Structural Mechanisms of Nucleosome Recognition by Linker Histones
Abstract not provided
Zhou, Bing-Rui↗
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The elastase-PK101 structure: Mechanism of an ultrasensitive activity-based probe revealed
Human neutrophil elastase (HNE) plays a central role in neutrophil host defense, but its broad specificity makes HNE a difficult target for both inhibitor and probe development. Recently, we identified the unnatural amino acid containing activity-based probe PK101, which exhibits astounding sensitivity and selectivity for HNE, yet completely lacks mechanistic explanation for its unique characteristics. Here, we present the crystal structure of the HNE-PK101 complex which not only reveals the basis for PK101 ultrasensitivity but also uncovers so far unrecognized HNE features. Strikingly, the Nle( O -Bzl) function in the P4 position of PK101 reveals and leverages an “exo-pocket” on HNE as a critical factor for selectivity. Furthermore, the PK101 P3 position harbors a methionine dioxide function, which mimics a post-translationally oxidized methionine residue and forms a critical hydrogen bond to the backbone amide of Gly219 of HNE. Gly219 resides in a Gly–Gly motif that is unique to HNE, yet compulsory for this interaction. Consequently, this feature enables HNE to accommodate substrates that have undergone methionine oxidation, which constitutes a hallmark post-translational modification of neutrophil signaling.
36 MATERIALS SCIENCE↗
Precision mechanical structure of an ultra-high-resolution spectrometer for inelastic X-ray scattering instrument
A method and an ultrahigh-resolution spectrometer including a precision mechanical structure for positioning inelastic X-ray scattering optics are provided. The spectrometer includes an X-ray monochromator and an X-ray analyzer, each including X-ray optics of a collimating (C) crystal, a pair of dispersing (D) element crystals, anomalous transmission filter (F) and a wavelength (W) selector crystal. A respective precision mechanical structure is provided with the X-ray monochromator and the X-ray analyzer. The precision mechanical structure includes a base plate, such as an aluminum base plate; positioning stages for D-crystal alignment; positioning stages with an incline sensor for C/F/W-crystal alignment, and the positioning stages including flexure-based high-stiffness structure.
36 MATERIALS SCIENCE↗
Development and Comparison of Mechanical Structures for FNAL 15 T Nb$_3$Sn Dipole Demonstrator
Main design challenges for 15 T accelerator magnets are large Lorentz forces at this field level. The large Lorentz forces generate high stresses in the coil and mechanical structure and, thus, need stress control to maintain them at the acceptable level for brittle Nb3Sn coils and other elements of magnet mechanical structure. To provide these conditions and achieve the design field in the FNAL 15 T dipole demonstrator, several mechanical structures have been developed and analysed. The possibilities and limitations of these designs are discussed in this paper
43 PARTICLE ACCELERATORS↗
Structural mechanisms of the Ih–II and II → Ic transitions between the crystalline phases of aqueous ice
Structural mechanisms are proposed for experimentally observed phase transitions between crystalline modifications of aqueous ice, Ih and II, as well as II and Ic. It is known that the Ih–II transition occurs with the conservation of large structural units (hexagonal channels) common for these ices. It is shown that the Ih → II transition may occur with the conservation of 5/6 of all hydrogen bonds in crystal, including all hydrogen bonds in the retained channels (3/4 of the total number of bonds in crystal) and 1/3 of the bonds between these channels (1/12 of the total number). The transformation of other hydrogen bonds between the retained channels leads to the occurrence of proton order in ice II. A structural mechanism is proposed to explain the transformation of single crystals of ice Ih either into single crystals of ice II or into crystalline twins of ice II with c axes rotated by 180° with respect to each other, which is often observed at the Ih → II transition. It is established that up to 7/12 of all hydrogen bonds are retained at the irreversible cooperative II → Ic transition.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Development, construction and tests of the Mu2e electromagnetic calorimeter mechanical structures
The “muon-to-electron conversion” (Mu2e) experiment at Fermilab will search for the charged lepton flavour violating neutrino-less coherent conversion of a muon into an electron in the field of an aluminum nucleus. The observation of this process would be the unambiguous evidence of the existence of physics beyond the standard model. Mu2e detectors comprise a straw-tracker, an electromagnetic calorimeter and an external veto for cosmic rays. In particular, the calorimeter provides excellent electron identification, a fast calorimetric online trigger, and complementary information to aid pattern recognition and track reconstruction. The detector has been designed as a state-of-the-art crystal calorimeter and employs 1348 pure Cesium Iodide (CsI) crystals readout by UV-extended silicon photosensors and fast front-end and digitization electronics. A design consisting of two identical annular matrices (named “disks”) positioned at the relative distance of 70 cm downstream the aluminum target along the muon beamline