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At least 451 records · Page 25

Improved Depiction Of Computed Unsteady Flows

PLOT4D and STREAKER programs increase ease of production and utility of animated depictions of unsteady flows simulated numerically by advanced computational fluid dynamics. Programs developed to maximize information displayed while minimizing amount stored. PLOT4D, an extended version of PLOT3D, used to depict steady three-dimensional flows, incorporates features making it more computationally efficient than to visualize unsteady flow as succession of steady flows, animating frame by frame. PLOT4D postprocesses numerical output of fluid-dynamical computation into maps of flow quantities on two-coordinate surfaces depicting cut through flow field or conform to body surface. STREAKER generates streaklines, close approximations of patterns traced by streams of dye or smoke released into simulated flows. Streaklines defined via spatial succession of endpoints of pathlines of massless particles released into flow. STREAKER computes endpoints by fourth-order Runge-Kutta integration of velocity vectors.

Smith, Merritt H.↗

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↗

Data-driven equation-free dynamics applied to many-protein complexes: The microtubule tip relaxation

Microtubules (MTs) constitute the largest components of the eukaryotic cytoskeleton and play crucial roles in various cellular processes, including mitosis and intracellular transport. The property allowing MTs to cater to such diverse roles is attributed to dynamic instability, which is coupled to the hydrolysis of GTP (guanosine-5'-triphosphate) to GDP (guanosine-5'-diphosphate) within the β-tubulin monomers. Understanding the equilibrium dynamics and the structural features of both GDP- and GTP-complexed MT tips, especially at an all-atom level, remains challenging for both experimental and computational methods because of their dynamic nature and the prohibitive computational demands of simulating large, many-protein systems. This study employs the “equation-free” multiscale computational method to accelerate the relaxation of all-atom simulations of MT tips toward their putative equilibrium conformation. Using large MT lattice systems (14 protofilaments × 8 heterodimers) comprising ~21-38 million atoms, we applied this multiscale approach to leapfrog through time and nearly double the computational efficiency in realizing relaxed all-atom conformations of GDP- and GTP-complexed MT tips. Commencing from an initial 4 μs unbiased all-atom simulation, we interleave coarse projective “equation-free” jumps with short bursts of all-atom molecular dynamics simulation to realize an additional effective simulation time of 1.875 μs. Our 5.875 μs of effective simulation trajectories for each system expose the subtle yet essential differences in the structures of MT tips as a function of whether β-tubulin monomer is complexed with GDP or GTP, as well as the lateral interactions within the MT tip, offering a refined understanding of features underlying MT dynamic instability. Furthermore, the approach presents a robust and generalizable framework for future explorations of large biomolecular systems at atomic resolution.

Wu, Jiangbo [University of Chicago, IL (United Sta↗

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2

SARS-CoV and SARS-CoV-2 bind to the human ACE2 receptor in practically identical conformations, although several residues of the receptor-binding domain (RBD) differ between them. Herein, we have used molecular dynamics (MD) simulations, machine learning (ML), and free-energy perturbation (FEP) calculations to elucidate the differences in binding by the two viruses. Although only subtle differences were observed from the initial MD simulations of the two RBD–ACE2 complexes, ML identified the individual residues with the most distinctive ACE2 interactions, many of which have been highlighted in previous experimental studies. FEP calculations quantified the corresponding differences in binding free energies to ACE2, and examination of MD trajectories provided structural explanations for these differences. Lastly, the energetics of emerging SARS-CoV-2 mutations were studied, showing that the affinity of the RBD for ACE2 is increased by N501Y and E484K mutations but is slightly decreased by K417N.

