Method for Improved Fluorescence Corrections for Molar Mass Characterization by Multiangle Light Scattering
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Biochemistry & Molecular Biology↗
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Analyzing the Quantum Approximate Optimization Algorithm: Ansätze, Symmetries, and Lie Algebras
The quantum approximate optimization algorithm (QAOA) has been proposed as a method to obtain approximate solutions for combinatorial optimization tasks. In this work, we study the underlying algebraic properties of three QAOA ansätze for the maximum-cut problem on connected graphs, while focusing on the generated Lie algebras as well as their invariant subspaces. Specifically, we analyze the standard QAOA ansatz as well as the orbit and multiangle ansätze. We are able to fully characterize the Lie algebras of the multiangle ansatz across arbitrary connected graphs, finding that they only fall into one of just six families. Aside from the cycle and path graphs, the Lie dimensions for every graph are exponentially large in the system size, meaning that multiangle ansätze are extremely prone to exhibiting barren plateaus. Then, a similar quasi-graph-independent Lie-algebraic characterization beyond the multiangle ansatz is impeded as the circuit exhibits additional “hidden” symmetries besides those naturally arising from a certain parity-superselection operator and all automorphisms of the considered graph. Disregarding the “hidden” symmetries, we can upper bound the dimensions of the orbit and the standard Lie algebras, and the dimensions of the associated invariant subspaces are determined via explicit character formulas. To finish, we conjecture that (for most graphs) the standard Lie algebras have only components that are either exponential or that grow, at most, polynomially with the system size. This would imply that the QAOA is either prone to barren plateaus or classically simulable. More generally, our work provides a symmetry framework and tools to analyze any desired variational quantum algorithm.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Quantum closures for neutrino moment transport
A computationally efficient method for calculating the transport of neutrino flavor in simulations is to use angular moments of the neutrino one-body reduced density matrix, i.e., “quantum moments.” As with any moment-based radiation transport method, a closure is needed if the infinite tower of moment evolution equations is truncated. We derive a general parametrization of a quantum closure and the limits the parameters must satisfy in order for the closure to be physical. We then derive from multiangle calculations the evolution of the closure parameters in two test cases which we then progressively insert into a moment evolution code and show how the parameters affect the moment results until the full multiangle results are reproduced. This parametrization paves the way to setting prescriptions for genuine quantum closures adapted to neutrino transport in a range of situations.
79 ASTRONOMY AND ASTROPHYSICS↗
Elucidating lipid nanoparticle properties and structure through biophysical analyses
Designing lipid nanoparticle (LNP) delivery systems with specific targeting, potency and minimal side effects is crucial for their clinical use. However, traditional characterization methods, such as dynamic light scattering, cannot accurately quantify physicochemical properties of LNPs and how these are influenced by the lipid composition and mixing method. Here, we structurally characterize polydisperse LNP formulations by applying emerging solution-based biophysical methods that have higher resolution and provide biophysical data beyond size and polydispersity. These techniques include sedimentation velocity analytical ultracentrifugation, field-flow fractionation followed by multiangle light scattering and size-exclusion chromatography in line with synchrotron small-angle X-ray scattering. Here, we show that LNPs have intrinsic polydispersity in size, RNA loading and shape, which depend on both the formulation technique and the lipid composition. Lastly, we predict LNP transfection in vitro and in vivo by examining the relationship between mRNA translation and physicochemical characteristics. Solution-based biophysical methods will be essential for determining LNP structure–function relationships, facilitating the creation of new design rules for LNPs.
