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DOE OSTI2024

Stable Non-equilibrium Structures in Chiral Nematics under Microfluidic Flow

Cholesteric liquid crystals (CLCs) are compelling responsive materials with applications in next-generation sensing, imaging, and display technologies. While electric fields and surface treatments have been used to manipulate the molecular organization and, subsequently, the optical properties of CLCs, their response to controlled fluid flow has remained largely unexplored. Here, in this study, we investigate the influence of microfluidic flow on the structure of thermotropic CLCs that can exhibit structural coloration. We demonstrate that the shear forces that arise from microfluidic flow align the helical axis of CLCs; alignment is a prerequisite for harnessing the promising photonic properties of CLCs. Moreover, we show that microfluidic flow can generate non-equilibrium structures exhibiting photonic band gaps that are inaccessible in the stationary cholesteric phase. Our findings have implications for the use of CLCs in applications involving flow processing such as additive manufacturing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain

Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1998

Effect of Swirl on Turbulent Structures in Supersonic Jets

Direct Numerical Simulation (DNS) is used to study the mechanism of generation and evolution of turbulence structures in a temporally evolving supersonic swirling round jet and also to examine the resulting acoustic radiations. Fourier spectral expansions are used in the streamwise and azimuthal directions and a 1-D b-spline Galerkin representation is used in the radial direction. Spectral-like accuracy is achieved using this numerical scheme. Direct numerical simulations, using the b-spline spectral method, are carried out starting from mean flow initial conditions which are perturbed by the most unstable linear stability eigenfunctions. It is observed that the initial helical instability waves evolve into helical vortices which eventually breakdown into smaller scales of turbulence. 'Rib' structures similar to those seen in incompressible mixing layer flow of Rogers and Moserl are observed. The jet core breakdown stage exhibits increased acoustic radiations.

Rao, Ram Mohan↗

NASA NTRS1998

Effect of Swirl on Turbulent Structures in Supersonic Jets

Rao, Ram Mohan↗

NASA NTRS1998

Effect of Swirl on Turbulent Structures in Supersonic Jets

Direct numerical simulation (DNS) is used to study the mechanism of generation and evolution of turbulence structures in a temporally evolving supersonic swirling round jet and also to examine the resulting acoustic radiations. Fourier spectral expansions are used in the streamwise and azimuthal directions and a 1-D b-spline Galerkin representation is used in the radial direction. Spectral-like accuracy is achieved using this numerical scheme. Direct numerical simulations, using the b-spline spectral method, are carried out starting from mean flow initial conditions which are perturbed by the most unstable linear stability eigenfunctions. It is observed that the initial.helical instability waves evolve into helical vortices which eventually breakdown into smaller scales of turbulence. 'Rib' structures similar to those seen in incompressible mixing layer flow of Rogers and Moser are observed. The jet core breakdown stage exhibits increased acoustic radiations.

Rao, Ram Mohan↗

DOE OSTI2023

Virus‐Based Pyroelectricity

Abstract The first observation of heat‐induced electrical potential generation on a virus and its detection through pyroelectricity are presented. Specifically, the authors investigate the pyroelectric properties of the M13 phage, which possesses inherent dipole structures derived from the noncentrosymmetric arrangement of the major coat protein (pVIII) with an α‐helical conformation. Unidirectional polarization of the phage is achieved through genetic engineering of the tail protein (pIII) and template‐assisted self‐assembly techniques. By modifying the pVIII proteins with varying numbers of glutamate residues, the structure‐dependent tunable pyroelectric properties of the phage are explored. The most polarized phage exhibits a pyroelectric coefficient of 0.13 µC m −2 °C −1 . Computational modeling and circular dichroism (CD) spectroscopy analysis confirm that the unfolding of α‐helices within the pVIII proteins leads to changes in phage polarization upon heating. Moreover, the phage is genetically modified to enable its pyroelectric function in diverse chemical environments. This phage‐based approach not only provides valuable insights into bio‐pyroelectricity but also opens up new opportunities for the detection of various viral particles. Furthermore, it holds great potential for the development of novel biomaterials for future applications in biosensors and bioelectric materials.

