Molecular Dynamics Simulations of Reverse Osmosis in Silica Nanopores
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11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
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Impact of magnetic and electric fields on the free energy to form a calcium carbonate ion-pair
Electromagnetic fields are used in water treatment and desalination to regulate scale formation and extend the lifetime of membranes. External electric and magnetic fields can promote or suppress mineral nucleation and growth. However, the molecular-scale mechanisms of such processes remain unknown. Computing the free energies needed to form ion pairs under external fields provides important insights into understanding the elemental steps during the initial formation of mineral scales. In this paper, we used molecular dynamics combined with metadynamics simulations to investigate the free energies of forming the [Ca–CO 3 ] 0 ion pair, a fundamental building block of carbonate scales, under a range of magnetic (up to 10 T) and electric (up to 10 V m −1 ) fields in water. The presence of constant magnetic or electric fields favored the ion pairing reaction and lowered the free energies by up to 3% to 6%. The internal energy and entropic components of the free energy showed significant changes and exhibited non-linear behavior with increasing field strength. The [Ca–CO 3 ] 0 ion pairing is an entropy-driven process in the absence of an external field, but the mechanism shifts to an internal energy-driven process under selected external fields, suggesting possible changes in the nucleation pathways.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection
In the indeterminate nodules of a model legume Medicago truncatula, ~700 nodule-specific cysteine-rich (NCR) peptides with conserved cysteine signature are expressed. NCR peptides are highly diverse in sequence, and some of these cationic peptides exhibit antimicrobial activity in vitro and in vivo. However, there is a lack of knowledge regarding their structural architecture, antifungal activity, and modes of action against plant fungal pathogens. Here, the three-dimensional NMR structure of the 36-amino acid NCR044 peptide was solved. This unique structure was largely disordered and highly dynamic with one four-residue α-helix and one three-residue antiparallel β-sheet stabilized by two disulfide bonds. NCR044 peptide also exhibited potent fungicidal activity against multiple plant fungal pathogens, including Botrytis cinerea and three Fusarium spp. It inhibited germination in quiescent spores of B. cinerea. In germlings, it breached the fungal plasma membrane and induced reactive oxygen species. It bound to multiple bioactive phosphoinositides in vitro. Time-lapse confocal and superresolution microscopy revealed strong fungal cell wall binding, penetration of the cell membrane at discrete foci, followed by gradual loss of turgor, subsequent accumulation in the cytoplasm, and elevated levels in nucleoli of germlings. Spray-applied NCR044 significantly reduced gray mold disease symptoms caused by the fungal pathogen B. cinerea in tomato and tobacco plants, and postharvest products. Our work illustrates the antifungal activity of a structurally unique NCR peptide against plant fungal pathogens and paves the way for future development of this class of peptides as a spray-on fungistat/fungicide.
59 BASIC BIOLOGICAL SCIENCES↗
Imidazolium-Type Anion Exchange Membranes for Improved Organic Acid Transport and Permselectivity in Electrodialysis
Most commercial anion exchange membranes (AEMs) deploy quaternary ammonium moieties. Alternative cation moieties have been explored in AEMs for fuel cells, but there are no studies focused examining alternative tethered cations in AEMs for ionic separations—such as organic acid anion transport via electrodialysis. H-cell and conductivity experiments demonstrate that tethered benzyl 1-methyl imidazolium groups in polysulfone AEMs enhance lactate conductivity by 49% and improved lactate anion flux by 24x when compared to a quaternary benzyl ammonium polysulfone AEM. An electrodialysis demonstration with the imidazolium-type AEM showed a 2x improvement in lactate anion flux and 20% improvement in permselectivity when benchmarked against the quaternary ammonium AEM. Molecular dynamics and 2D NOESY NMR revealed closer binding of lactate anions to the imidazolium cations when compared to the quaternary ammonium cation. It is posited that this closer binding is responsible to greater flux values observed with imidazolium-type AEM.