36 MATERIALS SCIENCE↗
Most of the rhamnogalacturonan-I from cultured Arabidopsis cell walls is covalently linked to arabinogalactan-protein
To characterize a purified rhamnogalacturonan-I (RG-I) containing both RG-I and arabinogalactan-protein (AGP) types of glycosyl residues, an AGP-specific β-1,3-galactanase that can cleave the AG backbone and release the AG sidechain was applied to this material. Carbohydrate analysis and NMR spectroscopy verified that the galactanase-released carbohydrate consists of RG-I covalently attached to the AG sidechain, proving a covalent linkage between RG-I and AGP. Size exclusion chromatography-multiangle light scattering-refractive index detection revealed that the galactanase-released RG-I has an average molecular weight of 41.6 kDa, which, together with the percentage of pectic sugars suggests an RG-I-AGP comprising one AGP covalently linked to two RG-I glycans. Carbohydrate analysis and NMR results of the RG-I-AGP, the galactanase-released glycans, and the RG lyase-released glycans demonstrated that the attached RG-I glycans are decorated with α-1,5-arabinan, β-1,4-galactan, xylose, and 4-O-Me-xylose sidechains. Furthermore, our measurement suggests that the covalently linked RG-I-AGP is the major component of the traditionally prepared RG-I.
59 BASIC BIOLOGICAL SCIENCES↗
The structure of high-Mg alkali-bearing aluminosilicate glasses investigated in situ at ambient and high pressure by multi-angle energy dispersive X-ray diffraction and infrared microspectroscopy
The structural properties of synthetic high-Mg alkali-bearing aluminosilicate glasses analogues of natural picritic-to-komatiitic magmas were investigated in situ by multiangle energy dispersive X-ray diffraction at 2.1 GPa and ambient pressure and by Fourier Transform infrared spectroscopy up to 5.4 GPa in a cycle of compression and decompression experiments. Our results show that the intermediate range ordering of the glass structure at 2.1 GPa is 3.14 Å, increasing to 3.19 Å when decompressed. The local structure shows T-O lengths of 1.66 Å (2.1 GPa) and 1.65 Å (ambient pressure), T-T distances of 3.19 Å at high pressure, which lengthen to 3.21 Å at ambient pressure, causing the T-O-T angle of 147° determined at 2.1 GPa to widen to 154° upon decompression. The deconvoluted infrared spectra result in the presence of Q 1 , Q 2 , Q 3 populations in the aluminosilicate spectral region, whose proportions remain relatively unchanged up to 5.4 GPa. The structural response of the investigated glasses to cold-compression does not involve changes in polymerization, but rather a shrinking and compaction of the structure as evidenced by the Qn species shifting to higher wavenumbers as a function of pressure. The structural properties determined from X-ray diffraction for this glass composition are discussed together with those of glasses emerging from previous studies to highlight a compositional dependence mainly dictated by the amount of SiO 2 and Al 2 O 3 .
glass structure↗
Chlorophyllase from Arabidopsis thaliana Reveals an Emerging Model for Controlling Chlorophyll Hydrolysis
Chlorophyll (Chl) is one of Nature’s most complex pigments to biosynthesize and derivatize. This pigment is vital for survival and also paradoxically toxic if overproduced or released from a protective protein scaffold. Therefore, along with the mass production of Chl, organisms also invest in mechanisms to control its degradation and recycling. One important enzyme that is involved in these latter processes is chlorophyllase. This enzyme is employed by numerous photosynthetic organisms to hydrolyze the phytol tail of Chl. Although traditionally thought to catalyze the first step of Chl degradation, recent work suggests that chlorophyllase is instead employed during times of abiotic stress or conditions that produce reactive oxygen species. However, the molecular details regarding how chlorophyllases are regulated to function under such conditions remain enigmatic. Here, we investigate the Arabidopsis thaliana chlorophyllase isoform AtCLH2 using site-directed mutagenesis, mass spectrometry, dynamic light scattering, size-exclusion multiangle light scattering, and both steady-state enzyme kinetic and thermal stability measurements. Through these experiments, we show that AtCLH2 exists as a monomer in solution and contains two disulfide bonds. One disulfide bond putatively maps to the active site, whereas the other links two N-terminal Cys residues together. These disulfide bonds are cleaved by chemical or chemical and protein-based reductants, respectively, and are integral to maintaining the activity, stability, and substrate scope of the enzyme. This work suggests that Cys residue oxidation in chlorophyllases is an emerging regulatory strategy for controlling the hydrolysis of Chl pigments.
