Structural insight into the novel iron-coordination and domain interactions of transferrin-1 from a
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Weber, Jacob J.↗
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Mechanistic Studies of a Primitive Homolog of Nitrogenase Involved in Coenzyme F430 Biosynthesis
Methyl-coenzyme M reductase (MCR) is the key enzyme in the biological formation and anaerobic oxidation of methane (AOM). Methane is a potent greenhouse gas and the major component of natural gas. Given the abundance of natural gas reserves in remote areas, there is great current interest in a scalable bio-based process for the conversion of methane to liquid fuel or other high-value commodity chemicals. MCR holds much promise for use in such a methane bioconversion strategy. However, MCR cannot currently be produced in an active form in a heterologous host, due in large part to the lack of genetic and biochemical information about the production of holo MCR. In an effort to overcome this deficiency, our laboratory elucidated the biosynthetic pathway of the unique nickel-containing coenzyme of MCR, F430. The key step in coenzyme F430 biosynthesis (Cfb) was found to involve an unprecedented reductive cyclization reaction that converts Ni-sirohydrochlorin a , c -diamide to 15,17 3 -seco-F430-17 3 -acid. This remarkable transformation, which involves a 6-electron reduction of the isobacteriochlorin ring system, cyclization of the c -acetamide side chain to form a γ-lactam ring, and the formation of 7 stereocenters, is catalyzed by a primitive homolog of nitrogenase (CfbCD). Nitrogenase is a two-component metalloenzyme that catalyzes the ATP-dependent reduction of dinitrogen to ammonia (nitrogen fixation). Homologs of nitrogenase are also involved in the biosynthesis of the photosynthetic pigments chlorophyll and bacteriochlorophyll. Phylogenetic analysis of the CfbCD complex suggests that it is representative of a more ancient lineage of the nitrogenase superfamily, and a thorough investigation of its structure and function is likely to shed light on the mechanisms and evolution of these important metalloenzymes that catalyze multi-electron redox reactions. Moreover, a detailed understanding of the mechanism of the CfbCD complex may aid in the development of specific inhibitors to help reduce natural greenhouse gas emissions and can be exploited for the heterologous production of MCR for methane bioconversion. Towards these goals, the following Specific Aims will be pursued to determine the: 1) Identity of the CfbCD reaction product. The exact reaction catalyzed by CfbCD, including the number of electrons transferred and whether it involves enzymatic cyclization, is unclear. Several approaches, including reaction stoichiometry measurements, spectroelectrochemistry, and magnetic resonance spectroscopy will be applied to elucidate the structure of the reaction product and establish whether CfbCD is a reductase or reductive cyclase. 2) Structure, conformational dynamics, and oligomerization state changes of CfbCD. Significant insight into the mechanism and allosteric regulation of CfbCD can be obtained by assessing changes in the structure and dynamics of the complex during the catalytic cycle. To accomplish this, a combination of size-exclusion chromatography, hydrogen-deuterium exchange mass spectrometry, molecular dynamics simulations, and high-resolution structural methods will be employed. 3) Source, order, and stereochemistry of proton additions during CfbCD catalysis. Details regarding the order and stereochemistry of proton additions during the CfbCD reaction will be uncovered using a combined spectroscopic and computational approach. Complementary mechanistic studies employing site-directed mutagenesis and substrate analogs will establish the identity of active site acid residues and the possible involvement of substrate-assisted catalysis during the CfbCD reaction.