36 MATERIALS SCIENCE↗
Reversible Switch in Charge Storage Enabled by Selective Ion Transport in Solid Electrolyte Interphase
Solid-electrolyte interphases (SEIs) in advanced rechargeable batteries ensure reversible electrode reactions at extreme potentials beyond the thermodynamic stability limits of electrolytes by insulating electrons while allowing working ions to transport. Such selective ion transport occurs naturally in biological cell membranes as a ubiquitous prerequisite of many life processes and a foundation of biodiversity. In addition, cell membranes can selectively open and close the ion channels in response to external stimuli (e.g., electrical, chemical, mechanical, thermal), giving rise to “gating” mechanisms that help manage intracellular reactions. We wondered whether the chemistry and structure of SEIs can mimic cell membranes, such that ion gating can be replicated. That is, can SEIs realize a reversible switching between two electrochemical behaviors, i.e., the ion intercalation chemistry of batteries and the ion adsorption of capacitors? Herein, we report such SEIs that result in thermally activated selective ion transport. The function of open/close gate switches is governed by the chemical and structural dynamics of SEIs under different thermal conditions, with precise behaviors as conducting and insulating interphases that enable battery and capacitive processes within a finite temperature window. Such an ion gating function is synergistically contributed by Arrhenius-activated ion transport and SEI dissolution/regrowth. Following the understanding of this new mechanism, we then develop an electrochemical method to heal the SEI layer in situ. As a result, the knowledge acquired in this work reveals the possibility of hitherto unknown biomimetic properties of SEIs, which will guide us to leverage such complexities to design better SEIs for future battery chemistries.
25 ENERGY STORAGE↗
Enriching Cations Using Electric Field Gradients Generated by Bipolar Electrodes in the Absence of Buffer
We discuss that ionic current gradients and corresponding electric field gradients formed at bipolar electrodes are useful for enriching cations up to ~350-fold at specific locations in microfluidic devices. The enrichment mechanism is determined by collecting current data, measuring solution conductivity, and by performing pH indicator experiments. These data reveal the dynamic nature of the enrichment mechanism. Specifically, they show the complex relationship between the ionic current gradients formed at the bipolar electrode and the extent of cation enrichment. Finally, we demonstrate cation enrichment is possible in buffer-free solutions containing up to 50.0 mM KCl. This finding is significant because it broadens the range of solutions in which membrane-free, electrochemical separations using bipolar electrodes can be performed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Predicting initial trans-membrane pressure across cycles in the ultrafiltration process using random forest
With growing freshwater scarcity, direct potable reuse (DPR) systems that reclaim wastewater for drinking are becoming increasingly important for sustainable water supply. Reliable operation requires minimizing downtime in ultrafiltration (UF) units, where membrane fouling leads to elevated trans-membrane pressure (TMP). This study develops data-driven regression models based on random forest (RF) and autoregressive (AR) approaches to forecast the initial TMP at the start of each UF filtration cycle in a pilot-scale DPR system. The RF model consistently outperforms baseline methods, including historical mean, last observation carried forward, and AR models, across multiple forecast horizons, achieving the lowest root mean square error. To evaluate how different classes of process variables contribute to TMP dynamics over time, we examine the feature importance of independent input variables across multiple forecast horizons. This analysis provides insight into the temporal relevance of operational and sensor-derived features, guiding control and monitoring strategies. Additionally, the impact of hyperparameter tuning on TMP prediction performance is assessed for both direct and recursive RF modelling approaches. The proposed RF framework establishes a robust foundation for predictive monitoring and real-time optimization of UF operations, supporting sustainable and reliable water reuse.
direct potable reuse↗
Gating of Hydrophobic Nanopores with Large Anions
In this report, understanding ion transport in nanoporous materials is critical to a wide variety of energy and environmental technologies, ranging from ion-selective membranes, drug delivery, and biosensing, to ion batteries and supercapacitors. While nanoscale transport is often described by continuum models that rely on a point charge description for ions and a homogeneous dielectric medium for the solvent, here, we show that transport of aqueous solutions at a hydrophobic interface can be highly dependent on the size and hydration strength of the solvated ions. Specifically, measurements of ion current through single silicon nitride nanopores that contain a hydrophobic-hydrophilic junction show that transport properties are dependent not only on applied voltage but also the type of anion. We find that in Cl - -contained solutions the nanopores only conducted ionic current above a negative voltage threshold. On the other hand, introduction of large polarizable anions, such as Br - and I - , facilitated the pore wetting, making the pore conductive at all examined voltages. Molecular dynamics simulations revealed that the large anions, Br - and I - , have a weaker solvation shell compared to that of Cl - , and consequently were prone to migrate from the aqueous solution to the hydrophobic surface, leading to the anion accumulation responsible for pore wetting. The results are essential for designing nanoporous systems that are selective to ions of the same charge, for realization of ion-induced wetting in hydrophobic pores, as well as for fundamental understanding on the role of ion hydration shell on the properties of solid/liquid interfaces.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural analyses of the PKA RIIβ holoenzyme containing the oncogenic DnaJB1-PKAc fusion protein reveal protomer asymmetry and fusion-induced allosteric perturbations in fibrolamellar hepatocellular carcinoma