59 BASIC BIOLOGICAL SCIENCES↗
Solution characterization of the dynamic conjugative entry exclusion protein TraG
The R100 plasmid and the secretion system it encodes are representative of F-like conjugative type IV secretion systems for the transmission of mobile DNA elements in gram-negative bacteria, serving as a major contributor to the spread of antibiotic resistance in bacterial pathogens. The TraG protein of F-like systems consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain, denoted TraG*. TraG* is essential in preventing redundant DNA transfer through a process termed entry exclusion. In the donor cell, it interacts with TraN to facilitate mating pair stabilization; however, if a mating pore forms between bacteria with identical plasmids, TraG* interacts with its cognate TraS in the inner membrane of the recipient bacterium to prevent redundant donor–donor conjugation. Structural studies of TraG* from the R100 plasmid have revealed the presence of a dynamic region between the N- and C-terminal domains of TraG. Thermofluor, circular dichroism, collision-induced unfolding–mass spectrometry, and size exclusion chromatography linked to multiangle light scattering and small angle x-ray scattering experiments indicated an N-terminal truncation mutant displayed higher stability and less disordered content relative to full-length TraG*. The 45 N-terminal residues of TraG* are hypothesized to serve as part of a flexible linker between the two independently functioning domains.
59 BASIC BIOLOGICAL SCIENCES↗
Hyperspectral interference tomography of nacre
Significance We invented an optical technique—hyperspectral interference tomography—that rapidly and nondestructively extracts nanoscale structural information across large samples of nacre (mother-of-pearl) and other layered materials by combining multiangle and polarization-resolved hyperspectral imaging with optical-interference modeling. We investigated nacre in mollusk shells from two different species, red abalone and rainbow abalone, and discovered a previously unknown relationship between the age of the mollusk and the thickness of aragonite tablets in nacre. Hyperspectral interference tomography will have applications in climate science, since nacre tablet thickness in fossil shells is a proxy for ancient seawater temperature, and in bioinspired mechanics, because the layered structure of nacre inspires engineered materials with exceptional strength and toughness.
47 OTHER INSTRUMENTATION↗
Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer
Neurofibromin is a tumor suppressor encoded by the NF1 gene, which is mutated in Rasopathy disease neurofibromatosis type I. Defects in NF1 lead to aberrant signaling through the RAS–mitogen-activated protein kinase pathway due to disruption of the neurofibromin GTPase-activating function on RAS family small GTPases. Very little is known about the function of most of the neurofibromin protein; to date, biochemical and structural data exist only for its GAP domain and a region containing a Sec-PH motif. To better understand the role of this large protein, here we carried out a series of biochemical and biophysical experiments, including size-exclusion chromatography–multiangle light scattering (SEC-MALS), small-angle X-ray and neutron scattering, and analytical ultracentrifugation, indicating that full-length neurofibromin forms a high-affinity dimer. We observed that neurofibromin dimerization also occurs in human cells and likely has biological and clinical implications. Analysis of purified full-length and truncated neurofibromin variants by negative-stain EM revealed the overall architecture of the dimer and predicted the potential interactions that contribute to the dimer interface. We could reconstitute structures resembling high-affinity full-length dimers by mixing N- and C-terminal protein domains in vitro. The reconstituted neurofibromin was capable of GTPase activation in vitro, and co-expression of the two domains in human cells effectively recapitulated the activity of full-length neurofibromin. Taken together, these results suggest how neurofibromin dimers might form and be stabilized within the cell.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
ULK complex organization in autophagy by a C-shaped FIP200 N-terminal domain dimer
The autophagy-initiating human ULK complex consists of the kinase ULK1/2, FIP200, ATG13, and ATG101. Hydrogen-deuterium exchange mass spectrometry was used to map their mutual interactions. The N-terminal 640 residues (NTD) of FIP200 interact with the C-terminal IDR of ATG13. Mutations in these regions abolish their interaction. Negative stain EM and multiangle light scattering showed that FIP200 is a dimer, while a single molecule each of the other subunits is present. The FIP200NTD is flexible in the absence of ATG13, but in its presence adopts the shape of the letter C ~20 nm across. The ULK1 EAT domain interacts loosely with the NTD dimer, while the ATG13:ATG101 HORMA dimer does not contact the NTD. Cryo-EM of the NTD dimer revealed a structural similarity to the scaffold domain of TBK1, suggesting an evolutionary similarity between the autophagy-initiating TBK1 kinase and the ULK1 kinase complex.