09 BIOMASS FUELS↗
Effective viscosities in a hydrodynamically expanding boost-invariant QCD plasma
Background: The near-equilibrium properties of a QCD plasma can be encoded into transport coefficients such as bulk and shear viscosity. In QCD, the ratio of these transport coefficients to entropy density, ζ/$\textit{s}$ and η/$\textit{s}$, depends nontrivially on the plasma's temperature. This is unlike in conformal systems where they take constant values such as η/$\textit{s}$ = 1/(4π). Purpose: In this work, we show that in a (0 + 1)D boost-invariant fluid with no transverse expansion, a temperature-dependent ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ can be described by an equivalent effective viscosity $\langleζ/s\rangle_{\text{eff}}$ or $\langleη/s\rangle_{\text{eff}}$. This effective viscosity combines the actual temperature-dependent ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ with the temperature profile of the fluid. Further, we extend the concept of effective viscosity in systems with transverse expansion and discuss how effective viscosities can be used to identify families of ζ/$\textit{s(T)}$ and η /$\textit{s(T)}$ that lead to similar hydrodynamic evolution. Methods: The Navier-Stokes relativistic hydrodynamic equations are used to provide a first definition of effective viscosity, in (0 + 1)D and (1 + 1)D. In the (0 + 1)D case, the analysis is extended to Israel-Stewart-type second-order hydrodynamics to clarify the effect of higher-order hydrodynamics corrections on the effective viscosity. Results: In a boost-invariant fluid with no transverse expansion [(0 + 1)D], the effective viscosity is expressed as a simple integral of ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ over temperature, with a weight determined by the speed of sound of the fluid. The result is general for any equation of state with a moderate temperature dependence of the speed of sound, including the QCD equation of state. This definition of effective viscosity can be used to identify infinite families of ζ/$\textit{s(T)}$ or η/$\textit{s(T)}$ that produce essentially indistinguishable temperature profiles. In a boost-invariant cylindrical system [(1 + 1)D], a similar definition of effective viscosity is obtained in terms of characteristic trajectories in time and transverse direction. This leads to an infinite number of constraints on an infinite functional space for ζ/$\textit{s(T)}$ and η/$\textit{s(T)}$. Realistic examples are presented by using a finite number of constraints on a finite functional space. Conclusions: The definition of effective viscosity in a (0 + 1)D system clarifies how infinite families of ζ/$\textit{s(T)}$ and η/$\textit{s(T)}$ can result in nearly identical hydrodynamic temperature profiles. By extending the study to a boost-invariant cylindrical [(1 + 1)D] fluid, we identify an approximate but more general definition of effective viscosity that highlights the potential and limits of the concept of effective viscosity in fluids with limited symmetries.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Superadditivity at large charge
The weak gravity conjecture has been invoked to conjecture that the dimensions of charged operators in a CFT should obey a superadditivity relation (sometimes referred to as convexity). In this paper, we study superadditivity of the operator spectrum in theories expanded about the semi-classical saddle point that dominates correlators of large charge operators. We explore this in two contexts. The first is a model with two scalar fields that carry different charges, at a non-trivial Wilson-Fisher fixed point. A careful analysis of the semi-classics for this two field model demonstrates that ‘quantum’ violations of superadditivity (those not forbidden by the conjecture) persist in the large charge regime. We then turn to study the general properties of CFTs at large charge as bottom-up EFTs. By a trial and error procedure we come up with a seemingly consistent family of examples violating the conjecture. In so doing the presence of a genuine dilaton field appears necessary. On the one hand our result demonstrates that the superadditivity conjecture cannot be proven purely on the basis of a bottom-up analysis. On the other hand, the need for a dilaton, with the corresponding infinite fine tuning, indicates the conjecture-violating EFTs are unlikely to be UV completable.