Kim, Han↗

DOE OSTI2024

HSV ‐1 ICP0 dimer domain adopts a novel β‐barrel fold

Abstract Infected cell protein 0 (ICP0) is an immediate‐early regulatory protein of herpes simplex virus 1 (HSV‐1) that possesses E3 ubiquitin ligase activity. ICP0 transactivates viral genes, in part, through its C‐terminal dimer domain (residues 555–767). Deletion of this dimer domain results in reduced viral gene expression, lytic infection, and reactivation from latency. Since ICP0's dimer domain is associated with its transactivation activity and efficient viral replication, we wanted to determine the structure of this specific domain. The C‐terminus of ICP0 was purified from bacteria and analyzed by X‐ray crystallography to solve its structure. Each subunit or monomer in the ICP0 dimer is composed of nine β‐strands and two α‐helices. Interestingly, two adjacent β‐strands from one monomer “reach” into the adjacent subunit during dimer formation, generating two β‐barrel‐like structures. Additionally, crystallographic analyses indicate a tetramer structure is formed from two β‐strands of each dimer, creating a “stacking” of the β‐barrels. The structural protein database searches indicate the fold or structure adopted by the ICP0 dimer is novel. The dimer is held together by an extensive network of hydrogen bonds. Computational analyses reveal that ICP0 can either form a dimer or bind to SUMO1 via its C‐terminal SUMO‐interacting motifs but not both. Understanding the structure of the dimer domain will provide insights into the activities of ICP0 and, ultimately, the HSV‐1 life cycle.

Biochemistry & Molecular Biology↗

DOE OSTI2022

Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering

Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light–absorbing (Pr)–to–far-red light–absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa. Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an “II”-framed close form of the Pfr state to an “O”-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Quark and gluon helicity evolution at small x: revised and updated

We revisit the problem of small Bjorken-x evolution of the gluon and flavor-singlet quark helicity distributions in the shock wave (s-channel) formalism. Earlier works on the subject in the same framework resulted in an evolution equation for the gluon field-strength F 12 and quark “axial current” $\overline{\psi}\gamma$ + γ 5 ψ operators (sandwiched between the appropriate light-cone Wilson lines) in the double-logarithmic approximation (summing powers of α s ln 2 (1/x) with α s the strong coupling constant). In this work, we observe that an important mixing of the above operators with another gluon operator, ${}_D{}^{\leftarrow i} {}_D{}^{i}$, also sandwiched between the light-cone Wilson lines (with the repeated transverse index i = 1, 2 summed over), was missing in the previous works. This operator has the physical meaning of the sub-eikonal (covariant) phase: its contribution to helicity evolution is shown to be proportional to another sub-eikonal operator, ${}_D{}^{i} {}_D{}^{\leftarrow i}$, which is related to the Jaffe-Manohar polarized gluon distribution. In this work we include this new operator into small-x helicity evolution, and construct novel evolution equations mixing all three operators (${}_D{}^{i} {}_D{}^{\leftarrow i}$, F 12 , and $\overline{\psi}\gamma$ + γ 5 ψ), generalizing the results of . We also construct closed double-logarithmic evolution equations in the large-N c and large-N c &N f limits, with N c and N f the numbers of quark colors and flavors, respectively. Solving the large-N c equations numerically we obtain the following small-x asymptotics of the quark and gluon helicity distributions ΔΣ and ΔG, along with the g 1 structure function, $$ \Delta \Sigma \left(x,{Q}^2\right)\sim \Delta G\left(x,{Q}^2\right)\sim {g}_1\left(x,{Q}^2\right)\sim {\left(\frac{1}{x}\right)}^{3.66\sqrt{\frac{\alpha_s{N}_c}{2\pi }}} $$ in complete agreement with the earlier work by Bartels, Ermolaev and Ryskin.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

RNA sculpting by the primordial Helix-clasp-Helix–Strand-Loop (HcH–SL) motif enforces chemical recognition enabling diverse KH domain functions

Not Available

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Deuteron off-resonance rotating frame relaxation for the characterization of slow motions in rotating and static solid-state proteins