59 BASIC BIOLOGICAL SCIENCES↗
An atypical BRCT–BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex
The XRCC1–DNA ligase IIIα complex (XL) is critical for DNA single-strand break repair, a key target for PARP inhibitors in cancer cells deficient in homologous recombination. Here, we combined biophysical approaches to gain insights into the shape and conformational flexibility of the XL as well as XRCC1 and DNA ligase IIIα (LigIIIα) alone. Structurally-guided mutational analyses based on the crystal structure of the human BRCT–BRCT heterodimer identified the network of salt bridges that together with the N-terminal extension of the XRCC1 C-terminal BRCT domain constitute the XL molecular interface. Coupling size exclusion chromatography with small angle X-ray scattering and multiangle light scattering (SEC-SAXS–MALS), we determined that the XL is more compact than either XRCC1 or LigIIIα, both of which form transient homodimers and are highly disordered. The reduced disorder and flexibility allowed us to build models of XL particles visualized by negative stain electron microscopy that predict close spatial organization between the LigIIIα catalytic core and both BRCT domains of XRCC1. Together our results identify an atypical BRCT–BRCT interaction as the stable nucleating core of the XL that links the flexible nick sensing and catalytic domains of LigIIIα to other protein partners of the flexible XRCC1 scaffold.
59 BASIC BIOLOGICAL SCIENCES↗
Detectability of collective neutrino oscillation signatures in the supernova explosion of a 8.8 M ⊙ star
In order to investigate the impact of collective neutrino oscillations (CNOs) on the neutrino signal from a nearby supernova, we perform three-flavor neutrino oscillation simulations employing the multiangle effect. The background hydrodynamic model is based on the neutrino hydrodynamic simulation of a 8.8 M ⊙ progenitor star. In this work, we find that CNO commences after some 100 ms post bounce. Before this, CNO is suppressed by matter-induced decoherence. In the inverted mass hierarchy, the spectrum of $\bar{ν}_e$ becomes softer after the onset of CNO. To evaluate the detectability of this modification, we define a hardness ratio between the number of high energy neutrino events and low energy neutrino events adopting a fixed critical energy. We show that Hyper-Kamiokande (HK) can distinguish the effect of CNO for supernova distances out to ~ 10 kpc. On the other hand, for the normal mass hierarchy, the spectrum of ν e becomes softer after the onset of CNO, and we show that DUNE can distinguish this feature for supernova distances out to ~ 10 kpc . More work is necessary to optimize the best value of critical energy for maximum sensitivity. We also show that if the spectrum of $\bar{ν}_e$ in HK becomes softer due to CNO, the spectrum of $ν_e$ in DUNE becomes harder, and vice versa. These synergistic observations in $\bar{ν}_e$ and $ν_e$, by HK and DUNE, respectively, will be an intriguing opportunity to test the occurrence of CNO.
79 ASTRONOMY AND ASTROPHYSICS↗
Bhatnagar-Gross-Krook subgrid model for neutrino quantum kinetics
Here, we present a new subgrid model for neutrino quantum kinetics, which is primarily designed to incorporate effects of collective neutrino oscillations into neutrino-radiation-hydrodynamic simulations for core-collapse supernovae and mergers of compact objects. We approximate the neutrino oscillation term in a quantum kinetic equation using the Bhatnagar-Gross-Krook (BGK) relaxation-time prescription, and the transport equation is directly applicable for classical neutrino transport schemes. The BGK model is motivated by recent theoretical indications that nonlinear phases of collective neutrino oscillations settle into quasisteady structures. We explicitly provide basic equations of the BGK subgrid model for both multiangle and moment-based neutrino transport to facilitate the implementation of the subgrid model in the existing neutrino transport schemes. We also show the capability of our BGK subgrid model by comparing it to fully quantum kinetic simulations for fast neutrino-flavor conversion. We find that the overall properties can be well reproduced in the subgrid model; the error of angular-averaged survival probability of neutrinos is within ~20%. By identifying the source of error, we also discuss perspectives to improve the accuracy of the subgrid model.