effective field theories↗
Deciphering the Cofilin Oligomers via Intermolecular Disulfide Bond Formation: A Coarse-Grained Molecular Dynamics Approach to Understanding Cofilin’s Regulation on Actin Filaments
Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experimental work suggests that cofilin also forms functionally distinct oligomers through thiol post-translational modification (PTM) that encourages actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. Here, we also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol post-translational modification cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Fourfold alkyl wrapping of a copper(II) porphyrin thwarts macrocycle π–π stacking in a compact supramolecular package
Porphyrins are valuable constituents in optoelectronic, catalytic, and other applications, yet control of intermolecular π–π stacking is invariably essential to attain the desired properties. Superstructures built onto the porphyrin, often via meso -aryl groups, can afford facial encumbrance that suppresses π–π stacking, although some molecular designs have provided insufficient facial coverage and many have entailed cumbersome syntheses. In this study, a copper(II) porphyrin bearing four meso substituents, namely, {10,20-bis[2,6-bis(octyloxy)phenyl]-5,15-dibromoporphinato}copper(II), [Cu(C 64 H 82 Br 2 N 4 O 4 )], was prepared by metalation of the corresponding free-base porphyrin and was characterized by single-crystal X-ray diffraction. The crystal structure reveals a dihedral angle of 111.1 (2)° for the plane of the meso -aryl group relative to the plane of the porphyrin, with both aryl groups tilted in the same direction. Each of the four octyloxy groups exhibits a gauche conformation for the –OCH 2 CH 2 – unit but is extended with four or five anti (–CH 2 CH 2 –/H) conformations thereafter, causing each octyl group to span the dimension of the macrocycle. In a global frame of reference where the two Br atoms define the north/south poles and the two aryl groups are at antipodes on the equator, two octyl groups of one aryl unit project over the northern hemisphere (covering pyrroles A and B ), whereas those of the other aryl unit project over the southern hemisphere (covering pyrroles C and D ). Together, the four octyl groups ensheath the two faces of the porphyrin in a self-wrapped assembly. The closest approach of the Cu atom to an octyl methylene C atom (position 6) is 3.5817 (18) Å, the mean separations of neighboring porphyrin planes are 8.059 (4) and 4.693 (8) Å along the a and c axes, respectively, and the center-to-center distances between the Cu atoms of neighboring porphyrins are 10.2725 (4), 12.2540 (6), and 12.7472 (6) Å along the a , b , and c axes, respectively. The Hirshfeld surface analysis and two-dimensional (2D) fingerprint plots provide information concerning contact interactions in the supramolecular assembly of the solid crystal.
Chemistry↗
Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure
The reaction mechanism of biomass decomposition by xylanases remains the subject of debate. Here, to clarify the mechanism, we investigated the glycosylation step of GH11 xylanase, an enzyme that catalyzes the hydrolysis of lignocellulosic hemicellulose (xylan). Making use of a recent neutron crystal structure, which revealed the protonation states of relevant residues, we used ab initio quantum mechanics/molecular mechanics (QM/MM) calculations to determine the detailed reaction mechanism of the glycosylation step. In particular, our focus is on the controversial question of whether or not an oxocarbenium ion intermediate is formed on the reaction pathway. The calculations support the validity of a basic retaining mechanism within a double-displacement scheme. The estimated free energy barrier of this reaction is ~18 kcal/mol with QM/MM-CCSD(T)/6-31(+)G**//MP2/6-31+G**/AMBER calculations, and the rate-determining step of the glycosylation is scission of the glycosidic bond after proton transfer from the acidic Glu177. The estimated lifetime of the oxocarbenium ion intermediate (on the order of tens of ps) and the secondary kinetic isotope effect suggest that there is no accumulation of this intermediate on the reaction path, although the intermediate can be transiently formed. In the enzyme–substrate (ES) complex, the carbohydrate structure of the xylose residue at the -1 subsite has a rather distorted (skewed) geometry, and this xylose unit at the active site has an apparent half-chair conformation when the oxocarbenium ion intermediate is formed. The major catalytic role of the protein environment is to orient residues that take part in the initial proton transfer. Because of a fine alignment of catalytic residues, the enzyme can accelerate the glycosylation reaction without paying a reorganization energy penalty.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Non-Gaussianities in collider energy flux