satisfies the Mu2e physics requirements. The hostile Mu2e operational conditions, in terms of radiation levels (total expected ionizing dose of 12 krad and a neutron fluence of 5 × 10$^{10}$ n/cm$^{2}$ @ 1 MeV$_{eq}$ (Si)/y), magnetic field intensity (1 T) and vacuum level (10$^{-4}$ Torr) have posed tight constraints on scintillating materials, sensors, electronics and on the design of the detector mechanical structures and material choice. The support structure of each 674 crystal matrix is composed of an aluminum hollow ring and parts made of open-cell vacuum-compatible carbon fiber. The photosensors and front-end electronics for the readout of each crystal are inserted in a machined copper holder and make a unique mechanical unit. The resulting 674 mechanical units are supported by a machined plate of vacuum-compatible plastic material. The plate also integrates the cooling system made of a network of copper lines flowing a low temperature radiation-hard fluid and placed in thermal contact with the copper holders to constitute a low resistance thermal bridge. The data acquisition electronics are hosted in aluminum custom crates positioned on the external lateral surface of the disks. The crates also integrate the electronics cooling system as lines running in parallel to the front-end system. In this paper we report on the calorimeter mechanical structure design, the mechanical and thermal simulations that have determined the design technological choices, and the status of component production, quality assurance tests and plans for assembly at Fermilab.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
MOOSE-Based Fast Reactor Core Bowing Capabilities: Coupled Structural Mechanics – Thermal Fluids Demonstration and Related Verification Efforts
Under the U.S. Department of Energy Office of Nuclear Energy’s Advanced Modeling and Simulation (NEAMS) Program, an integrated multiphysics approach is being developed to model the core bowing phenomena important to liquid metal-cooled fast reactors. Core bowing is an important passive safety mechanism in liquid metal-cooled fast reactors and involves multiphysics effects including radiation transport, fluid flow, heat transfer, and mechanical response to temperature and flux gradients. Verification and assessment efforts continued on the Multiphysics Object Oriented Simulation Environment (MOOSE) capabilities relevant for modeling thermo-mechanical core bowing behavior. IAEA Verification Problem 4, which was started in FY23, was further examined with MOOSE capabilities to rectify discrepancies observed in previous years when compared to IAEA benchmark participant data. Meshing and postprocessing capabilities in MOOSE were also advanced by other teams and utilized this year. A thermal fluids-structural mechanical coupling demonstration has performed on 7-assemblyand 19-assembly fast reactor assembly configurations using MOOSE. Subchannel capabilities are used to calculate coolant temperature, and heat conduction capabilities calculate duct wall temperature as well as heat transfer through the inter-assembly gap. Structural mechanical capabilities then deform the mesh, accounting for contact between assemblies, according to the temperature gradients calculated by the thermal solvers. Power distributions are imposed rather than calculated to demonstrate different deformations.
22 GENERAL STUDIES OF NUCLEAR REACTORS↗
Design and assembling status of the Mu2e electromagnetic calorimeter mechanical structures
The muon-to-electron conversion (Mu2e) experiment at Fermilab will search for the Charged Lepton Flavour Violating neutrino-less coherent conversion of a muon into an electron in the field of an aluminum nucleus. The observation of this process would be the unambiguous evidence of physics beyond the Standard Model. The detector has been designed as a state-of-the-art crystal calorimeter and employs 1348 pure Cesium Iodide (CsI) crystals readout by UV-extended silicon photosensors and fast front-end and digitization electronics. A design consisting of two identical annular matrices (named disks ) positioned at the relative distance of 70 cm, downstream the aluminum target along the muon beamline, satisfies the Mu2e physics requirements. The hostile Mu2e operational conditions, in terms of radiation levels (total ionizing dose of 12 krad and a neutron fluence of 5 10^{10} n/cm2 @ 1 MeVeq (Si)/y), magnetic field intensity (1 T) and vacuum level (10−4 Torr) have posed tight constraints on the design of the detector mechanical structures and materials choice. The support structure of the two 674 crystal matrices employs two aluminum hollow rings and parts made of open- cell vacuum-compatible carbon fiber. The photosensors and service front-end electronics for each crystal are assembled in a unique mechanical unit inserted in a machined copper holder. The 674 units are supported by a machined plate made of vacuum-compatible plastic material. The plate also integrates the cooling system made of a network of copper lines flowing a low temperature radiation-hard fluid and placed in thermal con- tact with the copper holders. The data acquisition electronics is hosted in aluminum custom crates positioned on the external lateral surface of the two disks. The crates also integrate the electronics cooling system. In this poster we will review the constraints on the calorimeter mechanical structures, the technological choices, and the status of assembling at Fermilab.
