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Theoretical Model Study of Interplay of Coulomb Interaction and Electron-Phonon Interaction in the Thermal Properties of Monolayer Graphene
We propose here a tight-binding (TB) model Hamiltonian for monolayer graphene-on-substrate describing the nearest-neighbor-hopping, on-site Coulomb interaction on the sub-lattices and the electron-phonon interaction under the high-frequency limit of phonon vibration. Applying Lang-Firsov canonical transformation, the electron and phonon systems are decoupled in the atomic Hamiltonian, such that the effective Coulomb interaction and effective nearest-neighbor-hopping integral respectively appear as U-tilde =U−2t{sub 1}λ and t-tilde {sub 1}=t{sub 1}e{sup ((−t{sub 1}λ)/(ω{sub 0}))}, where U, t{sub 1}, λ and ω{sub 0} are respectively Coulomb energy, nearest-neighbor-hopping integral, electron-phonon (e-ph) coupling and phonon frequency. The effective Coulomb interaction in the Hamiltonian is considered within mean-field approximation. The Hamiltonian is solved by Zubarev’s Green’s function technique. The temperature-dependent electronic entropy and specific heat are calculated from the free energy of graphene system and are computed numerically. The temperature-dependent electronic specific heat exhibits a charge gap peak at room temperature arising due to the effect of Coulomb interaction and electron-phonon interaction. The evolution of these peaks in specific heat is investigated by varying the model parameters of the system.
Interactions between displacement cascade and dislocation and their influences on Peierls stress in Fe-20Cr-25Ni alloys
The interactions between dislocations and displacement cascades are investigated using molecular dynamics simulations. The primary knock-on atoms (PKAs) are placed at different distances to edge and screw dislocation lines. Specifically, an fcc Fe-20Cr-25Ni system is studied; the alloy is the based alloy for Alloy 709. The number of defects is calculated using Wigner-Seitz analysis in order to illustrate the effect of dislocations on cascades. The displacement cascades in systems containing dislocations tend to generate more total defects compared with bulk systems, but eventually lead to less surviving defects in the materials matrix due to interactions with dislocations. The changes in atomic structures of the dislocations after interacting with cascades are analyzed to understand how the primary damage affects dislocations. The displacement cascade potentially causes dislocation climb in edge dislocations and cross-slip in screw dislocations, which could serve as additional mechanisms contributing to the radiation-induced hardening (RIH) compared with conventional RIH models. To reveal this, Peierls stresses are calculated before and after cascades using molecular static simulations. This study provides critical information of how defect production and dislocations are correlated, especially when total dose is high, which needs to be taken into account in upper scale models, such as mean-field rate theory.
The Primary Interaction Compton Couple algorithm for sorting GRETINA/GRETA interaction points
The Primary Interaction Compton Couple (PICC) algorithm is presented in this work. The algorithm is used to determine the first-interaction-point position for $γ$-ray events in GRETINA. The first-interaction-point position is crucial for in-beam $γ$-ray spectroscopy experiments with fast beams due to the effect of Doppler broadening on the in-beam energy resolution. The development of the algorithm and its performance compared to a tracking algorithm and the Main Interaction assumption is presented. The PICC algorithm is demonstrated with real data to outperform the $γ$-ray energy tracking algorithm used for comparison here and the Main Interaction assumption in first-interaction-point determinations.
Protein–Mineral Interactions: Molecular Dynamics Simulations Capture Importance of Variations in Mineral Surface Composition and Structure
Molecular dynamics simulations, conventional and metadynamics, were performed to determine the interaction of model protein Gb1 over kaolinite (001), Na+-montmorillonite (001), Ca2+-montmorillonite (001), goethite (100), and Na+-birnessite (001) mineral surfaces. Gb1, a small (56 residue) protein with a well-characterized solution-state nuclear magnetic resonance (NMR) structure and having α-helix, four-fold β-sheet, and hydrophobic core features, is used as a model protein to study protein soil mineral interactions and gain insights on structural changes and potential degradation of protein. From our simulations, we observe little change to the hydrated Gb1 structure over the kaolinite, montmorillonite, and goethite surfaces relative to its solvated structure without these mineral surfaces present. Over the Na+-birnessite basal surface, however, the Gb1 structure is highly disturbed as a result of interaction with this birnessite surface. Unraveling of the Gb1 β-sheet at specific turns and a partial unraveling of the α-helix is observed over birnessite, which suggests specific vulnerable residue sites for oxidation or hydrolysis possibly leading to fragmentation.
Interparticle Interactions in Dilute Solutions of Polyelectrolyte Complex Micelles.