The microscopic dynamics of particle collisions is imprinted into the statistical properties of asymptotic energy flux, much like the dynamics of inflation is imprinted into the cosmic microwave background. This energy flux is characterized by correlation functions < E(n → 1 )…E(n → k ) > of energy flow operators E(n → ). There has been significant recent progress in studying energy flux, including the calculation of multi-point correlation functions and their direct measurement inside high-energy jets at the Large Hadron Collider (LHC). In this paper, we build on these advances by defining a notion of “celestial non-gaussianity” as a ratio of the three-point function to a product of two-point functions. We show that this celestial non-gaussianity is under perturbative control within jets at the LHC, allowing us to cleanly access the non-gaussian interactions of quarks and gluons. We find good agreement between perturbative calculations of the non-gaussianity and a charged-particle-based analysis using CMS Open Data, and we observe a strong non-gaussianity peaked in the “flattened triangle” regime. The ability to robustly study three-point correlations is a significant step in advancing our understanding of jet substructure at the LHC. We anticipate that the celestial non-gaussianity, and its generalizations, will play an important role in the development of higher-order parton showers simulations and in the hunt for ever more subtle signals of potential new physics within jets.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
The Gross-Neveu-Yukawa archipelago
We perform a bootstrap analysis of a mixed system of four-point functions of bosonic and fermionic operators in parity-preserving 3d CFTs with O(N) global symmetry. Our results provide rigorous bounds on the scaling dimensions of the O(N)-symmetric Gross-Neveu-Yukawa (GNY) fixed points, constraining these theories to live in isolated islands in the space of CFT data. We focus on the cases N = 1, 2, 4, 8, which have applications to phase transitions in condensed matter systems, and compare our bounds to previous analytical and numerical results.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N -1-Phenylethyl Sidechains
N-substituted glycines (polypeptoids) containing chiral hydrophobic sidechains are known to fold into biomimetic alpha helices. These helix formers often produce conformationally heterogeneous structures and are difficult to characterize at a sub-nanometer resolution. Previously, peptoid N-1-phenylethyl (S)-enantiomer sidechains (Nspe) were inferred from various experiments to form right-handed helices and (R)-enantiomers (Nrpe), left-handed helices. Prior computational work for N(s/r)pe oligomers has struggled to reproduce this trend. Herein, quantum mechanics calculations and molecular dynamics simulations are used to understand the origins of this discrepancy. Results from DFT and molecular mechanics calculations on a variety of Nspe and Nrpe oligomers as a function of chain length are in agreement, showing that Nspe and Nrpe prefer left- and right-handed helices, respectively. Additional metadynamics simulations are used to study Nrpe and Nspe oligomers folding in water. These results show that the free-energy driving forces for assembly into a helical backbone configuration are very small (within ~k B T). Lastly, we compare DFT calculations for other experimentally characterized peptoid sidechains, N(r/s)sb, N(r/s)tbe, and N(r/s)npe. In this analysis, we show that peptoid sidechains determined to be more robust experimentally (tbe and npe) have helical preferences opposite the trend seen in less robust assemblies formed by N(r/s)pe and N(r/s)sb chemistries. Furthermore, the more robust tbe and nnpe favor the (S)-enantiomer to right-handed and the (R)-enantiomers to left-handed helices.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A natural mutation between SARS-CoV-2 and SARS-CoV determines neutralization by a cross-reactive antibody
Epitopes that are conserved among SARS-like coronaviruses are attractive targets for design of cross-reactive vaccines and therapeutics. CR3022 is a SARS-CoV neutralizing antibody to a highly conserved epitope on the receptor binding domain (RBD) on the spike protein that is able to cross-react with SARS-CoV-2, but with lower affinity. Using x-ray crystallography, mutagenesis, and binding experiments, we illustrate that of four amino acid differences in the CR3022 epitope between SARS-CoV-2 and SARS-CoV, a single mutation P384A fully determines the affinity difference. CR3022 does not neutralize SARS-CoV-2, but the increased affinity to SARS-CoV-2 P384A mutant now enables neutralization with a similar potency to SARS-CoV. We further investigated CR3022 interaction with the SARS-CoV spike protein by negative-stain EM and cryo-EM. Three CR3022 Fabs bind per trimer with the RBD observed in different up-conformations due to considerable flexibility of the RBD. In one of these conformations, quaternary interactions are made by CR3022 to the N-terminal domain (NTD) of an adjacent subunit. Overall, this study provides insights into antigenic variation and potential cross-neutralizing epitopes on SARS-like viruses.