Pasciuto, D.↗
Development, construction and qualification tests of the mechanical structures of the electromagnetic calorimeter of the Mu2e experiment at Fermilab
The “muon-to-electron conversion” (Mu2e) experiment at Fermilab will search for the Charged Lepton Flavour Violating neutrino-less coherent conversion of a muon into an electron in the field of an aluminum nucleus. The observation of this process would be the unambiguous evidence of physics beyond the Standard Model. Mu2e detectors comprise a straw-tracker, an electromagnetic calorimeter and an external veto for cosmic rays. The calorimeter provides excellent electron identification, complementary information to aid pattern recognition and track reconstruction, and a fast calorimetric online trigger. The detector has been designed as a state-of-the-art crystal calorimeter and employs 1340 pure Cesium Iodide (CsI) crystals readout by UV-extended silicon photosensors and fast front-end and digitization electronics. A design consisting of two identical annular matrices (named “disks”) positioned at the relative distance of 70 cm downstream the aluminum target along the muon beamline satisfies the Mu2e physics requirements.The hostile Mu2e operational conditions, in terms of radiation levels (total ionizing dose of 12 krad and a neutron fluence of 5x1010 n/cm2 @ 1 MeVeq (Si)/y), magnetic field intensity (1 T) and vacuum level (10$^{-4}$ Torr) have posed tight constraints on the design of the detector mechanical structures and materials choice. The support structure of the two 670 crystal matrices employs two aluminum hollow rings and parts made of open-cell vacuum-compatible carbon fiber. The photosensors and service front-end electronics for each crystal are assembled in a unique mechanical unit inserted in a machined copper holder. The 670 units are supported by a machined plate made of vacuum-compatible plastic material. The plate also integrates the cooling system made of a network of copper lines flowing a low temperature radiation-hard fluid and placed in thermal contact with the copper holders to constitute a low resistance thermal bridge. The data acquisition electronics is hosted in aluminum custom crates positioned on the external lateral surface of the two disks. The crates also integrate the electronics cooling system as lines running in parallel to the front-end system.The constraints on the calorimeter mechanical structures design, the development from the conceptual design to the specifications of all the structural components, the status of components production and the components quality assurance tests are presented.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Full scale structural, mechanical and dynamical properties of HIV-1 liposomes
Enveloped viruses are enclosed by a lipid membrane inside of which are all of the components necessary for the virus life cycle; viral proteins, the viral genome and metabolites. Viral envelopes are lipid bilayers that adopt morphologies ranging from spheres to tubes. The envelope is derived from the host cell during viral replication. Thus, the composition of the bilayer depends on the complex constitution of lipids from the host-cell’s organelle(s) where assembly and/or budding of the viral particle occurs. Here, molecular dynamics (MD) simulations of authentic, asymmetric HIV-1 liposomes are used to derive a unique level of resolution of its full-scale structure, mechanics and dynamics. Analysis of the structural properties reveal the distribution of thicknesses of the bilayers over the entire liposome as well as its global fluctuations. Moreover, full-scale mechanical analyses are employed to derive the global bending rigidity of HIV-1 liposomes. Finally, dynamical properties of the lipid molecules reveal important relationships between their 3D diffusion, the location of lipid-rafts and the asymmetrical composition of the envelope. Overall, our simulations reveal complex relationships between the rich lipid composition of the HIV-1 liposome and its structural, mechanical and dynamical properties with critical consequences to different stages of HIV-1’s life cycle.
