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Nonconventional NMR Spin-Coupling Constants in Oligosaccharide Conformational Modeling: Structural Dependencies Determined from Density Functional Theory Calculations
Nonconventional NMR spin-coupling constants were investigated to determine their potential as conformational constraints in MA’AT modeling of the O-glycosidic linkages of oligosaccharides. Four ( 1 J C1',H1' , 1 J C1',C2' , 2 J C1',H2' , and 2 J C2',H1' ) and eight ( 1 J C4,H4 , 1 J C3,C4 , 1 J C4,C5 , 2 J C3,H4 , 2 J C4,H3 , 2 J C5,H4 , 2 J C4,H5 , and 2 J C3,C5 ) spin-couplings in methyl β-d-galactopyranosyl-(1→4)-β-d-glucopyranoside (methyl β-lactoside) were calculated using density functional theory (DFT) to determine their dependencies on O-glycosidic linkage C–O torsion angles, $\phi$ and ψ, respectively. Long-range 4 J H1',H4 was also examined as a potential conformational constraint of either $\phi$ or ψ. Secondary effects of exocyclic (hydroxyl) C–O bond rotation within or proximal to these coupling pathways were investigated. Based on the findings of methyl β-lactoside, analogous J-couplings were studied in five additional two-bond O-glycosidic linkages [βGlcNAc-(1→4)-βMan, 2-deoxy-βGlc-(1→4)-βGlc, αMan-(1→3)-βMan, αMan-(1→2)-αMan, and βGlcNAc(1→2)-αMan] to determine whether the coupling behaviors observed in methyl β-lactoside were more broadly observed. Of the 13 nonconventional J-couplings studied, 7 exhibit properties that may be useful in future MA’AT modeling of O-glycosidic linkages, none of which involve coupling pathways that include the linkage C–O bonds. The findings also provide new insights into the general effects of exocyclic C–O bond conformation on the magnitude of experimental spin-couplings in saccharides and other hydroxyl-containing molecules.
Using geometric simulation software ‘GASP’ to model conformational flexibility in a family of zinc metal–organic frameworks
Here, a new tripodal tricarboxylic acid ligand, 4,4'-(4'-(4'-carboxy-[1,1'-biphenyl]-4-yl)-[2,2':6',2''-terpyridine]-5,5''-diyl)-dibenzoic acid (H 3 cbt ), was synthesised using a three-step convergent strategy. Subsequent reactions with zinc( II ) nitrate hexahydrate yielded three metal–organic frameworks (MOFs). The three MOFs, [Zn(H cbt )]·4DMF ( 1 ), [Zn(H cbt )]·4DMSO·1.5H 2 O·DMF ( 2 ), and [Zn(H cbt )]·2DMF·3H 2 O ( 3 ), each adopt flexible interdigitated 2D net topologies. Framework 1 has DMF-filled channels that retain porosity upon desolvation, with a measured BET surface area of 248 m 2 g -1 . Framework 2 possesses larger DMSO-containing channels that collapse upon desolvation, resulting in near-equivalent porosity values to framework 1 . In silico calculations and topological considerations determined using the geometric simulation software GASP dictate that framework 2 can feasibly alter conformation to approximate 1 , but cannot perfectly replicate the interdigitated motif. Framework 3 formed when wet solvents were used to synthesise 1 . Interestingly, the interdigitated structure of 3 contains a unique carboxylate binding mode that precludes its subsequent adoption by either 1 or 2 upon their exposure to water. This diverse array of structural considerations recommends this MOF family for modelling using GASP. Interrogating frameworks 1–3 using this software provided insights that justified experimentally observed conformational trends, as well as barriers to interconversion between members of this MOF family. In a broader sense, this work demonstrates the wider applicability of GASP software to modelling structural changes within flexible MOF materials.
Advancements in modeling conformally doped X-MSND radiation imagers
Not Available
Reconciling MA'AT and molecular dynamics models of linkage conformation in oligosaccharides
MA'AT conformational models of the phi torsion angles of O -glycosidic linkages differ from those obtained from MD simulation.
