Geometric and electrostatic modeling using molecular rigidity functions
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59 BASIC BIOLOGICAL SCIENCES↗
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Multiscale Persistent Functions for Biomolecular Structure Characterization
Here in this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions (MRFs) with persistent homology analysis, so as to construct a series of multiscale persistent functions, particularly multiscale persistent entropies, for structure characterization. To clarify the fundamental idea of our method, the multiscale persistent entropy (MPE) model is discussed in great detail. Mathematically, unlike the previous persistent entropy (Chintakunta et al. in Pattern Recognit 48(2):391–401, 2015; Merelli et al. in Entropy 17(10):6872–6892, 2015; Rucco et al. in: Proceedings of ECCS 2014, Springer, pp 117–128, 2016), a special resolution parameter is incorporated into our model. Various scales can be achieved by tuning its value. Physically, our MPE can be used in conformational entropy evaluation. More specifically, it is found that our method incorporates in it a natural classification scheme. This is achieved through a density filtration of an MRF built from angular distributions. To further validate our model, a systematical comparison with the traditional entropy evaluation model is done. Additionally, it is found that our model is able to preserve the intrinsic topological features of biomolecular data much better than traditional approaches, particularly for resolutions in the intermediate range. Moreover, by comparing with traditional entropies from various grid sizes, bond angle-based methods and a persistent homology-based support vector machine method (Cang et al. in Mol Based Math Biol 3:140–162, 2015), we find that our MPE method gives the best results in terms of average true positive rate in a classic protein structure classification test. More interestingly, all-alpha and all-beta protein classes can be clearly separated from each other with zero error only in our model. Finally, a special protein structure index (PSI) is proposed, for the first time, to describe the “regularity” of protein structures. Basically, a protein structure is deemed as regular if it has a consistent and orderly configuration. Our PSI model is tested on a database of 110 proteins; we find that structures with larger portions of loops and intrinsically disorder regions are always associated with larger PSI, meaning an irregular configuration, while proteins with larger portions of secondary structures, i.e., alpha-helix or beta-sheet, have smaller PSI. Essentially, PSI can be used to describe the “regularity” information in any systems.
59 BASIC BIOLOGICAL SCIENCES↗
Gaussian processes for inferring parton distributions
The extraction of parton distribution functions (PDFs) from experimental or lattice QCD data is an ill-posed inverse problem, where regularization strongly impacts both systematic uncertainties and the reliability of the results. We study a framework based on Gaussian Process Regression (GPR) to reconstruct PDFs from lattice QCD matrix elements. Within a Bayesian framework, Gaussian processes serve as flexible priors that encode uncertainties, correlations, and constraints without imposing rigid functional forms. We investigate a wide range of kernel choices, mean functions, and hyperparameter treatments. We quantify information gained from the data using the Kullback-Leibler divergence. Synthetic data tests demonstrate the consistency and robustness of the method. Our study establishes GPR as a systematic and non-parametric approach to PDF reconstruction, offering controlled uncertainty estimates and reduced model bias in lattice QCD analyses.
hadronic spectroscopy↗
An electrostatic spectral neighbor analysis potential for lithium nitride
Machine-learned interatomic potentials based on local environment descriptors represent a transformative leap over traditional potentials based on rigid functional forms in terms of prediction accuracy. However, a challenge in their application to ionic systems is the treatment of long-ranged electrostatics. Here, we present a highly accurate electrostatic Spectral Neighbor Analysis Potential (eSNAP) for ionic α-Li 3 N, a prototypical lithium superionic conductor of interest as a solid electrolyte or coating for rechargeable lithium-ion batteries. We show that the optimized eSNAP model substantially outperforms traditional Coulomb–Buckingham potential in the prediction of energies and forces, as well as various properties, such as lattice constants, elastic constants, and phonon dispersion curves. We also demonstrate the application of eSNAP in long-time, large-scale Li diffusion studies in Li 3 N, providing atomistic insights into measures of concerted ionic motion (e.g., the Haven ratio) and grain boundary diffusion. This work aims at providing an approach to developing quantum-accurate force fields for multi-component ionic systems under the SNAP formalism, enabling large-scale atomistic simulations for such systems.