59 BASIC BIOLOGICAL SCIENCES↗
Effect of Molybdenum Content on Structural, Mechanical, and Tribological Properties of Hot Isostatically Pressed β-Type Titanium Alloys for Orthopedic Applications
Aiming to develop alloys with better properties for orthopedic applications, the focus of the present research was to evaluate the effect of Mo at.% content on structural, mechanical, and tribological properties of hot isostatically pressed Ti-xMo (x = 4, 8, 12, 15, and 20 at.%) alloys. The structural evolution, mechanical properties, and tribological behavior of the nanostructured Ti-xMo alloys were evaluated using x-ray diffraction, scanning electron microscope, and ball-on-disk tribometer. Wear tests were conducted under different applied loads of 2, 8, and 16 N. Experimental results indicated that the structural evolution and morphological changes of the milled alloys were sensitive to their molybdenum (Mo) content. The morphological characterization showed that the crystallite size and the particle size decreased with increasing Mo content (at.%) reaching the lowest values of 27 and 26 nm in the case of Ti-15Mo and Ti-20Mo, respectively. On the other hand, the coefficient of friction and wear rates were found to be decreasing with increasing Mo content.
36 MATERIALS SCIENCE↗
The electronic structure, mechanical and thermodynamic properties of Mo{sub 2}XB{sub 2} and MoX{sub 2}B{sub 4} (X = Fe, Co, Ni) ternary borides
The mechanical properties, electronic structure and thermodynamic properties of the Mo{sub 2}XB{sub 2} and MoX{sub 2}B{sub 4} (X = Fe, Co, Ni) ternary borides were calculated by first-principles methods. The elastic constants show that these ternary borides are mechanically stable. Formation enthalpy of Mo{sub 2}XB{sub 2} and MoX{sub 2}B{sub 4} (X = Fe, Co, Ni) ternary borides are at the range of −118.09 kJ/mol to −40.14 kJ/mol. The electronic structures and chemical bonding characteristics are analyzed by the density of states. Mo{sub 2}FeB{sub 2} has the largest shear and Young's modulus because of its strong chemical bonding, and the values are 204.3 GPa and 500.3 GPa, respectively. MoCo{sub 2}B{sub 4} shows the lowest degree of anisotropy due to the lack of strong direction in the bonding. The Debye temperature of MoFe{sub 2}B{sub 4} is the largest among the six phases, which means that MoFe{sub 2}B{sub 4} possesses the best thermal conductivity. Enthalpy shows an approximately linear function of the temperature above 300 K. The entropy of these compounds increase rapidly when the temperature is below 450 K. The Gibbs free energy decreases with the increase in temperature. MoCo{sub 2}B{sub 4} has the lowest Gibbs free energy, which indicates the strongest formation ability in Mo{sub 2}XB{sub 2} and MoX{sub 2}B{sub 4} (X = Fe, Co, Ni) ternary borides.
36 MATERIALS SCIENCE↗
Ab-initio study of structural, mechanical and electronic properties of functionalized carbon nanotubes
We present exemplary results of extensive studies of structural, mechanical and electronic properties of covalent functionalization of carbon nanotubes (CNTs). We report new results for metallic (9,0), and semiconducting (10,0) single-wall carbon nanotubes (CNT) functionalized with -COOH, -OH, and both groups with concentration up to 12.5%. Our studies are performed in the framework of the density functional theory (DFT). We discuss here the stability, local and global changes in structure, elastic moduli (Young's, Shear, and Bulk), electronic structure and resulting band gaps, as a function of the density of the adsorbed molecules.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Structural, Mechanical, and Electrical Behavior of Ceramic-Reinforced Copper Metal Matrix Hybrid Composites
This article presents the structural, mechanical, and electrical behavior of ceramic-reinforced copper metal matrix hybrid composites developed by stir-casting technique. Commercial copper was used as matrix, and different weight percentages of boron carbide (B{sub 4}C), with constant weight percentage of tungsten carbide, boron nitride, and chromium, were used as reinforcements. Copper hybrid composites were characterized by high-resolution x-ray diffraction, optical microscope, scanning electron microscope, energy-dispersive analysis of x-ray, high-resolution scanning electron microscope, and Fourier transform infrared spectroscopy. Density, hardness, tensile strength, compressive strength, and electrical conductivity were also analyzed. These hybrid composites show improved mechanical properties such as hardness, tensile strength, and compressive strength, while relatively lower density and electrical conductivity were observed.