The application of dilute solutions of poly electrolyte complex (PEC) micelles for delivering therapeutic nucleic acids into disease sites has gained momentum. This Letter reports a detailed characterization of PEC micelles in dilute solutions including their internal structures and the determination of the interparticle interactions. The polymer concentration ranges from 0.1 to 0.5 wt %, a regime where micelle-micelle interactions are infrequent. We employ synchrotron small-angle X-ray scattering (SAXS) to simultaneously probe the morphology, internal structure, and radius of gyration (R-g) of the self-assemblies formed by charged diblock polyelectrolytes and homopolyelectrolytes. The emerging appearance of the structure factor in SAXS profiles with the increasing polymer concentration demonstrates the presence of the repulsive intermicellar correlations, which is further confirmed by the differences between the "reciprocal R-g" estimated by Guinier approximation and the "real space R-g" determined by pair distribution functions. We find that the soft corona chains tethered on the surface of phase-separated complex domains are compressed when micelles come close to the point where a hard-sphere interaction takes over. These findings contribute to the fundamental understanding of the structure and space-filling constraints in the complexation-driven self-assemblies and advance the rational design of cationic polymer-based nonviral gene delivery vectors.
Plasmon–Exciton Interactions Probed Using Spatial Coentrapment of Nanoparticles by Topological Singularities
We study plasmon-exciton interaction by using topological singularities to spatially confine, selectively deliver, cotrap and optically probe colloidal semiconductor and plasmonic nanoparticles. The interaction is monitored in a single quantum system in the bulk of a liquid crystal medium where nanoparticles are manipulated and nanoconfined far from dielectric interfaces using laser tweezers and topological configurations containing singularities. When quantum dot-in-a-rod particles are spatially colocated with a plasmonic gold nanoburst particle in a topological singularity core, its fluorescence increases because blinking is significantly suppressed and the radiative decay rate increases by nearly an order of magnitude owing to the Purcell effect. We argue that the blinking suppression is the result of the radiative rate change that mitigates Auger recombination and quantum dot ionization, consequently reducing nonradiative recombination. Our work demonstrates that topological singularities are an effective platform for studying and controlling plasmon-exciton interactions.
Cellulose–hemicellulose interactions at elevated temperatures increase cellulose recalcitrance to biological conversion
It has been previously shown that cellulose-lignin droplets’ strong interactions, resulting from lignin coalescence and redisposition on cellulose surface during thermochemical pretreatments, increase cellulose recalcitrance to biological conversion, especially at commercially viable low enzyme loadings. However, information on the impact of cellulose–hemicellulose interactions on cellulose recalcitrance following relevant pretreatment conditions are scarce. Here, to investigate the effects of plausible hemicellulose precipitation and re-association with cellulose on cellulose conversion, different pretreatments were applied to pure Avicel® PH101 cellulose alone and Avicel mixed with model hemicellulose compounds followed by enzymatic hydrolysis of resulting solids at both low and high enzyme loadings. Solids produced by pretreatment of Avicel mixed with hemicelluloses (AMH) were found to contain about 2 to 14.6% of exogenous, precipitated hemicelluloses and showed a remarkably much lower digestibility (up to 60%) than their respective controls. However, the exogenous hemicellulosic residues that associated with Avicel following high temperature pretreatments resulted in greater losses in cellulose conversion than those formed at low temperatures, suggesting that temperature plays a strong role in the strength of cellulose–hemicellulose association. Molecular dynamics simulations of hemicellulosic xylan and cellulose were found to further support this temperature effect as the xylan–cellulose interactions were found to substantially increase at elevated temperatures. Furthermore, exogenous, precipitated hemicelluloses in pretreated AMH solids resulted in a larger drop in cellulose conversion than the delignified lignocellulosic biomass containing comparably much higher natural hemicellulose amounts. In conclusion, increased cellulase loadings or supplementation of cellulase with xylanases enhanced cellulose conversion for most pretreated AMH solids; however, this approach was less effective for solids containing mannan polysaccharides, suggesting stronger association of cellulose with (hetero) mannans or lack of enzymes in the mixture required to hydrolyze such polysaccharides.