36 MATERIALS SCIENCE↗
Excited state electron transfer in A 2 and A 2 B 2 functionalized zinc porphyrins carrying rigid and flexible β -pyrrole π-extended substituents
Optical absorption and emission, electrochemical, and photochemical properties of peripherally functionalized with flexible and rigid π-extended substituents on A 2 and A 2 B 2 type zinc porphyrins is investigated. The significance of rigid π-substituents over flexible ones in governing the spectral properties is unraveled. Flexible π-substituents on the porphyrin ring caused appreciable spectral broadening compared to porphyrin carrying rigid π-substituents. Further, supramolecular dyads are formed by coordinating phenyl imidazole functionalized fullerene, C 60 Im. Here, the calculated binding constants for the 1:1 complexes is in the order of 2–7 × 10 5 M −1 suggesting stable complex formation. Free-energy calculations performed according to the Rehm–Weller approach suggested possibility of excited state electron transfer in these dyads. Femtosecond transient absorption studies of the dyads performed in o-dichlorobenzene showed evidence of occurrence of electron transfer from the singlet-excited state that was in competition with the intersystem crossing process to populate the triplet-excited state of porphyrins.
A2 and A2B2 functionalized zinc↗
Intermediate scattering functions of a rigid body monoclonal antibody protein in solution studied by dissipative particle dynamic simulation
In the past decade, there was increased research interest in studying internal motions of flexible proteins in solution using Neutron Spin Echo (NSE) as NSE can simultaneously probe the dynamics at the length and time scales comparable to protein domain motions. However, the collective intermediate scattering function (ISF) measured by NSE has the contributions from translational, rotational, and internal motions, which are rather complicated to be separated. Widely used NSE theories to interpret experimental data usually assume that the translational and rotational motions of a rigid particle are decoupled and independent to each other. To evaluate the accuracy of this approximation for monoclonal antibody (mAb) proteins in solution, dissipative particle dynamic computer simulation is used here to simulate a rigid-body mAb for up to about 200 ns. The total ISF together with the ISFs due to only the translational and rotational motions as well as their corresponding effective diffusion coefficients is calculated. The aforementioned approximation introduces appreciable errors to the calculated effective diffusion coefficients and the ISFs. For the effective diffusion coefficient, the error introduced by this approximation can be as large as about 10% even though the overall agreement is considered reasonable. Thus, we need to be cautious when interpreting the data with a small signal change. In addition, the accuracy of the calculated ISFs due to the finite computer simulation time is also discussed.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Polymers with controlled assembly and rigidity made with click-functional peptide bundles
The engineering of biological molecules is a key concept in the design of highly functional, sophisticated soft materials. Biomolecules exhibit a wide range of functions and structures, including chemical recognition (of enzyme substrates or adhesive ligands, for example), exquisite nanostructures (composed of peptides, proteins or nucleic acids), and unusual mechanical properties (such as silk-like strength, stiffness, viscoelasticity and resiliency). Here we combine the computational design of physical (noncovalent) interactions with pathway-dependent, hierarchical ‘click’ covalent assembly to produce hybrid synthetic peptide-based polymers. The nanometre-scale monomeric units of these polymers are homotetrameric, α-helical bundles of low-molecular-weight peptides. These bundled monomers, or ‘bundlemers’, can be designed to provide complete control of the stability, size and spatial display of chemical functionalities. The protein-like structure of the bundle allows precise positioning of covalent linkages between the ends of distinct bundlemers, resulting in polymers with interesting and controllable physical characteristics, such as rigid rods, semiflexible or kinked chains, and thermally responsive hydrogel networks. Chain stiffness can be controlled by varying only the linkage. Moreover, by controlling the amino acid sequence along the bundlemer periphery, we use specific amino acid side chains, including non-natural ‘click’ chemistry functionalities, to conjugate moieties into a desired pattern, enabling the creation of a wide variety of hybrid nanomaterials.
36 MATERIALS SCIENCE↗
Thermally stable and self-healable lignin-based polyester
The increased use of plastics and the associated environmental impact has catalyzed research on the development of bio-derived polymers. Bio-based polyesters have gained increased attention due to the abundance of their starting materials and ease of processing. Lignin is naturally occurring in biomass with rich carbon content, whose functionality and rigidity make it an ideal bio-derived candidate for bio-based polyesters. Herein, a lignin-based polyester with good thermal stability and self-repairability was synthesized from carboxylated lignin and epoxidized soybean oil. The synthesized lignin/epoxidized soybean oil (ESO) vitrimer was brittle such that its mechanical performance could not be recorded. However, when polyethylene glycol (PEG) was incorporated as a plasticizer, polymer samples exhibited acceptable ductility. From thermomechanical analysis of the synthesized polyesters, the plasticizer did not impair thermal stability of polymers, but greatly enhanced mechanical properties. Notably, all samples exhibited stability at high temperatures, and good glass transition temperatures (51.0 ± 0.9–78.0 ± 1.2 °C). The highest tensile strength (3.983 ± 0.1 MPa) and storage modulus (1463.67 ± 12.6 MPa) were recorded for the polyester containing 6 % w/w PEG. Moreover, the polymer samples exhibited self-healing capability at 180 °C. This work expands on valorization of lignin through the synthesis of bio-derived materials.