59 BASIC BIOLOGICAL SCIENCES↗
Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong
Abstract Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare, and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among 5 locations and found they achieve close to the same levels of accuracy as Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also implemented a method of uncertainty quantification called conformalized quantile regression that we demonstrate has similar patterns of sensitivity to model misspecification as Bayesian highest posterior density (HPD) and greatly overlap with HPDs, but have lower precision (more conservative). Finally, we trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of region-specific epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster after training. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models.
Evolutionary Biology↗
Star Block Copolymers at Homopolymer Interfaces: Conformation and Compatibilization
Star block copolymers (s-BCPs), comprised of multiple linear diblock copolymers joined at a central point, are shown to segregate to the interface between two immiscible homopolymers that are identical to the blocks of the s-BCPs. The s-BCPs undergo a configurational transition at the interface, with different blocks of copolymers being embedded in their respective homopolymers, thereby bridging the interface and promoting adhesion. A series of 4-arm s-BCPs were synthesized with hydrogenated or deuterated polystyrene (PS/dPS) as the core block and poly(2-vinylpyridine) (P2VP) as the corona block, which was directly placed at the interface between the two homopolymers. Neutron reflectivity (NR) was used to determine the concentration profiles of the PS homopolymer, s-BCP core blocks, and P2VP total segments under equilibrium. The investigation varies the molecular weight (MW) and the total number of s-BCPs at the interface. Self-consistent-field theory (SCFT) was also employed to calculate the concentration profiles of the components at the interface, which were in excellent agreement with experimental results. The NR showed that the interfacial width between the homopolymers increased with the increasing number of s-BCPs at the interface up to a saturation limit. Beyond this limit, additional s-BCPs were released into the corona-miscible phase as unimolecular micelles. For a comparable interlayer thickness of s-BCPs at the interface, lower MW s-BCPs generated a broader interface. SCFT analysis suggested that, at the same packing density, the arms of the low MW s-BCPs align more parallel to the interface, while the arms of high MW s-BCPs adopt a more normal orientation, like their linear BCP counterparts. Furthermore, it was also observed that the core blocks, constrained by the junction points, were oriented more parallel and closer to the interface than the corona blocks. The phase behavior of the polymer blends revealed that s-BCP additives can efficiently reduce the domain size, with the low MW yielding smaller domain sizes due to the greater reduction in the interfacial energy and the high MW arresting phase separation due to their higher binding energy and a jamming of the interfacial assemblies. Asymmetric double cantilever beam (ADCB) tests demonstrated that s-BCPs promoted adhesion more efficiently than their linear BCP counterparts due to stronger binding energy per molecule, suggesting a more efficient compatibilizer for polymer upcycling. In conclusion, the results from these studies provide fundamental insights into the assembly of s-BCPs at homopolymer interfaces, the reduction of domain size, and promotion of adhesion, providing a strategy for the use of s-BCPs as stealth surfactants and universal compatibilizers.