36 MATERIALS SCIENCE↗
Structural, mechanical, and magnetic properties of GaFe{sub 3}N thin films
Using the density-functional theory, the structural, mechanical, and magnetic properties were investigated for different GaFe{sub 3}N configurations: ferromagnetic, ferrimagnetic, paramagnetic, and nonmagnetic. Ferrimagnetic and high-spin ferromagnetic states exhibit the lowest energy and are the competing ground states as the total energy difference is 0.3 meV/atom only. All theoretically predicted values could be fully confirmed by experiments. For this, the authors synthesized phase pure, homogeneous, and continuous GaFe{sub 3}N films by combinatorial reactive direct current magnetron sputtering. Despite the low melting point of gallium, the authors succeeded in the growth of GaFe{sub 3}N films at a temperature of 500 °C. Those thin films exhibit a lattice parameter of 3.794 Å and an elastic modulus of 226 ± 20 GPa. Magnetic susceptibility measurements evidence a magnetic phase transitions at 8.0 ± 0.1 K. The nearly saturated magnetic moment at ±5 T is about 1.6 μB/Fe and is close to the theoretically determined magnetic moment for a ferrimagnetic ordering (1.72 μB/Fe).
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Nanoscale structure, mechanics and growth of epidermal cell walls
This article briefly reviews recent advances in nano-scale and micro-scale assessments of primary cell wall structure, mechanical behaviors and expansive growth. Cellulose microfibrils have hydrophobic and hydrophilic faces which may selectively bind different matrix polysaccharides and adjacent microfibrils. Furthermore, these distinctive binding interactions may guide partially aligned cellulose microfibrils in primary cell walls to form a planar, load-bearing network within each lamella of polylamellate walls. Consideration of expansive growth of cross-lamellate walls leads to a surprising inference: side-by-side sliding of microfibrils may be a key rate-limiting physical step, potentially targeted by specific wall loosening agents. Atomic force microscopy shows different patterns of microfibril movement during force-driven extension versus enzymatic loosening. Consequently, simulations of cell growth as elastic deformation of isotropic cell walls may need to be augmented to incorporate the distinctive behavior of growing cell walls.
59 BASIC BIOLOGICAL SCIENCES↗
Geometry-aware framework for deep energy method: An application to structural mechanics with hyperelastic materials
Here, in this work, we introduce a novel physics-informed framework named the Geometry-Aware Deep Energy Method (GADEM) for solving structural mechanics problems on different geometries. As the weak form of the physical system equation (or the energy-based approach) has demonstrated clear advantages compared to the strong form for solving solid mechanics problems, GADEM employs the weak form and aims to infer the solution on multiple shapes of geometries. Integrating a geometry-aware framework into an energy-based method results in an effective physics-informed deep learning model in terms of accuracy and computational cost. Different ways to represent the geometric information and to encode the geometric latent vectors are investigated in this work. We introduce a loss function of GADEM which is minimized based on the potential energy of all considered geometries. An adaptive learning method is also employed for the sampling of collocation points to enhance the performance of GADEM. We present some applications of GADEM to solve solid mechanics problems, including a loading simulation of a toy tire involving contact mechanics and large deformation hyperelasticity. The numerical results of this work demonstrate the remarkable capability of GADEM to infer the solution on various and new shapes of geometries using only one trained model.
97 MATHEMATICS AND COMPUTING↗
Brush-Coated Nanoparticle Polymer Thin Films: structure-mechanical-optical properties
Our work was devoted to understanding the structure and properties of a class of thin film polymer nanocomposites (PNCs). PNCs are composed of polymer hosts into which nanoparticles (metallic nanoparticles, quantum dots, nanorods, C 60 , nanotubes) are incorporated. PNCs exhibit a diverse range of functional properties (optical, electronic, mechanical, biomedical, structural), determined in part by the chemical composition of the polymer host and the type of nanoparticle. The properties PNCs rely not only on specific functional, size-dependent, behavior of the nanoparticles, but also on the dispersion, and organizational order in some cases, inter-nanoparticle separation distances, and on relative interactions between the nanoparticles and the host. Therefore the scientific challenges associated with understanding the interrelations between the structure and function/properties of PNCs are far more complex than may be understood based only on the knowledge of the compositions of the constituents. The challenges of understanding the structure-function behavior of PNCs are further compounded by the fact that control of the dispersion of the nanoparticles within the polymer hosts is difficult; one must learn how to disperse inorganic particles within an organic host. The goal of this proposal was to develop an understanding of the connection between the structure and the thermal (glass transition), mechanical and optical properties of a specific class of PNCs. Specifically PNCs composed of polymer chain grafted gold nanoparticles within polymer hosts. A major objective was to understand how to develop basic principles that enable the fabrication of functional materials possessing optimized morphologies and combinations of materials properties.
36 MATERIALS SCIENCE↗