Here, we demonstrate the feasibility of deuterium solid-state NMR off-resonance rotating frame relaxation measurements for studies of slow motions in biomolecular solids. The pulse sequence, which includes adiabatic pulses for magnetization alignment, is illustrated for static and magic-angle spinning conditions away from rotary resonances. We apply the measurements for three systems with selective deuterium labels at methyl groups: a) a model compound, Fluorenylmethyloxycarbonyl methionine-D 3 amino acid, for which the principles of the measurements and corresponding motional modeling based on rotameric interconversions are demonstrated; b) amyloid-β 1-40 fibrils labeled at a single alanine methyl group located in the disordered N-terminal domain. This system has been extensively studied in prior work and here serves as a test of the method for complex biological systems. The essential features of the dynamics consist of large-scale rearrangements of the disordered N-terminal domain and the conformational exchange between the free and bound forms of the domain, the latter one due to transient interactions with the structured core of the fibrils. and c) a 15-residue helical peptide which belongs to the predicted α-helical domain near the N-terminus of apolipoprotein B. The peptide is solvated with triolein and incorporates a selectively labeled leucine methyl groups. The method permits model refinement, indicating rotameric interconversions with a distribution of rate constants.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

In situ observation of the magnetization configuration and reversal in cylindrical nanowires

Curvilinear magnetic structures often have unique magnetic behavior compared to their rectilinear counterparts. This is due to the unique curvilinear boundary conditions as well as the curvature induced Dzyaloshinskii–Moriya-like interaction and the curvature induced anisotropy. The effects of a curvilinear geometry are best studied in 3D structures, where the curvature can have a significant spatial extent. Of these 3D structures, the simplest structure to study is the cylindrical nanowire. Here, we have simulated the magnetization reversal in cylindrical NiFe nanowires and present in situ Lorentz TEM images to support the findings of the simulations. We studied the domain formation and reversal of nanowires with two distinct diameters that give rise to a different reversal behavior. We have, thus, found that the zero-field magnetization configuration in these wires can take on a double helix type of configuration. The reversal in these structures then proceeds through the winding and unwinding of these helical configurations rather than through domain wall propagation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Large-eddy simulations of turbulent flows in arrays of helical- and straight-bladed vertical-axis wind turbines

Effects of helical-shaped blades on the flow characteristics and power production of finite-length wind farms composed of vertical-axis wind turbines (VAWTs) are studied numerically using large-eddy simulation (LES). Two helical-bladed VAWTs (with opposite blade twist angles) are studied against one straight-bladed VAWT in different array configurations with coarse, intermediate, and tight spacings. Statistical analysis of the LES data shows that the helical-bladed VAWTs can improve the mean power production in the fully developed region of the array by about 4.94%–7.33% compared with the corresponding straight-bladed VAWT cases. The helical-bladed VAWTs also cover the azimuth angle more smoothly during the rotation, resulting in about 47.6%–60.1% reduction in the temporal fluctuation of the VAWT power output. Using the helical-bladed VAWTs also reduces the fatigue load on the structure by significantly reducing the spanwise bending moment (relative to the bottom base), which may improve the longevity of the VAWT system to reduce the long-term maintenance cost.

17 WIND ENERGY↗

DOE OSTI2026

Rapidity-dependent spin decomposition of the nucleon

We revisit the two-dimensional Fourier transform of generalized parton distributions (GPDs) at nonzero skewness. At 𝜂 = 0 it reduces to the standard impact-parameter density, while at 𝜂 ≠ 0 it is an off-forward amplitude that we interpret as a genuine parton–nucleon correlation. Its overall strength (the transverse-plane integral of the density) is fixed by the GPD at the kinematic point 𝑡 =−𝑐 𝜂 =−4⁢𝜂 2 ⁢𝑚$^{2}_{𝑁}$/(1 − 𝜂 2 ) and decreases monotonically with the rapidity gap Δ⁢𝑦 = ln⁡[(1+𝜂)/(1−𝜂)] = 2 artanh⁡(𝜂). This rapidity dependence implies rapidity-modified Ji identities that connect helicity, orbital, and total angular momenta of the correlation in closed form. To quantify these effects, we construct leading-twist quark and gluon GPDs in a string-based conformal framework: conformal moments are parametrized by linear open- and closed-string Regge trajectories with slopes constrained by parton distribution functions (PDFs), hadron/glueball spectroscopy, and form-factor data, and GPDs are reconstructed over the full (𝑥,𝜂,𝑡) domain by Mellin-Barnes inversion with next-to-leading order evolution. We find qualitative agreement (and fair quantitative agreement within quoted uncertainties) for several moments and selected nonsinglet 𝑥-space channels at 𝜇 = 2 GeV when compared with lattice QCD, while we also identify channels with visible tension and discuss likely sources (PDF priors and 𝑡-slope systematics).