interface↗
Coupling sensor to enzyme in the voltage sensing phosphatase
Voltage-sensing phosphatases (VSPs) dephosphorylate phosphoinositide (PIP) signaling lipids in response to membrane depolarization. VSPs possess an S4-containing voltage sensor domain (VSD), resembling that of voltage-gated cation channels, and a lipid phosphatase domain (PD). The mechanism by which voltage turns on enzyme activity is unclear. Structural analysis and modeling suggest several sites of VSD-PD interaction that could couple voltage sensing to catalysis. Voltage clamp fluorometry reveals voltage-driven rearrangements in three sites implicated earlier in enzyme activation—the VSD-PD linker, gating loop and R loop—as well as the N-terminal domain, which has not yet been explored. N-terminus mutations perturb both rearrangements in the other segments and enzyme activity. Our results provide a model for a dynamic assembly by which S4 controls the catalytic site.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
String-based parametrization of nucleon GPDs at any skewness: A comparison to lattice QCD
We introduce a string-based parametrization for nucleon quark and gluon generalized parton distributions (GPDs) valid at all skewness values. The conformal moments of the GPDs are expressed as sums of the spin-j nucleon A-form factor and the skewness-dependent spin-j nucleon D-form factor. This representation, which fulfills the polynomiality condition (due to Lorentz invariance) and does not rely on model-specific assumptions, is derived from t-channel string exchanges in anti-de Sitter spaces. The spin-j nucleon D-form factor is closely related to the spin-j nucleon A-form factor. We use the Mellin moments from empirical parton distributions to model the spin-j nucleon A-form factors. Using only five Regge slope parameters, fixed from the electromagnetic and gravitational form factors, our string-based parametrization generates accurate singlet, nonsinglet, isovector, and flavor-separated nucleon quark GPDs, along with symmetric nucleon gluon GPDs from their Mellin-Barnes integral representations. Our isovector nucleon quark GPD is in agreement with existing lattice data. Our string-based parametrization should facilitate the empirical extraction and global analysis of nucleon GPDs in exclusive processes, bypassing the deconvolution challenge.
Electron-ion collisions↗
Tailoring the Interfacial Interactions of Porous Polymer Membranes to Accelerate Atomic Layer Deposition: The Latent Path to Antifouling Membranes
Atomic layer deposition (ALD) is a powerful strategy to engineer hybrid organic-inorganic membranes with emergent functionalities. The combination of atomic-level thickness control, a wide materials palette, and unprecedented conformality allows the physiochemical properties (e.g., hydrophilicity) of mesoporous polymer membranes to be precisely tuned. The nucleation of ALD material growth on polymer surfaces relies on Lewis acid-base interactions and remains an overlooked motif with tremendous potential to accelerate ALD nucleation and growth. Strategies to enhance these interactions could enable desirable properties such as antifouling behavior to be imparted on inert polymer surfaces that lack the necessary functional groups for ALD nucleation. Here, in this study, we demonstrate that the reactivity of polyacrylonitrile (PAN) membranes toward ALD metal oxide (MO) precursors with Lewis acid characteristics is enhanced by introducing strong Lewis base functional groups (amidoxime: Am) on the PAN backbone (Am-PAN). The resulting Lewis acid-base interactions accelerate the MO nucleation in Am-PAN and reduce the number of deposition cycles required to achieve hydrophilicity compared with the untreated PAN membrane. Unveiling the reaction mechanism, in situ Fourier transform infrared (FTIR) spectroscopy measurements established enhanced interaction dynamics between the ALD MO precursors and the Am-PAN membrane, unlike the PAN membrane. Spectroscopic ellipsometry and thermogravimetric analysis measurements revealed higher MO loadings in Am-PAN membranes compared to PAN membranes for the same number of ALD cycles. We found that strong Lewis acid-base interactions accelerated the ALD for a range of materials including Al 2 O 3 , TiO 2 , SnO 2 , and ZnO. More broadly, our work demonstrates that tailoring metal-precursor-polymer interactions is a powerful strategy to accelerate and modulate the ALD. We used this design strategy to fabricate Al 2 O 3 -Am-PAN hybrid membranes that showed 2-fold higher antifouling capability compared to pristine PAN membranes prepared with an equivalent number of Al 2 O 3 ALD cycles. Our approach expands the scope of design options for fouling-resistant porous hybrid inorganic-organic membranes and may ultimately reduce the operational costs of water treatment.