79 ASTRONOMY AND ASTROPHYSICS↗
Advection algorithms for quantum neutrino moment transport
Neutrino transport in compact objects is an inherently challenging multidimensional problem. Here, this difficulty is compounded if one includes flavor transformation—an intrinsically quantum phenomenon requiring one to follow the coherence between flavors and thus necessitating the introduction of complex numbers. To reduce the computational burden, simulations of compact objects that include neutrino transport often make use of momentum-angle-integrated moments (the lowest order ones being commonly referred to as the energy density and flux) and these quantities can be generalized to include neutrino flavor, i.e., they become quantum moments. Numerous finite-volume approaches to solving the moment evolution equations for classical neutrino transport have been developed based on solving a Riemann problem at cell interfaces. In this paper we describe our generalization of a Riemann solver for quantum moments, specifically decomposing complex numbers in terms of a (signed) magnitude and phase instead of real and imaginary parts. We then test our new algorithm in numerous cases showing a neutrino fast flavor instability, varying from toy models with analytic solutions to snapshots from neutron star merger simulations. Compared to previous algorithms for neutrino transport with flavor mixing, we find uniformly smaller growth rates of the flavor transformation along with concomitantly larger length-scales, and that the results are a better match with the growth rates seen from multiangle codes.
79 ASTRONOMY AND ASTROPHYSICS↗
Hydrometeor Shape Variability in Snowfall as Retrieved from Polarimetric Radar Measurements
A polarimetric radar–based method for retrieving atmospheric ice particle shapes is applied to snowfall measurements by a scanning Ka-band radar deployed at Oliktok Point, Alaska (70.495°N, 149.883°W). The mean aspect ratio, which is defined by the hydrometeor minor-to-major dimension ratio for a spheroidal particle model, is retrieved as a particle shape parameter. The radar variables used for aspect ratio profile retrievals include reflectivity, differential reflectivity, and the copolar correlation coefficient. The retrievals indicate that hydrometeors with mean aspect ratios below 0.2–0.3 are usually present in regions with air temperatures warmer than approximately from –17° to –15°C, corresponding to a regime that has been shown to be favorable for growth of pristine ice crystals of planar habits. Radar reflectivities corresponding to the lowest mean aspect ratios are generally between –10 and 10 dBZ. For colder temperatures, mean aspect ratios are typically in a range between 0.3 and 0.8. There is a tendency for hydrometeor aspect ratios to increase as particles transition from altitudes in the temperature range from –17° to –15°C toward the ground. Furthermore, this increase is believed to result from aggregation and riming processes that cause particles to become more spherical and is associated with areas demonstrating differential reflectivity decreases with increasing reflectivity. Aspect ratio retrievals at the lowest altitudes are consistent with in situ measurements obtained using a surface-based multiangle snowflake camera. Pronounced gradients in particle aspect ratio profiles are observed at altitudes at which there is a change in the dominant hydrometeor species, as inferred by spectral measurements from a vertically pointing Doppler radar.
54 ENVIRONMENTAL SCIENCES↗
Retrieval of the complex-valued refractive index of germanium near the M 4,5 absorption edge
The complex-valued index of refraction of germanium in the extreme ultraviolet (XUV) is measured by multiangle reflectance of synchrotron radiation. The resulting index of refraction is higher resolution than previously measured values. It reveals new structures attributed to transitions from the 3d-core orbitals to the $Σ^{c}_{5,2}$ and the $X^{c}_{5,2}$ conduction bands. Additionally, it is shown that the problem of total external reflection, which renders multi-angle reflectance measurements insensitive to the complex-valued refractive index at grazing incidence, can be overcome by employing measurements at angles of incidence away from the critical angle.
36 MATERIALS SCIENCE↗