The DESI One-Percent Survey: A Concise Model for the Galactic Conformity of Emission-line Galaxies
Galactic conformity is the phenomenon whereby a galaxy of a certain physical property is correlated with its neighbors of the same property, implying a possible causal relationship. Here, the observed auto correlations of emission-line galaxies (ELGs) from the highly complete DESI One-Percent Survey exhibit a strong clustering signal on small scales, providing clear evidence for the conformity effect of ELGs. Building upon the original subhalo abundance-matching (SHAM) method developed by Gao et al., we propose a concise conformity model to improve the ELG–halo connection. In this model, the number of satellite ELGs is boosted by a factor of ~5 in the halos whose central galaxies are ELGs. We show that the mean ELG satellite number in such central halos is still smaller than 1 and that the model does not significantly increase the overall satellite fraction. With this model, we can well recover the ELG auto correlations to the smallest scales explored with the current data (i.e., r p > 0.03 Mpc h –1 in real space and at s > 0.3 Mpc h –1 in redshift space), while the cross correlations between luminous red galaxies and ELGs are nearly unchanged. Although our SHAM model has only eight parameters, we further verify that it can accurately describe the ELG clustering in the entire redshift range from z = 0.8 to 1.6. We therefore expect that this method can be used to generate high-quality ELG lightcone mocks for DESI.
CFT and lattice correlators near an RG domain wall between minimal models
Conformal interfaces separating two conformal field theories (CFTs) provide maps between different CFTs, and naturally exist in nature as domain walls between different phases. One particularly interesting construction of a conformal interface is the renormalization group (RG) domain wall between CFTs. For a given Virasoro minimal model \mathcal{M}_{k+3,k+2} ℳ k + 3 , k + 2 , an RG domain wall can be generated by a specific deformation which triggers an RG flow towards its adjacent Virasoro minimal model \mathcal{M}_{k+2,k+1} ℳ k + 2 , k + 1 with the deformation turned on over part of the space. An algebraic construction of this domain wall was proposed by Gaiotto in [J. High Energy Phys. 12, 103 (2012)]. In this paper, we will provide a study of this RG domain wall for the minimal case k=2 k = 2 , which can be thought of as a nonperturbative check of the construction. In this case the wall is separating the Tricritical Ising Model (TIM) CFT and the Ising Model (IM) CFT. We will check the analytical results of correlation functions from the RG brane construction with the numerical density matrix renormalization group (DMRG) calculation using a lattice model proposed in [arXiv.1206.1332, Science 344, 280 (2014)], and find a perfect agreement. We comment on possible experimental realizations of this RG domain wall.
Standard Model in conformal geometry: Local vs gauged scale invariance
Here, we discuss comparatively local versus gauged Weyl symmetry beyond Standard Model (SM) and Einstein gravity and their geometric interpretation. The SM and Einstein gravity admit a natural embedding in Weyl integrable geometry which is a special limit of Weyl conformal (non-metric) geometry. The theory has a local Weyl scale symmetry but no associated gauge boson. Unlike previous models with such symmetry, this embedding is truly minimal i.e. with no additional fields beyond SM and underlying geometry. This theory is compared to a similar minimal embedding of SM and Einstein gravity in Weyl conformal geometry (SMW) which has a full gauged scale invariance, with an associated Weyl gauge boson. At large field values, both theories give realistic, Starobinsky–Higgs like inflation. The broken phase of the current model is the decoupling limit of the massive Weyl gauge boson of the broken phase of SMW, while the local scale symmetry of the current model is part of the larger gauged scale symmetry of SMW. Hence, the current theory has a gauge embedding in SMW. Unlike in the SMW, we note that in models with local scale symmetry the associated current is trivial, which is a concern for the physical meaning of this symmetry. Therefore, the SMW is a more fundamental UV completion of SM in a full gauge theory of scale invariance that generates Einstein gravity in the (spontaneously) broken phase, as an effective theory.
Gravitational waves from supercooled phase transitions in conformal Majoron models of neutrino mass
We study supercooled first-order phase transitions above the QCD scale in a wide class of conformal Majoron-like U(1)′ models that explain the totality of active neutrino oscillation data and produce a detectable stochastic gravitational wave background (SGWB) at LIGO, LISA and ET. We place constraints on the U(1)′ breaking scale and gauge coupling using current LIGO-Virgo-Kagra data. We find that strong supercooling can be ruled out in large regions of parameter space if a SGWB is not detected by these experiments. A null signal at LIGO and ET will disfavor a type-I seesaw scale above 10 14 GeV, while a positive signal is a signature of heavy right-handed neutrinos. On the other hand, LISA will be sensitive to seesaw scales as low as a TeV, and could detect a SGWB even if the right-handed neutrinos are decoupled.