60 APPLIED LIFE SCIENCES↗

Critical role of structural order in bipolar redox-active molecules for organic redox flow batteries

Bipolar redox-active molecules (BRMs) have been suggested as a means to address crossover related issues in all-organic redox flow batteries (RFBs). In such species, electron donors (anolytes) and electron acceptors (catholytes) are linked by a chain, and the same chemical composition is used in both anode and cathode compartments to reduce chemical gradients and unbalanced ion transport. The resultant RFBs resemble the aqueous vanadium RFBs, but offer greater design flexibility and potentially more favorable electrochemical and physicochemical properties. Yet the complex trade-offs in these properties have been a complication. Here we developed a fundamental rubric to uncover the likely origins in the performance metrics of these BRMs that are salient for their use in RFBs. Methylene linked phenothiazine and phthalimide moieties were employed as model BRMs and variations in their properties and molecular conformations were evaluated by systematically varying the methylene linker. Our results revealed that even minimalistic changes in the linker length resulted in dramatic oscillations in the solubility and stability. Using crystallography, quantum chemistry, and molecular dynamics, we clarify that the seemingly fluctuating behavior is due to (1) the inter- and intra-molecular charge transfer between the donor and acceptor through bond or/and through space; (2) the formation of distinctive packing/clustering motifs. Both interactions are strongly dependent on the molecular conformation. As these structural factors modify the electronic structure of both electroactive functional groups and do not change monotonically, the structure–property response in BRMs is often complex. Finally, accordingly, these behaviors need to be taken into account in developing BRMs and knowledge of these structural factors will allow the more rational design of BRMs for grid-scale energy storage.

25 ENERGY STORAGE↗

Scaling Theory of Neutral Sequence-Specific Polyampholytes

The primary sequence of charged monomers in a polyampholyte has a profound effect on its conformational properties. In this work, theory and simulations are used to predict how the sequence influences the single-chain behavior of globally neutral polyampholytes (PAs) under salt-free conditions. We consider PAs with Markov statistics of charges, where charge “blockiness” is defined by the correlation λ along the chain. These PAs cover a wide spectrum of primary sequences ranging from alternating (λ = –1) to ideally random (λ = 0) to diblock (λ → 1). In a theta solvent, sufficiently long PAs of any primary sequence form globules, but their internal structure, as well as the position and sharpness of the coil–globule transition, crucially depends on λ. Further, using scaling arguments, we demonstrate that the excess charge of the globule correlation volume (blob) increases with increasing λ, thereby inducing stronger Coulomb attractions between neighboring blobs of opposite charge and leading to higher density PA globules. Scaling predictions are supported by the results of the random phase approximation (RPA) and coarse-grained molecular dynamics simulations. A generalization to good and poor solvents is presented that enables the construction of the resulting scaling diagram of PA conformations in terms of solvent quality and charge blockiness, thereby providing a comprehensive molecular understanding of the role of the PA primary sequence in the chain structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Visualizing group II intron dynamics between the first and second steps of splicing

Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5’-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Light scalar meson and decay constant in SU(3) gauge theory with eight dynamical flavors

The SU(3) gauge theory with N f = 8 nearly massless Dirac fermions has long been of theoretical and phenomenological interest due to the near-conformality arising from its proximity to the conformal window. One particularly interesting feature is the emergence of a relatively light, stable flavor-singlet scalar meson σ ( J P C = 0 + + ) in contrast to the N f = 2 theory QCD. In this work, we study the finite-volume dependence of the σ meson correlation function computed in lattice gauge theory and determine the σ meson mass and decay constant extrapolated to the infinite-volume limit. We also determine the infinite-volume mass and decay constant of the flavor-nonsinglet scalar meson a 0 . Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗

The Influence of Alkyl Spacers and Molecular Weight on the Charge Transport and Storage Properties of Oxy‐Bithiophene‐Based Conjugated Polymers