36 MATERIALS SCIENCE↗
First-Principles Quantum Transport Modeling of Spin-Transfer and Spin-Orbit Torques in Magnetic Multilayers
A unified approach for computing (i) spin-transfer torque in magnetic trilayers like spin valve and magnetic tunnel junction, where injected charge current flows perpendicularly to interfaces, and (ii) spin-orbit torque in magnetic bilayers of the type ferromagnet/spin-orbit-coupled material, where injected charge current flows parallel to the interface, was reviewed. The experimentally explored and technologically relevant spin-orbit-coupled materials include 5d heavy metals, topological insulators, Weyl semimetals, and transition metal dichalcogenides. This approach requires to construct the torque operator for a given Hamiltonian of the device and the steady-state nonequilibrium density matrix, where the latter is expressed in terms of the nonequilibrium Green’s functions and split into three contributions. Tracing these contributions with the torque operator automatically yields field-like and damping-like components of spin-transfer torque or spin-orbit torque vector, which is particularly advantageous for spin-orbit torque where the direction of these components depends on the unknown-in-advance orientation of the current-driven nonequilibrium spin density in the presence of spin-orbit coupling. Illustrative examples are provided by computing spin-transfer torque in a one-dimensional toy model of a magnetic tunnel junction and realistic Co/Cu/Co spin valve, both of which are described by first-principles Hamiltonians obtained from noncollinear density functional theory calculations, as well as by computing spin-orbit torque in a ferromagnetic layer described by a tight-binding Hamiltonian which includes spin-orbit proximity effect within ferromagnetic monolayers assumed to be generated by the adjacent monolayer transition metal dichalcogenide. In addition, it is shown here how spin-orbit proximity effect, quantified by computing (via first-principles retarded Green’s function) spectral functions and spin textures on monolayers of realistic ferromagnetic material like Co in contact with heavy metal or monolayer transition metal dichalcogenide, can be tailored to enhance the magnitude of spin-orbit torque. Furthermore, errors made in the calculation of spin-transfer torque are quantified when using Hamiltonian from collinear density functional theory, with rigidly rotated magnetic moments to create noncollinear magnetization configurations, instead of proper (but computationally more expensive) self-consistent Hamiltonian obtained from noncollinear density functional theory.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Rigid-Rod Sulfonated Polyamide as an Aqueous-Processable Binder for Li-Ion Battery Electrodes
Polymer binders are important components of most battery electrodes, ensuring high performance and long-term durability. Increasing demand for lithium-ion batteries in the automotive, stationary power, and portable electronics industries calls for a greener binder to replace poly(vinylidene difluoride) (PVDF). We evaluate the performance of aqueous solution-processed electrodes prepared with a rigid-rod polymer binder, poly(2,2'-disulfonyl-4,4'-benzidine terephthalamide) (PBDT). The polyamide backbone and double-helical configuration of PBDT give rise to its mechanical strength and rigidity, and its functional nature (H-bonding amides and sulfonates) can provide specific binding with electrode particles. LiFePO 4 electrodes prepared with 3 wt% PBDT show mechanical integrity and cycling stability, achieving over 1000 cycles at 4C rate with negligible capacity decay. These electrodes demonstrate comparable rate performance with their PVDF counterparts while eliminating fluorine from the electrode as well as the organic solvents needed for processing. Furthermore, this study reveals that PBDT holds great potential as a binder for advanced sustainable batteries.
25 ENERGY STORAGE↗
First Analysis of Earth's Stratospheric γ ‐Ray Emission in Geographical Coordinates With Fermi LAT
Abstract From low‐Earth orbit, the Earth is an extremely bright γ ‐ray source compared to distant astrophysical objects. The high‐energy γ ‐ray emission, from the Earth's upper atmosphere, is produced by the interactions between cosmic rays (CRs) and air molecules. As CRs are predominantly charged particles, the geomagnetic field acts as a spectrometer, forbidding CRs below a certain energy to arrive and interact with the atmosphere at a given geomagnetic location from a given direction. We use photon data between 0.2 and 20 GeV as observed by the Fermi Large Area Telescope (LAT) to create, for the first time, stratospheric γ ‐ray emission maps of the Earth in the geographical coordinate system, for different viewing directions from LAT altitude. These maps confirm a strong association between measured γ ‐ray fluxes and geomagnetic cutoffs for CRs. We also report the spectrum of the Earth's stratospheric γ ‐ray emission in cardinal directions and use the geomagnetic spectrometer effect to infer the atmosphere's yield function of γ rays per incoming CR proton as a function of CR rigidity at the altitude of the Fermi spacecraft. This work is relevant to the study of near‐Earth radiation exposure for astronauts and spacecraft, modeling the geomagnetic field, and CR‐air interactions.