CO 2 plume evolution in a depleted natural gas reservoir: Modeling of conformance uncertainty reduction over time
Uncertainty in the long-term fate of CO 2 injected for geologic carbon sequestration (GCS) is a significant barrier to the adoption of GCS as a greenhouse-gas emission-mitigation for industry and regulatory agencies alike. Here, we present a modeling study that demonstrates that the uncertainty in forecasts of GCS site performance decreases over time as monitoring data are used to update operational models. We consider a case study of GCS in a depleted natural gas reservoir, with CO 2 injection occurring over 20 years, with a 50-year post-injection site care period. We constructed a detailed model to generate the actual model output, which is considered synthetic observation data. A series of simpler operational models based on limited data and assumptions about how an operator would model such a site are then run and compared against actual model output at specific monitoring points after one year, two years, etc. The operational model is updated and improved using the synthetic observation data from the actual model at the same time intervals. Model parameter values and model features needed to be updated over time to improve matches to the actual model. These kinds of model adjustments would be a normal part of reservoir engineering and site management at GCS sites. Uncertainty in two key measures related to site performance decreases with time: extent of the CO 2 plume up-dip migration, and radial extent of the pressure pulse. This conclusion should help allay the concerns of industry and regulators about uncertainty in long-term fate of CO 2 at GCS sites.
Solving the 2D SUSY Gross-Neveu-Yukawa model with conformal truncation
We use Lightcone Conformal Truncation to analyze the RG flow of the two-dimensional supersymmetric Gross-Neveu-Yukawa theory, i.e. the theory of a real scalar superfield with a $\mathbb{Z}$ 2 -symmetric cubic superpotential, aka the 2d Wess-Zumino model. The theory depends on a single dimensionless coupling $\overline{g}$, and is expected to have a critical point at a tuned value ${\overline{g}}_{\ast }$ where it flows in the IR to the Tricritical Ising Model (TIM); the theory spontaneously breaks the $\mathbb{Z}$ 2 symmetry on one side of this phase transition, and breaks SUSY on the other side. We calculate the spectrum of energies as a function of $\overline{g}$ and see the gap close as the critical point is approached, and numerically read off the critical exponent ν in TIM. Beyond the critical point, the gap remains nearly zero, in agreement with the expectation of a massless Goldstino. We also study spectral functions of local operators on both sides of the phase transition and compare to analytic predictions where possible. In particular, we use the Zamolodchikov C -function to map the entire phase diagram of the theory. Crucial to this analysis is the fact that our truncation is able to preserve supersymmetry sufficiently to avoid any additional fine tuning.
Achieving geometric accuracy in FFT-based micromechanical models using conformal grid
Owing to its efficiency, simplicity and robustness, the FFT-based method has become the standard for computation of mechanical fields in a heterogeneous periodic unit cell. One of the main disadvantages of the FFT-based method is the inaccurate representation of the initial microstructure on a regular grid of voxels, which can be alleviated through the use of distorted initial grids. Here, in this paper, a method for generation of distorted initial grids conforming to the microstructural features (e.g. straight/curved boundaries) is proposed. The method determines the positions of the grid nodes in the initial configuration by solving a system of springs connecting the nodes. Microstructures consisting of layers, Voronoi tessellation and circular/spherical inclusions are considered, and mechanical fields simulated using the FFT-based method. It is found that distorted initial grids, conforming to the microstructural features, lead to more accurate mechanical fields in comparison to the corresponding non-distorted initial grid solution. The effect of initial grid distortion on the convergence of the FFT-based method is analyzed and discussed.
MA’AT Analysis of Aldofuranosyl Rings: Unbiased Modeling of Conformational Equilibria and Dynamics in Solution
Not provided.