Conjugated polymers (CPs) with polar side chains can conduct electronic and ionic charges simultaneously, making them promising for bioelectronics, electrocatalysis and energy storage. Recent work showed that adding alkyl spacers between CP backbones and polar side chains improved electronic charge carrier mobility, reduced swelling and enhanced stability, without compromising ion transport. However, how alkyl spacers impact polymer backbone conformation and, subsequently, electronic properties remain unclear. In this work, we design two oxy-bithiophene-based CP series, each featuring progressively extended alkyl spacer lengths and two distinct molecular weight (MW) distributions. Using operando characterisations, we evaluate the (spectro)electrochemical and swelling properties of the polymer thin films, and their performance in organic field-effect transistors and organic electrochemical transistors. Surprisingly, alkyl spacers negatively impact the hole mobility of our polymers, with higher MW amplifying this effect. Using molecular dynamics simulations, we show that it is thermodynamically favourable for adjacent non-polar alkyl spacers to aggregate in polar electrolytes, leading to backbone twisting. Further spectroscopic measurements corroborate this prediction. Our findings demonstrate the active interactions between side chain structure, MW and electrolyte/solvent polarity in influencing polymer performance, underscoring the importance of considering solvation environment effects on polymer conformation when designing new mixed conducting CPs for electrochemical applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sequential polymer infusion into solid substrates (SPISS): Impact of processing on sorbent CO 2 adsorption properties

Solid sorbents made of small amine molecules and polyamines infused into mesoporous substrates are promising materials for CO 2 capture technologies. To date, their preparation is mainly based on wet infusion with focus on increasing amine content by varying the structure of the amine sorbent and designing solid substrates of various pore parameters. Less explored in the field are changes in processing to afford efficient CO 2 sorbents. In this study, branched poly(ethylenimine) (bPEI, M w = 800 Da) alone and blends with linear poly(propylenimine) (LPPI, M n = 6,700 Da) are infused into solid SBA-15 substrates by a method that varies the solution processing called sequential polymer infusion into solid substrates (SPISS). The reference 40 % bPEI-SBA-15 samples are split by two methods: split batch in dry suspension (SBD) and split batch in liquid suspension (SBL). Sequentially, alcoholic 10% of bPEI (non-blends) and 10% of LPPI (blends) solutions are introduced to afford the desired products. Under dry conditions, the resulting 50% bPEI-SBA-15 SBD & SBL sorbents display high CO 2 capacities up to 3.47 mmol CO 2 /g SiO 2 for simulated flue gas (10% CO 2 ) and 2.62 mmol CO 2 /g SiO 2 for direct air capture (DAC, 400 ppm CO 2 ). Under humid DAC conditions the CO 2 performance is further enhanced with an uptake of 4.62 mmol CO 2 /gSiO 2 and amine efficiency of 0.22 mmol CO 2 /mmol N. Subjected to extended temperature swing adsorption kinetic cycling (20 cycles), the SPISS samples display stable working capacities and retain over 70% (blends) and over 90% (non-blends) of their initial 12 h adsorption performance. LPPI is demonstrated to be an effective water sorption limiting agent using dynamic vapor sorption measurements. Solid state NMR techniques reveal important insights into the dynamics of the amine polymers confined into SBA-15 pores, as impacted by processing conditions. The results suggest that the conformation of the polymers is different depending on the processing method, displaying relatively tight (SBD) and loose (SBL) packing. Finally, the simple solution processing approaches presented here show that processing variations may guide the design of solid amine sorbents with desirable properties relevant for integration into CO 2 capture technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Identification and Description of a Silicic Volcaniclastic Layer in Gale Crater, Mars, Using Active Neutron Interrogation

