gaussian Process Regression (GPR), a non-parametric kernel-based probabilistic machine learning modeling paradigm, to learn the mapping functions relating to the morphogenetic programs that generate and maintain the final organ shape. We calibrated and tested the method on cross-sections of Drosophila wing imaginal discs, a highly informative model organ system, to study mechanisms that regulate epithelial processes that range from development to cancer. As a specific test case, the parameter estimation framework successfully infers the underlying changes in core parameters needed to match simulation data with time series imaging data of wing discs perturbed with collagenase. Unexpectedly, the framework also identifies multiple distinct parameter sets that generate shapes similar to wild-type organ shapes. This platform enables an efficient, global sensitivity analysis to support the necessity of both actomyosin contractility and basal ECM stiffness to generate and maintain the curved shape of the wing imaginal disc. The optimization framework, combined with fixed tissue imaging, identified that Piezo, a mechanosensitive ion channel, impacts fold formation by regulating the apical-basal balance of actomyosin contractility and elasticity of ECM. This framework is extensible toward reverse-engineering the morphogenesis of any organ system and can be utilized in real-time control of complex multicellular systems.

Machine Learning-Enabled Development of Accurate Force Fields for Refrigerants.

Hydrofluorocarbon (HFC) refrigerants with zero ozone-depleting potential have replaced chlorofluorocarbons and are now ubiquitous. However, some HFCs have high global warming potential, which has led to calls by governments to phase out these HFCs. Technologies to recycle and repurpose these HFCs need to be developed. Therefore, thermophysical properties of HFCs are needed over a wide range of conditions. Molecular simulations can help understand and predict the thermophysical properties of HFCs. The prediction capability of a molecular simulation is directly tied to the accuracy of the force field. In this work, we applied and refined a machine learning-based workflow to optimize the Lennard-Jones parameters of classical HFC force fields for HFC-143a (CF3CH3), HFC-134a (CH2FCF3), R-50 (CH4), R-170 (C2H6), and R-14 (CF4). Our workflow involves liquid density iterations with molecular dynamics simulations and vapor-liquid equilibrium (VLE) iterations with Gibbs ensemble Monte Carlo simulations. Support vector machine classifiers and Gaussian process surrogate models save months of simulation time and can efficiently select optimal parameters from half a million distinct parameter sets. Excellent agreement as evidenced by low mean absolute percent errors (MAPEs) of simulated liquid density (ranging from 0.3% to 3.4%), vapor density (ranging from 1.4% to 2.6%), vapor pressure (ranging from 1.3% to 2.8%), and enthalpy of vaporization (ranging from 0.5% to 2.7%) relative to experiments was obtained for the recommended parameter set of each refrigerant. The performance of each new parameter set was superior or similar to the best force field in the literature.

Hybrid Data-Driven Discovery of High-Performance Silver Selenide-Based Thermoelectric Composites.

Optimizing material compositions often enhances thermoelectric performances. However, the large selection of possible base elements and dopants results in a vast composition design space that is too large to systematically search using solely domain knowledge. To address this challenge, a hybrid data-driven strategy that integrates Bayesian optimization (BO) and Gaussian process regression (GPR) is proposed to optimize the composition of five elements (Ag, Se, S, Cu, and Te) in AgSe-based thermoelectric materials. Data is collected from the literature to provide prior knowledge for the initial GPR model, which is updated by actively collected experimental data during the iteration between BO and experiments. Within seven iterations, the optimized AgSe-based materials prepared using a simple high-throughput ink mixing and blade coating method deliver a high power factor of 2100 µW m-1 K-2 , which is a 75% improvement from the baseline composite (nominal composition of Ag2 Se1 ). The success of this study provides opportunities to generalize the demonstrated active machine learning technique to accelerate the development and optimization of a wide range of material systems with reduced experimental trials.