36 MATERIALS SCIENCE↗
Experimental and analytical study of the hydrodynamic and single and two-phase convective heat transfer performance of flexible PDMS microchannels with micropillar arrays
Various copper and silicon based thermal management systems are used in the cooling of electronics. However, the rigid nature of these materials along with their high thermal and electrical conductivity pose a difficulty in developing direct contact embedded flexible cooling systems that can offer robust cooling performance. The low density, thermal stability, chemical inertness, and electrical insulation of Polydimethylsiloxane (PDMS) make it an ideal material to develop lightweight direct contact thermal management systems for electronics. Its ease of fabrication with tunable flexibility provides the opportunity to go beyond traditional electronics and develop advanced active and passive thermal management systems for a wide–range of applications in foldable and wearable electronics, liquid cooling garments, microgravity, and electric motors. In this study, a flexible PDMS based microchannel with micropillar arrays, which enhance the thermal performance of the device through capillary-assisted flow, has been developed. The hydrodynamic and convection heat transfer performance of three PDMS wick pillar geometries, ranging from a porosity of 0.8–0.91, are investigated and compared under single-phase and two-phase conditions. Dielectric coolant FC-3283 is employed and permeability measurements are made for mass fluxes ranging from 53 kg/m 2 s to 369 kg/m 2 s. Given its conformability, the device demonstrates a deviation from Darcy’s Law, within the laminar regime, with an increasing permeability with mass flux at the rate of ~0.5–0.8 Darcy/(kg/m 2 s). A semi-analytical model has been developed and reported to quantify the conformability of the device. The heat transfer performance is experimentally evaluated using the same dielectric fluid for mass flux ranging from 105 kg/m 2 s to 420 kg/m 2 s with heat fluxes ranging from 1.5 W/cm 2 to 16 W/cm 2 . Heat transfer coefficients of up to 7000 W/m 2 K are observed, which are comparable to copper and silicon microchannels. The effect of porosity on the single phase thermal performance has been evaluated against the pumping power to provide a basis for thermal management system design. Finally, high-speed imaging is performed to study the two-phase flow characteristics to provide insight into the vapor formation and removal.
42 ENGINEERING↗
Findings on Subtask 3.1 - Bakken Rich Gas Enhanced Oil Recovery Project
Total in-place oil for the Bakken petroleum system (BPS) (which includes the Bakken and Three Forks Formations) has been estimated to be 600 billion barrels (bbl). However, BPS wells have decline rates as high as 85% over the first 3 years of their lives, and primary recovery factors typically range from 3% to 10% of original oil in place. Given the low initial recovery rates, even small incremental productivity improvements could dramatically increase technically recoverable oil in the BPS. One potential solution is enhanced oil recovery (EOR) using gas injection, such as carbon dioxide (CO2) or hydrocarbon (HC) gases. While commonly used in conventional reservoirs, CO2 EOR in unconventional tight oil reservoirs has been limited to pilot tests. EOR using rich gas (mixture of methane, ethane, and propane) has also been employed in numerous pilots in several unconventional plays and has recently been successfully applied in the Eagle Ford play. If successful, large-scale gas-based EOR in the BPS could dramatically increase oil productivity and recovery factors and extend the life of the play for decades. While CO2 may be a technically suitable working fluid for EOR in the BPS, supplies are limited and costs for using CO2 in EOR pilots are prohibitively high. Meanwhile, produced gas flaring has presented challenges for BPS operators in North Dakota. Analysis conducted by the North Dakota Pipeline Authority indicates that the current gas-gathering infrastructure in North Dakota is insufficient to accommodate all of the associated gas that is produced from the BPS. The geographically isolated location of North Dakota relative to large natural gas markets, combined with suppressed natural gas prices, has made it economically challenging for industry to invest capital in expanding gas-gathering infrastructure in the state. These circumstances led to a research program conducted by the Energy & Environmental Research Center (EERC) in partnership with Liberty Resources Management Company LLC (LR) to examine the potential to use rich gas injection for EOR and mitigate flaring. A rich gas EOR pilot test was designed and executed by LR at its Stomping Horse development area in Williams County, North Dakota. From July 2018 through May 2019, a total of 160 million standard cubic feet (MMscf) of rich produced gas was injected into the BPS using five different wells in a sequential injection strategy. LR’s Leon–Gohrick drill spacing unit (DSU) was used as the test site. Regulatory oversight