The Dynamic Albedo of Neutrons instrument aboard the Mars Science Laboratory rover, Curiosity, has been used to map a stratigraphically-conformable layer of high-SiO 2 material in Gale crater. Previous work has shown this material contains tridymite, a high-temperature/low-pressure felsic mineral, interpreted to have a volcanic source rock. We describe several characteristics including orientation, extent, hydration, and geochemistry, consistent with a volcaniclastic material conformably deposited within a lacustrine mudstone succession. Relationships with widely dispersed alteration features and orbital detections of hydrated SiO 2 suggest that this high-SiO 2 layer extends at least 17 km laterally. Mineralogical abundances previously reported for this high-SiO 2 material indicated that hydrous species were restricted to the amorphous (non-crystalline) fraction, which is dominated by SiO2. The low mean bulk hydration of this high-SiO 2 layer (1.85 ± 0.13 wt.% water-equivalent hydrogen) is consistent with silicic glass in addition to opal-A and opal- CT. Persistent volcanic glass and tridymite in addition to opal in an ancient sedimentary unit indicates that the conversion to more ordered forms of crystalline SiO 2 has not proceeded to completion and that this material has had only limited exposure to water since it originally erupted, despite having been transported in a uviolacustrine system. Our results, including the conformable nature, large areal extent, and presence of vol- canic glass, indicate that this high-SiO 2 material is derived from the product of evolved magma on Mars. This is the rst identi cation of a silicic volcaniclastic layer on another planet, and has important implications for magma evolution mechanisms on single-plate planets.

58 GEOSCIENCES↗

Improving resolution and resolvability of single-particle cryoEM structures using Gaussian mixture models

Cryogenic electron microscopy is widely used in structural biology, but its resolution is often limited by the dynamics of the macromolecule. Here, we developed a refinement protocol based on Gaussian mixture models that integrates particle orientation and conformation estimation, and improves the alignment for flexible domains of protein structures. We demonstrated this protocol on multiple datasets, resulting in improved resolution and resolvability, locally and globally, by visual and quantitative measures.

59 BASIC BIOLOGICAL SCIENCES↗

Stoichiometry of the large conductance bacterial mechanosensitive channel of E. coli. A biochemical study

MscL, a 15 kDa transmembrane protein, is the only component involved in the formation of a 3 nS channel in the inner membrane of Escherichia coli that opens in response to mechanical or osmotic stress. While previous data had suggested that the functional MscL complex might be a hexamer, a recent crystallographic study of the MscL homologue from M. tuberculosis reveals a pentameric structure. The present work further examines the stoichiometry of the E. coli MscL using a variety of biochemical approaches. Detergent-purified 6His-MscL in solution and MscL in the membrane could be chemically crosslinked with the products displaying ladderlike patterns on SDS gels. Three crosslinking agents (EDC, DMS, and DMA) used at saturating concentrations invariably generated pentamers as the largest product. DSS produced additional bands corresponding to larger complexes although the pentamer band appeared to be the predominant product at high levels of crosslinker. It is not clear whether these extra bands reflect a difference in the crosslinking chemistry of DSS or whether its spacer arm is the longest of those used, or a combination of both facts. For the detergent-solubilized 6His-MscL both sedimentation equilibrium and gel chromatography showed the presence of multiple species. Thus the longer spacer arm could permit both intra- and intercomplex linkages. Nonetheless, the patterns obtained with all agents are consistent with and strongly suggest a pentameric organization for the MscL channel. Expression of MscL as genetically engineered double or triple subunit tandems yields low numbers of functional channels as compared to expressed monomers. The double-tandem assemblies must have an even number of subunits and crosslinking in the membrane confirmed hexamerization. Gel chromatography clearly demonstrated that the channels formed from the double tandems were larger than those formed from WT MscL, consistent with the native channel being pentameric. The observation that both double and triple tandems form channels of normal conductance implies that the pentameric assembly is to some degree independent of the number of subunit repeats in the polypeptide precursor. The channel is thus a pentameric core with the 'extra' subunits left out of the functional complex. From sedimentation equilibrium and size-exclusion chromatography, we also conclude that MscL complexes are not in a dynamic equilibrium with monomers, but are pre-assembled; and thus, their gating properties must result from changes in the conformation of the entire complex induced by the mechanical stress.