Gauge-gravity dualities↗

DOE OSTI2022

X-ray pulse generation with ultra-fast flipping of its orbital angular momentum

A method to temporally tailor the properties of X-ray radiation carrying Orbital Angular Momentum (OAM) is presented. In simulations, an electron beam is prepared with a temporally modulated micro-bunching structure which, when radiating at the second harmonic in a helical undulator, generates OAM light with a corresponding temporally modulated intensity. This method is shown to generate attosecond pulse trains of OAM light without the need for any additional external optics, making the wavelength range tunable. In addition to the OAM pulse train, the method can be adapted to generate radiation where the handedness of the OAM mode may also be temporally modulated (flipped).

43 PARTICLE ACCELERATORS↗

NASA NTRS1995

Solar flares controlled by helicity conservation

The energy release in a class of solar flares is studied on the assumption that during burst events in highly conducting plasma the magnetic helicity of plasma is approximately conserved. The available energy release under a solar flare controlled by the helicity conservation is shown to be defined by the magnetic structure of the associated prominence. The approach throws light on some solar flare enigmas: the role of the associated prominence. The approach throws light on some solar flare enigmas: the role of the associated prominences; the discontinuation of the reconnection of magnetic lines long before the complete reconnection of participated fields occurs; the existence of quiet prominences which, in spite of their usual optical appearance, do not initiate any flare events; the small energy release under a solar flare in comparison with the stockpile of magnetic energy in surrounding fields. The predicted scale of the energy release is in a fair agreement with observations.

Gliner, Erast B.↗

NASA NTRS2005

Elastic Response of Crimped Collagen Fibrils

A physiologic constitutive expression is presented in algorithmic format for the elastic response of wavy collagen fibrils found in soft connective tissues. The model is based on the observation that crimped fibrils have a three-dimensional structure at the micrometer scale that we approximate as a helical spring. The symmetry of this waveform allows the force/displacement relationship derived from Castigliano's theorem to be solved in closed form. Model predictions are in good agreement with experimental observations for mitral-valve chordae tendineae

Freed, Alan D.↗

DOE OSTI2021

Proceedings of RIKEN BNL Research Center Workshop: Small-x Physics in the EIC Era [Slides]

Understanding the high energy limit of hadronic and nuclear collisions is at the forefront of nuclear and particle physics. When boosted to ultrahigh energies, all hadrons and nuclei eventually transform into a universal form of matter called the Color Glass Condensate (CGC). The CGC is characterized by the high density (saturation) of small-x gluons which leads to distinct experimental signatures. Tantalizing hints of the CGC have been observed at HERA, RHIC and the LHC, but the prospects for the discovery of the CGC are more promising at future experiments such as the Electron-Ion Collider (EIC) at BNL Indeed, according to the National Science Academy report published in 2019, one of the three major goals of the EIC is to address the nature of the gluon saturation. (The other two are the mass and spin structure of the nucleons.) With this in mind, the small-x community is gearing up to meet the challenges of the EIC era. Over the past several years, there has been impressive progress in the next-to-leading order (NLO) calculations in the CGC framework of various observables such as single hadron production in proton-nucleus collisions, inclusive and exclusive dijet and trijet production in Deep Inelastic Scattering (DIS), jet-plus-photon production in DIS, etc. We expect that NLO calculations will be the standard tool to confront future experimental data at the EIC. Another emerging trend of the community is the interplay between small-x physics and spin physics. The RHIC result for the gluon helicity ΔG has underscored the necessity to understand the longitudinal spin structure of the proton at small-x. There have been theoretical indications that a significant fraction of spin and orbital angular momentum is stored in the small-x region. As for the transversely polarized proton, a surprising new connection between the gluon Sivers function at small-x and the QCD Odderon has been pointed out and its implications at the EIC has been discussed. In view of these developments, we think it is timely to organize a dedicated workshop on small-x physics to summarize the present status of the field and to discuss future directions. A major focus of this workshop will be to identify outstanding problems that could significantly benefit from collaborative efforts amongst scientists working on formal, phenomenological, and computational aspects of small-x physics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