Disentangling the Effects of Vapor Pressure Deficit and Soil Water Availability on Canopy Conductance in a Seasonal Tropical Forest During the 2015 El Niño Drought
In land models used in Earth system models, vegetation water stress is heuristically related to soil water matric potential, and root water uptake in soil layers is simply proportional to root density to meet the transpiration demand. The efficiency of roots utilizing deeper soil water under water stress cannot be well represented, but it is of critical importance for transpiration regulation and carbon flux. To improve modeling of tropical forest response to drought, a plant hydrodynamic scheme (HYDRO), adapted from a trait-based model in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), has been implemented in the Energy Exascale Earth System Model (E3SM) Land Model (ELM) to represent the hydraulic dynamics and root water uptake strategy. The adapted model conforms to the big-leaf photosynthesis model in ELM. Vegetation water stress in the model is a function of prognostic leaf water potential and is used to regulate stomatal conductance. Point simulations were performed at two tropical forest sites in the Amazon and Panama. Model sensitivity to the numerical solver, plant hydraulic traits, soil properties, and atmospheric forcing has been evaluated. Our results showed that, even though water stress factors calculated at our study sites using HYDRO are comparable to that simulated by the heuristic water stress model, soil moisture prediction is improved with soil water redistributions through roots. Simulated results using HYDRO is not as sensitive to plant hydraulic traits measured for different tree species as to the soil properties and atmospheric forcing. Simplified numerical solver may cause inaccuracy as to where roots uptake water. This study suggests that plant hydrodynamic representation is critical for improved simulations of soil moisture under water stresses.
A curated benchmark for cofolding models on kinase conformational states
Abstract Protein kinases are critical drug targets, requiring therapeutics that can modulate their active and inactive conformational states. While cofolding models can generate global folds directly from kinase sequences and ligand SMILES strings, these models have not yet been tested on their ability to recover ligand-induced-fit conformational states of the kinase proteins. Here, we introduce KinConfBench, a curated benchmark of 2225 high-quality human kinase chains to evaluate the ability of four state-of-the-art cofolding models—Boltz-2, Chai-1, Protenix, and RoseTTAFold-All-Atom—to recover both canonical and rare conformational states. We show that geometric success metrics of a ligand pose in the active site do not correlate strongly with the correct kinase conformational state, motivating a new set of dynamical benchmarks for assessing cofolding models. While all four cofolding models achieve ~60–80% prediction accuracy for kinase conformational classification, they exhibit severe mode collapse when performing multiple inferences, show negligible structural diversity in sampling induced-fit motions, and display a prevalent “apo-drift” in which most cofolding models predominantly predict the kinase to be in its ligand-free state. Our results highlight that capturing ligand-induced protein conformational diversity, not just geometric fit, is critical for next-generation structure-based drug discovery.
Development of Accelerated Steady-state Test Capsule Experiments to Replicate EBR-II Fuel Behavior Using BISON Fuel Performance Analysis
Here in this work, BISON fuel performance calculations were performed to predict the fuel behavior of accelerated burnup U-Pu-Zr fuel, with temperature operation conditions of the fuel and the cladding mirroring conditions within EBR-II fuel pins. The temperature operating conditions within the FAST accelerated burnup rods were aimed at replicating EBR-II X447/X447A fuel surface and inner cladding surface temperatures. Due to the FAST capsule design, these temperatures can be replicated with fission rate densities being significantly increased. fuel performance modeling has not been assessed for novel experiments such as accelerated burnup utilizing the FAST capsule within ATR. This is an important step in understanding accelerated irradiation methods as many performance models are empirical models conforming to the results of PIE but do not always include physical models that would represent the changes in irradiation tests.
Towards a Quintic Ginzburg-Landau Description of the (2,7) Minimal Model
We discuss dimensional continuation of the massless scalar field theory with the 𝑖𝜙 5 interaction term. It preserves the so-called 𝒫𝒯 symmetry, which acts by 𝜙 →−𝜙 accompanied by 𝑖 →−𝑖. Below its upper critical dimension 10/3, this theory has interacting infrared fixed points. We argue that the fixed point in 𝑑 = 2 describes the nonunitary minimal conformal model 𝑀(2,7). We identify the operators 𝜙 and 𝜙 2 with the Virasoro primaries 𝜙 1,2 and 𝜙 1,3 , respectively, and 𝑖𝜙 3 with a quasiprimary operator, which is a Virasoro descendant of 𝜙 1,3 . Our identifications appear to be consistent with the operator product expansions and with considerations based on integrability. Using constrained Padé extrapolations, we provide estimates of the critical exponents in 𝑑 = 3. We also comment on possible lattice descriptions of 𝑀(2,7) and discuss RG flows to and from this conformal field theory (CFT). Finally, we conjecture that the minimal models 𝑀(2,2𝑛 +1) are described by the massless scalar field theories with the 𝑖𝜙 2𝑛−1 interaction terms.