When the J-domain of the heat shock protein DnaJB1 is fused to the catalytic (C) subunit of cAMP-dependent protein kinase (PKA), replacing exon 1, this fusion protein, J-C subunit (J-C), becomes the driver of fibrolamellar hepatocellular carcinoma (FL-HCC). Here, we use cryo-electron microscopy (cryo-EM) to characterize J-C bound to RIIβ, the major PKA regulatory (R) subunit in liver, thus reporting the first cryo-EM structure of any PKA holoenzyme. We report several differences in both structure and dynamics that could not be captured by the conventional crystallography approaches used to obtain prior structures. Most striking is the asymmetry caused by the absence of the second cyclic nucleotide binding (CNB) domain and the J-domain in one of the RIIβ:J-C protomers. Using molecular dynamics (MD) simulations, we discovered that this asymmetry is already present in the wild-type (WT) RIIβ 2 C 2 but had been masked in the previous crystal structure. This asymmetry may link to the intrinsic allosteric regulation of all PKA holoenzymes and could also explain why most disease mutations in PKA regulatory subunits are dominant negative. The cryo-EM structure, combined with small-angle X-ray scattering (SAXS), also allowed us to predict the general position of the Dimerization/Docking (D/D) domain, which is essential for localization and interacting with membrane-anchored A-Kinase-Anchoring Proteins (AKAPs). This position provides a multivalent mechanism for interaction of the RIIβ holoenzyme with membranes and would be perturbed in the oncogenic fusion protein. The J-domain also alters several biochemical properties of the RIIβ holoenzyme: It is easier to activate with cAMP, and the cooperativity is reduced. These results provide new insights into how the finely tuned allosteric PKA signaling network is disrupted by the oncogenic J-C subunit, ultimately leading to the development of FL-HCC.
59 BASIC BIOLOGICAL SCIENCES↗
Ion permeation in potassium ion channels
The study of ion channels dates back to the 1950s and the groundbreaking electrophysiology work of Hodgin and Huxley, who used giant squid axons to probe how action potentials in neurons were initiated and propagated. More recently, several experiments using different structural biology techniques and approaches have been conducted to try to understand how potassium ions permeate through the selectivity filter of potassium ion channels. Two mechanisms of permeation have been proposed, and each of the two mechanisms is supported by different experiments. The key structural biology experiments conducted so far to try to understand how ion permeation takes place in potassium ion channels are reviewed and discussed. Protein crystallography has made, and continues to make, key contributions in this field, often through the use of anomalous scattering. Other structural biology techniques used to study the contents of the selectivity filter include solid-state nuclear magnetic resonance and two-dimensional infrared spectroscopy, both of which make clever use of isotopic labeling techniques, while molecular-dynamics simulations of ion flow through the selectivity filter have been enabled by the growing number of potassium ion channel structures deposited in the Protein Data Bank.
59 BASIC BIOLOGICAL SCIENCES↗
Crowded electrolytes containing redoxmers in different states of charge: Solution structure, properties, and fundamental limits on energy density
Nonaqueous redox flow batteries use liquid electrolytes containing redox-active organic molecules (redoxmers) as their energy storage medium. To maximize energy density, the redoxmer concentration needs to be maximized while maintaining low viscosity and high ionic conductivity. During charge, a redoxmer molecule pairs with an ion in the electrolyte while another ion migrates across the membrane to maintain electric neutrality. In a crowded electrolyte, this reconstitution changes physical and chemical properties of the solution. To explore these behaviors, a phenothiazine redoxmer fully miscible with acetonitrile was used, and electrochemical charge was mimicked by chemical oxidation. The solutions were examined using small-angle X-ray scattering, nuclear magnetic resonance, and conductometry and modeled using classical molecular dynamics. Overall, our study indicates that physical and structural properties of redoxmer solutions in both states of charge make it exceedingly difficult to increase the redoxmer concentrations over 2 M at any temperature without compromising dynamic properties of such solutions. The cause for this limitation is proximity to a gel-like regime in which fluidity, diffusivity, and ionic conductivity exponentially decrease with increasing concentration. This tendency is compounded by non-Arrhenius behavior of the electrolyte: a small increase in the concentration outruns gains in fluidity and conductivity at a higher temperature. Thus the properties of crowded electrolytes generally make it impossible to operate when gel-like behavior sets in. Pushing the redoxmer concentration to 2.5-3 M might be possible for small redoxmer molecules, but it would require the use of ionic liquid electrolytes at 340-360 K. (C) 2021 Elsevier B.V. All rights reserved.