NASA Discipline Cell Biology↗

Charge transfer rate constants for the carotenoid-porphyrin-C 60 molecular triad dissolved in tetrahydrofuran: The spin-boson model vs the linearized semiclassical approximation

Charge transfer rate constants were calculated for the carotenoid-porphyrin-C 60 (CPC 60 ) molecular triad dissolved in explicit tetrahydrofuran. The calculation was based on mapping the all-atom anharmonic Hamiltonian of this system onto the spin-boson Hamiltonian. The mapping was based on discretizing the spectral density from the time correlation function of the donor–acceptor potential energy gap, as obtained from all-atom molecular dynamics simulations. Different spin-boson Hamiltonians were constructed for each of the possible transitions between the three excited electronic states in two different triad conformations. The rate constants of three possible transitions were calculated via the quantum-mechanically exact Fermi’s golden rule (FGR), as well as a progression of more approximate expressions that lead to the classical Marcus expression. The advantage of the spin-boson approach is that once the mapping is established, the quantum-mechanically exact FGR and the hierarchy of approximations are known in closed form. The classical Marcus charge transfer rate constants obtained with the spin-boson Hamiltonians were found to reproduce those obtained from all-atom simulations with the linearized semiclassical approximation, thereby confirming the equivalence of the two approaches for this system. Furthermore, within the spin-boson Hamiltonian, we also found that the quantum-mechanically exact FGR rate constants were significantly enhanced compared to the classical Marcus theory rate constants for two out of three transitions in one of the two conformations under consideration. The results confirm that mapping to the spin-boson model can yield accurate predictions for charge transfer rate constants in a system as complex as CPC 60 dissolved in tetrahydrofuran.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Smoothed boundary method for simulating incompressible flow in complex geometries

Simulating flow through porous media with explicit considerations of complex microstructures is very challenging using conventional sharp-interface methods because of the difficulties in generating meshes conformal to complex geometries. In this work, a diffuse interface embedded boundary method known as the Smoothed Boundary Method (SBM) is utilized to facilitate simulations of fluid dynamics involving complex geometries. In diffuse-interface methods, the geometry is described by a domain parameter. The SBM allows the straightforward reformulation of the time-dependent Navier-Stokes equations in terms of this domain parameter, using only algebraic identities. Thus, enforcing the appropriate boundary conditions at the irregular embedded boundary is greatly simplified. Adaptive mesh refinement is used to increase the accuracy of the diffuse interface method by allowing thinner interfacial thickness to be used in the domain parameter. Here, the SBM-formulated Navier-Stokes equations are solved with the Finite Difference Method on refined mesh systems. Sharp-interface Finite Element Method simulations using the commercial software COMSOL on body-conforming meshes are also provided for comparison. Favorable agreement between the two methods is observed. Since it is no longer necessary for the mesh to conform to the complex geometry, the grid system for the SBM simulations can be generated rapidly and without additional manual interventions, making the entire simulation process more expedient.

36 MATERIALS SCIENCE↗

Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: a benchmark Quantum Monte Carlo study

The accurate description of non-covalent interactions is critical for understanding the structure, dynamics, and eventual function of biomolecules. The adenine dimer serves as a benchmark system for computational methods due to its role in nucleic acid structures and its rich conformational landscape. In this study, we employ benchmark diffusion quantum Monte Carlo (DMC) methods to investigate the relative energies and role of electron correlation on a set of adenine dimer conformations generated via a search of the potential energy landscape using the global optimizer algorithm. Relative DMC energies are compared against a wide range of density functional theory (DFT) approximation results. We find that although most of the DFT functionals perform well for low-energy structures, their accuracy varies significantly for higher-energy conformations, including stacked and T-shaped structures. A large fraction of the variation is due to the treatment of the van der Waals interaction. BLYP, B3LYP, and PBE0 significantly improve with added D4 dispersion, while the recent r2SCAN-D4 and ωB97M-V functionals show the least scatter and closest agreement with the DMC. These findings highlight the delicate nature of these interactions in biomolecular systems and provide guidance for simulations of their structure and dynamics and for the development of machine learned interatomic potentials.

Washburn, Laurel [ORNL] (ORCID:0000000324179335)↗