Madlee, S.↗
Correlating Local Compositions and Structures with the Macroscopic Optical Properties of Ce 3+ -Doped CaSc 2 O 4 , an Efficient Green-Emitting Phosphor
Calcium scandate (CaSc 2 O 4 ) substituted with small amounts (<1%) of Ce 3+ is a recently discovered bright-green-emitting phosphor with favorable light absorption and emission properties and robust temperature stability that make it well-suited for solid-state white-lighting applications. Combined analyses of scattering, solid-state nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR), and photoluminescence measurements establish the compositional and structural origins of the macroscopic optical properties of this phosphor material. Simultaneous refinements of synchrotron X-ray and neutron diffraction data of Ce 3+ -doped CaSc 2 O 4 enable the average crystal structure to be determined, which is shown to correspond to an exceedingly rigid host structure, as corroborated by density functional theory (DFT) calculations. Such structural rigidity leads to high quantum efficiency, which is optimized by the substitution of as little as 0.5 mol % of Ce 3+ for Ca 2+ ions, with higher extents of Ce 3+ substitution leading to decreased photoluminescent quantum yields. Solid-state 43 Ca and 45 Sc magic-angle spinning (MAS) NMR spectra are sensitive to the effects of the paramagnetic Ce 3+ dopant ions on nearby atoms in the host structure and yield evidence for local structural distortions. EPR measurements provide direct insights on structures of the Ce 3+ ions, as a function of Ce 3+ substitution. The combined scattering and spectroscopic analyses yield detailed new understanding of the local and long-range structures of Ce 3+ -doped CaSc 2 O 4 , which account for the sensitive composition-dependent optical properties of this important phosphor material.
36 MATERIALS SCIENCE↗
Dry Printing Pure Copper with High Conductivity and Adhesion for Flexible Electronics
Additive manufacturing of functional devices on various rigid and flexible substrates is rising rapidly due to their design flexibility, rapid manufacturing, and lower cost. Current printing technologies are ink-based and focused on printing silver (Ag) as conductive lines due to its matured ink formulation process, low sintering temperature, ease of printing, and low oxidation rate. However, Ag is the 68th most abundant element on Earth, while copper (Cu) is the 25th, making it much cheaper (>100×) while having a comparable conductivity to Ag. Therefore, printing Cu has become technologically and economically more attractive than Ag. Nevertheless, Cu printing is still a significant challenge in ink-based printing methods due to the higher sintering temperature relative to the glass-transition temperature of most flexible substrates, the higher oxidation rate, the challenging ink formulation process, and ink stability concerns. Here, we demonstrate printing highly conductive Cu on flexible polyimide substrates using a dry printing technique. Cu nanoparticles (~3–30 nm) are generated by on-demand laser ablation of a solid Cu target inside the printer head and under argon background gas. These Cu nanoparticles are then transported through a nozzle and onto the substrate, where they are laser-sintered in real time. The argon gas plays three critical roles in laser plume condensation for nanoparticle generation, transport, and sheath gas to avoid oxidation during sintering. The sintered nanoparticles thus show high electrical conductivity and mechanical stability under static and cyclic tests. Our dry printing technique can potentially revolutionize how electronic devices and sensors are additively manufactured for earth and space applications.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Arene Substitution Design for Controlled Conformational Changes of Dibenzocycloocta-1,5-dienes
We report that the agile eight-mernbered cycloalkane can be stabilized by fusing two rigid benzene rings, substituted with proper functional groups. The conformational change of dibenzocycloocta-1,S-diene (DBCOD), a rigid-flexible-rigidorganic moiety, from Boat to Chair conformation requires an activation energy of 42 kJ/mol that is substantially lower than that of existing submolecular shape-changing unit. Experimental data corroborated by theory calculations demonstrate that intramolecular hydrogen bonding can stabilize Boat whereas electron repulsive interaction from opposing ester substituents favors Chair. Intramolecular hydrogen bonding, formed by 1,10-diamide substitution stabilizes Boat, spiking the temperature at which Boat and Chair can readily interchange from -60 °C to 60 °C. Concomitantly this intramolecular attraction raises the energy barrier from 42 kJ/mol of unsubstituted DBCOD to 68 kJ/mol of diamide-substituted DBCOD. Remarkably, this value falls within the range of the activation energy of highly efficient enzyme catalyzed biological reactions. With shape changes once considered only possible with high-energy, our work reveals a potential pathway exemplified by a specific submolecular structure to achieve low-energy driven shape changes for the first time. Together with intrinsic cycle stability and high energy output systems that would have incurred damage under high-energy stimuli, could particularly benefit from this new kind of low-energy driven shape-changing mechanism. This work has laid the basis to construct systems for low-energy driven stimuli-responsive applications, hitherto a challenge to overcome.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Coexistence of Multilayered Phases of Confined Water: The Importance of Flexible Confining Surfaces