25 ENERGY STORAGE↗
Engineered selective biotoxin‐binding hydrogels for toxin sequestration
The development of synthetic selective membranes that separate materials of similar sizes, charges, and/or polarities remains a difficult challenge, and looking towards biology provides inspiration for new designs. In this work, a series of cholera toxin binding peptides (CTBPs) are identified, spanning a range of binding inhibitions, and integrated into chemically cross-linked cholera toxin binding gels (CTBGs) via thiol-Michael polycondensation reactions. All gels demonstrate rheological profiles consistent with elastic solids. The CTBGs are probed via small-angle neutron scattering and exhibit a correlation length, ξ, smaller than most proteins (1.3–2.5 nm). Thus, an effective entropic mesh is formed to block non-targeted proteins. However, the CTBGs have a dynamic mesh size, Ξ, that is larger than cholera toxin (CT) to allow the transport of target proteins. The CTBGs with the highest binding inhibitions both show high selectivity and permeation of CT, rejecting all other tested proteins. In total, two new highly selective CTBGs are synthesized and validated for use in cholera toxin remediation. Together, this platform demonstrates the wide applicability of selectively-diffusive materials for difficult separations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Lattice chain theories for dynamics of acoustic flexural phonons in nonpolar nanomaterials
Knowledge of lattice dynamics of acoustic flexural phonons is critically important in understanding the mechanical, electrical, and thermal properties of nanomaterials. However, the general nature of acoustic flexural phonons for the span of possible nanomaterials and the dependence of these on microscopic material properties remain unclear. Therefore, we develop general lattice chain theories to understand acoustic flexural vibrations in covalent and van der Waals lattices. Furthermore, the analytic theories suggest that the flexure branch has quadratic dispersion for low dimensional lattices in the long-wavelength limit, quite different from linear branches in bulk van der Waals bonded lattices like graphite. Surprisingly, interlayer van der Waals interactions in multilayer lattices do not determine the behavior of the flexural dispersion. The bonds of covalent interactions in multilayer and buckled monolayer lattices play different roles in determining the flexural dispersion with those in flat monolayer lattices, e.g., graphene. Further, based on the correspondence between microscopic and continuum dynamics, we provide a universal and effective approach to characterize the intrinsic bending rigidity of low dimensional nanomaterials using dispersion data.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DNA Strand Displacement Driven Molecular Additive Manufacturing (DSD-MAM)
The goal of this project was to validate two-dimensional molecular printers, initially selfassembled from DNA and then actuated by externally driven cycles of DNA strand displacement, as prototype integrated nanosystems for molecular additive manufacturing. Novel functionalities of these nanomachines were explored during this project, including the following: nanometer-precision positioning mechanisms based on DNA strand displacement with multivalent interactions for discrete stepping or else diffusive capture; integration of independently moving layers of DNA origami to achieve 2D controllable motion; integration of spatial positioning with deposition functionality. The principal importance of this project was to provide an essential step in the development of a new technology for atomically precise manufacturing. Our first generation molecular 2D printer offers several advantages over conventional DNA-origami patterning, such as faster prototyping, faster dynamic rearrangement of patterns, and the ability to respond with feedback. We anticipate that our first-generation molecular printers may inspire future generations of molecular printers with iterative improvements in robustness and throughput. Potential applications of atomically precise manufacturing include the following: photovoltaics; photosynthetic and fuel cells; thermoelectrics and anisotropic heat spreaders; solid-state lighting; molecular electronic and plasmonic circuits; selectively preamble membranes; self-repairing materials with high strength-to-weight and fracture resistance.
36 MATERIALS SCIENCE↗
Mapping the Interfacial Chemistry and Structure of Partially Fluorinated Bottlebrush Polymers and Their Linear Analogues
Polymer interfaces are key to a range of applications including membranes for chemical separations, hydrophobic coatings, and passivating layers for antifouling. While important, challenges remain in probing the interfacial monolayer where the molecular ordering and orientation can change depending on the chemical makeup or processing conditions. In this work, we leverage surface specific vibrational sum frequency generation (SFG) and the associated dependence on molecular symmetry to elucidate the ordering and orientations of key functional groups for poly(2,2,2-trifluoroethyl methacrylate) bottlebrush polymers and their linear polymer analogues. These measurements were framed by atomistic molecular dynamic simulations to provide a complementary physical picture of the gas–polymer interface. Simulations and SFG measurements show that methacrylate backbones are buried beneath a layer of trifluoroethyl containing side groups that result in structurally similar interfaces regardless of the polymer molecular weight or architecture. The average orientational angles of the trifluoroethyl containing side groups differ depending on polymer linear and bottlebrush architectures, suggesting that the surface groups can reorient via available rotational degrees of freedom. Results show that the surfaces of the bottlebrush and linear polymer samples do not strongly depend on molecular weight or architecture. As such, one cannot rely on increasing the molecular weight or altering the architecture to tune surface properties. This insight into the polymer interfacial structure is expected to advance the design of new material interfaces with tailored chemical/functional properties.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Integrated and dynamic multi-spectroscopic in situ imaging of plant metabolism at the level of subcellular compartments. Final Report
The goals of this project was to develop integrated multi-spectral molecular imaging technologies (Raman, fluorescence, and mass spectrometry), that can assess, and image metabolic processes at the cellular and subcellular levels of plant organs. These imaging technologies were developed in the context of computational capabilities that integrated multi-spectral images with genome scale models of metabolism. The integrated molecular imaging technologies were developed in the biological context of autophagy that remodels membrane lipid topologies, which control spatially defined subcellular regions within plant cells and optimizes plant biomass productivity during environmental stresses that can limit biomass productivity.