was provided by the North Dakota Industrial Commission (NDIC). Technical support was provided by the EERC through a series of laboratory, modeling, and field-based activities, and additional post-pilot research activities incorporated learnings from the test, developed new laboratory data, improved fracture modeling methods, and developed machine learning and big data analytics. The results from the Stomping Horse rich gas EOR pilot activities indicate that developing an effective, economical EOR approach for the BPS will require more field tests. Another key lesson learned from the Stomping Horse tests is that detailed pre- and posttest data on reservoir conditions and fluids production are essential. Robust reservoir characterization provides information that is crucial to creating realistic geomodels and conducting valid dynamic simulations of potential EOR scenarios. A detailed understanding of the completions and production history of offset wells is also necessary for valid test result interpretations. This knowledge is essential to designing the operational parameters of injectivity tests and interpreting the results. A conformance control strategy is also essential to success. Laboratory-based examinations of rich gas interactions with reservoir fluids and rocks were conducted, with an emphasis on determining the ability to mobilize oil in the tight reservoir rocks and shales of the BPS. Injection fluid composition was shown to have a positive impact on reducing reservoir oil minimum miscibility pressure (MMP), reducing interfacial tension (IFT), and altering wettability. IFT and contact angle measurements demonstrated that wettability can be altered in the presence of rich gas, suggesting the potential to improve oil recovery. Iterative modeling of surface infrastructure and reservoir performance using data generated by the various project activities was conducted. A geologic model of the Stomping Horse area was built; history-matched oil, gas, and water production was used in simulations of various EOR scenarios. Early programmatic modeling results were used to support LR’s design and operation of the EOR pilot and to provide insight regarding optimization of future commercial-scale BPS EOR design and operations. Post-pilot modeling focused on alternative methods of understanding complex fracture networks and accelerating simulation time. These led to improved simulation run times and provide excellent history-matching results. Several of these iterative models were used as the bases for developing algorithms into machine learning and big data analytics. History matching in reservoir simulation is time-consuming and computer processing-intensive. Machine learning algorithms were created, and an automated history-matching tool was developed. A large set of synthetic reservoir simulations were created to generate well responses (oil, gas, and water production, well bottomhole pressure [BHP], and tracer or propane breakthrough) for a set of EOR operating parameters that included offset well status (open or closed), injectate (rich gas or propane), injection rate, and injection well BHP. A user interface was developed to provide real-time visualization. Machine learning-based models were developed to provide rapid forecasting of well performance given a set of user-defined EOR operating parameters. These predictive models allow the user to modify the offset well status, injection rate, and injection well BHP and rapidly forecast future production performance. The combination of real-time visualization tools with real-time forecasting tools provides a framework for real-time control—operational changes that the EOR site operator can enact (e.g., changing gas injection rates) to affect the observed performance and potentially improve the EOR outcome. There is great reason to be optimistic about the future of EOR in the Bakken. The results of the laboratory studies suggest significant potential for high rates of oil mobilization using produced field gas injection under the right conditions. The results of the lab studies, combined with rigorous statistical analysis of well production data and associated modeling efforts, confirm the notion that fluid mobility within the reservoir is controlled by fractures. As more knowledge is gained about the nature and distribution of fracture networks in the Bakken, the industry will be in a better position to predict and, ultimately, influence fluid mobility. New field tests are necessary to develop a more complete understanding of those conditions. Thoughtful and creatively engineered field tests within a well-characterized geologic setting will yield the fundamental knowledge needed to take Bakken oil production to the next level. This subtask was cofunded through the EERC–U.S. Department of Energy Joint Program on Research and Development for Fossil Energy-Related Resources Cooperative Agreement No. DE-FE0024233. Nonfederal funding was provided by the North Dakota Industrial Commission’s Oil and Gas Research Program and Computer Modelling Group.
04 OIL SHALES AND TAR SANDS↗