Flexible nanoscale confinement is critical to understanding the role that bending fluctuations play on biological processes where soft interfaces are ubiquitous or to exploit confinement effects in engineered systems where inherently flexible 2D materials are pervasively employed. Here, using molecular dynamics simulations, we compare the phase behavior of water confined between flexible and rigid graphene sheets as a function of the in-plane density, ρ2D. We find that both cases show commensurate mono-, bi-, and trilayered states; however, the water phase in those states and the transitions between them are qualitatively different for the rigid and flexible cases. The rigid systems exhibit discontinuous transitions between an ( n )-layer and an ( n +1)-layer state at particular values of ρ2D, whereas under flexible confinement, the graphene sheets bend to accommodate an ( n )-layer and an (n+1)-layer state coexisting in equilibrium at the same density. We show that the flexible walls introduce a very different sequence of ice phases and their phase coexistence with vapor and liquid phases than that observed with rigid walls. We discuss the applicability of these results to real experimental systems to shed light on the role of flexible confinement and its interplay with commensurability effects.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Dynamical Transition of Collective Motions in Dry Proteins
Water is widely assumed to be essential for protein dynamics and function. In particular, the well-documented “dynamical” transition at ~ 200 K , at which the protein changes from a rigid, nonfunctional form to a flexible, functional state, as detected in hydrogenated protein by incoherent neutron scattering, requires hydration. We report on coherent neutron scattering experiments on perdeuterated proteins and reveal that a transition occurs in dry proteins at the same temperature resulting primarily from the collective heavy-atom motions. Furthermore, the dynamical transition discovered is intrinsic to the energy landscape of dry proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Functional composites by programming entropy-driven nanosheet growth
Here, nanomaterials must be systematically designed to be technologically viable. Driven by optimizing intermolecular interactions, current designs are too rigid to plug in new chemical functionalities and cannot mitigate condition differences during integration. Despite extensive optimization of building blocks and treatments, accessing nanostructures with the required feature sizes and chemistries is difficult. Programming their growth across the nano-to-macro hierarchy also remains challenging, if not impossible. To address these limitations, we should shift to entropy-driven assemblies to gain design flexibility, as seen in high-entropy alloys, and program nanomaterial growth to kinetically match target feature sizes to the mobility of the system during processing. In tis report, following a micro-then-nano growth sequence in ternary composite blends composed of block-copolymer-based supramolecules, small molecules and nanoparticles, we successfully fabricate high-performance barrier materials composed of more than 200 stacked nanosheets (125 nm sheet thickness) with a defect density less than 0.056 µm -2 and about 98% efficiency in controlling the defect type. Contrary to common perception, polymer-chain entanglements are advantageous to realize long-range order, accelerate the fabrication process (<30 min) and satisfy specific requirements to advance multilayered film technology. This study showcases the feasibility, necessity and unlimited opportunities to transform laboratory nanoscience into nanotechnology through systems engineering of self-assembly.
42 ENGINEERING↗
Constraining the Charge-Sign and Rigidity-Dependence of Solar Modulation
Our ability to identify the sources of cosmic rays and understand how these particles propagate through the interstellar medium is hindered by the combined effects of the solar wind and its embedded magnetic field, collectively known as solar modulation. In this paper, we build upon our previous work to model and constrain the effects of solar modulation on the cosmic-ray spectrum, using data from AMS-02 and BESS Polar II collected between 2007 and 2012, during which the heliospheric magnetic field was in a state of negative polarity. Our model uses measurements of the heliospheric magnetic field and the tilt angle of the heliospheric current sheet to accurately predict the effects of solar modulation as a function of time, charge, and rigidity. By incorporating data from a period of negative polarity, we have been able to robustly observe and constrain the charge-dependent effects of solar modulation.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