09 BIOMASS FUELS↗
The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing
The synthesis of exopolysaccharides as biofilm matrix components by pathogens is a crucial factor for chronic infections and antibiotic resistance. Many periplasmic proteins involved in polymer processing and secretion in Gram-negative synthase dependent exopolysaccharide biosynthetic systems have been individually characterized. The operons responsible for the production of PNAG, alginate, cellulose and the Pel polysaccharide each contain a gene that encodes an outer membrane associated tetratricopeptide repeat (TPR) domain containing protein. While the TPR domain has been shown to bind other periplasmic proteins, the functional consequences of these interactions for the polymer remain poorly understood. Herein, we show that the C-terminal TPR region of PgaA interacts with the de-N-acetylase domain of PgaB, and increases its deacetylase activity. Additionally, we found that when the two proteins form a complex, the glycoside hydrolase activity of PgaB is also increased. To better understand structure-function relationships we determined the crystal structure of a stable TPR module, which has a conserved groove formed by three repeat motifs. Tryptophan quenching, mass spectrometry analysis and molecular dynamics simulation studies suggest that the crystallized TPR module can bind PNAG/dPNAG via its electronegative groove on the concave surface, and potentially guide the polymer through the periplasm towards the porin for export. Our results suggest a scaffolding role for the TPR domain that combines PNAG/dPNAG translocation with the modulation of its chemical structure by PgaB.
59 BASIC BIOLOGICAL SCIENCES↗
Structure-Based Design of Dual Bactericidal and Bacteria-Releasing Nanosurfaces
Here, we report synergistic nanostructured surfaces combining bactericidal and bacteria-releasing properties. A polystyrene-block-poly(methyl methacrylate) (PS-block-PMMA) diblock copolymer is used to fabricate vertically oriented cylindrical PS structures (“PS nanopillars”) on silicon substrates. The results demonstrate that the PS nanopillars (with a height of about 10 nm, size of about 50 nm, and spacing of about 70 nm) exhibit highly effective bactericidal and bacteria-releasing properties (“dual properties”) against Escherichia coli for at least 36 h of immersion in an E. coli solution. Interestingly, the PS nanopillars coated with a thin layer (≈3 nm thick) of titanium oxide (TiO 2 ) (“TiO 2 nanopillars”) show much improved dual properties against E. coli (a Gram-negative bacterium) compared to the PS nanopillars. Moreover, the dual properties emerge against Listeria monocytogenes (a Gram-positive bacterium). To understand the mechanisms underlying the multifaceted property of the nanopillars, coarse-grained molecular dynamics (MD) simulations of a lipid bilayer (as a simplified model for E. coli) in contact with a substrate containing hexagonally packed hydrophilic nanopillars were performed. The MD results demonstrate that when the bacterium–substrate interaction is strong, the lipid heads adsorb onto the nanopillar surfaces, conforming the shape of a lipid bilayer to the structure/curvature of nanopillars and generating high stress concentrations within the membrane (i.e., the driving force for rupture) at the edge of the nanopillars. Membrane rupture begins with the formation of pores between nanopillars (i.e., bactericidal activity) and ultimately leads to the membrane withdrawal from the nanopillar surface (i.e., bacteria-releasing activity). In the case of Gram-positive bacteria, the adhesion area to the pillar surface is limited due to the inherent stiffness of the bacteria, creating higher stress concentrations within a bacterial cell wall. In conclusion, the present study provides insight into the mechanism underlying the “adhesion-mediated” multifaceted property of nanosurfaces, which is crucial for the development of next-generation antibacterial surface coatings for relevant medical applications.
36 MATERIALS SCIENCE↗