Photoelectron spectroscopy and computational investigations of the electronic structures and noncovalent interactions of cyclodextrin-closo-dodecaborate anion complexes x-CD·B12X122- (x = a, ß, y; X = H, F)
We report a joint negative ion photoelectron spectroscopy (NIPES) and computational study on the electronic structures and noncovalent interactions of a series of cyclodextrin-closo-dodecaborate dianion complexes, ?-CD·B12X122- (? = a, ß, ?; X = H, F). The measured vertical / adiabatic detachment energies (VDEs / ADEs) are 1.15/0.93, 3.55/3.20, 3.90/3.60, and 3.85/3.60 eV for B12H122- and its a-, ß-, ?-CD complexes, respectively; while the corresponding values are 1.90/1.70, 4.00/3.60, 4.33/3.95, and 4.30/3.85 eV for the X = F case. These results show that the inclusion of B12X122- into the CD cavities greatly increase the electronic stability of the dianions. The effect of electronic stabilization for ß-CD is roughly the same as for ?-CD, both being considerably stronger than that for a-CD. Density functional theory (DFT) based geometry optimization reveals that B12X122- are inserted into CDs increasingly deeper from a-CD to ?-CD. The calculated VDEs and ADEs agree with the experiments well, particularly, reproducing the electron binding energy (EBE) trends. The molecular orbital analyses indicate that the most loosely bound photodetached electrons origin from the guest B12X122- moieties. In addition to a shift of all signals to larger EBE, significant changes in the signal patterns are observed. At low EBE, this is due to the splitting of highly degenerate B12X122- orbitals, while at high EBE, photodetachment from CD oxygens contributes to the new bands. The guest B12X122- and host CD nocovalent, size-specific interaction based on the independent gradient model (IGM) and energy decomposition analysis (EDA), is dominated by electrostatic interactions. The analysis further unravels unambiguiously the existence of dihydrogen bonding and how it affects the total energy that stabilizes the host-guest complexes of CDs·B12H122- compared to the general hydrogen bonding interaction in CDs·B12F122-. This work clearly exhibits strong influences on the electronic structures of dodecaborates upon clustering with CDs, with both size (a-, ß-, ?-) and molecular (X = H or F) specificities, thus providing critical molecular-level information on the cyclodextrin-closo-dodecaborate interactions of interest to medical applications, e.g. Boron neutron capature therapy. The NIPES experiments done at PNNL were supported by the U.S. Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Bioscience (X.-B.W.) and was performed at the EMSL, a national scientific user facility sponsored by DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. H.S. and Z.S. acknowledge the funding support of National Natural Science Foundation of China (Nos.11727810, 61720106009 and 21603074), the Science and Technology Commission of Shanghai Municipality (Nos. 19JC1412200), and the Program of Introducing Talents of Discipline to Universities 111 project (B12024). Z. L. thanks the China Scholarship Council (CSC) for financial support. We acknowledge the ECNU Multifunctional Platform for Innovation (001) and HPC Research Computing Team for providing computational and storage resources. J.W. acknowledges support from the Alexander von Humboldt foundation (Feodor Lynen Fellowship and Rückkehrerstipendium), a Freigeist fellowship of the Volkswagenfoundation and Prof. Vladimir A. Azov for helpful discussions.
On the representation of many-body interactions in water
Recent work has shown that the many-body expansion of the interaction energy can be used to develop analytical representations of global potential energy surfaces (PESs) for water. In this study, the role of short- and long-range interactions at different orders is investigated by analyzing water potentials that treat the leading terms of the many-body expansion through implicit (i.e., TTM3-F and TTM4-F PESs) and explicit (i.e., WHBB and MB-pol PESs) representations. It is found that explicit short-range representations of 2-body and 3-body interactions along with a physically correct incorporation of short- and long-range contributions are necessary for an accurate representation of the water interactions from the gas to the condensed phase. Similarly, a complete many-body representation of the dipole moment surface is found to be crucial to reproducing the correct intensities of the infrared spectrum of liquid water.
Galvano-rotational effect induced by electroweak interactions in pulsars
We study electroweakly interacting particles in rotating matter. The existence of the electric current along the axis of the matter rotation is predicted in this system. This new galvano-rotational effect is caused by the parity violating interaction between massless charged particles in the rotating matter. We start with the exact solution of the Dirac equation for a fermion involved in the electroweak interaction in the rotating frame. This equation includes the noninertial effects. Then, using the obtained solution, we derive the induced electric current which turns out to flow along the rotation axis. We study the possibility of the appearance of the galvano-rotational effect in dense matter of compact astrophysical objects. The particular example of neutron and hypothetical quark stars is discussed. It is shown that, using this effect, one can expect the generation of toroidal magnetic fields comparable with poloidal ones in old millisecond pulsars. We also briefly discuss the generation of the magnetic helicity in these stars. Finally we analyze the possibility to apply the galvano-rotational effect for the description of the asymmetric neutrino emission from a neutron star to explain pulsars kicks.
Complementary test of the dark matter self-interaction in dark U(1) model by direct and indirect dark matter detection
The halo dark matter (DM) can be captured by the Sun if its final velocity after the collision with a nucleus in the Sun is less than the escape velocity. We consider a selfinteracting dark matter (SIDM) model where U(1) gauge symmetry is introduced to account for the DM self-interaction. Such a model naturally leads to isospin violating DM-nucleon interaction, although isospin symmetric interaction is still allowed as a special case. We present the IceCube-PINGU 2σ sensitivity to the parameter range of the above model with 5 years of search for neutrino signature from DM annihilation in the Sun. This indirect detection complements the direct detection by probing those SIDM parameter ranges which are either the region for very small m{sub χ} or the region opened up due to isospin violations.
Evidence for dark matter interactions in cosmological precision data?
We study a two-parameter extension of the cosmological standard model ΛCDM in which cold dark matter interacts with a new form of dark radiation. The two parameters correspond to the energy density in the dark radiation fluid Δ N fluid and the interaction strength between dark matter and dark radiation. The interactions give rise to a very weak "dark matter drag" which damps the growth of matter density perturbations throughout radiation domination, allowing to reconcile the tension between predictions of large scale structure from the CMB and direct measurements of σ 8 . We perform a precision fit to Planck CMB data, BAO, large scale structure, and direct measurements of the expansion rate of the universe today. Our model lowers the χ-squared relative to ΛCDM by about 12, corresponding to a preference for non-zero dark matter drag by more than 3σ. Particle physics models which naturally produce a dark matter drag of the required form include the recently proposed non-Abelian dark matter model in which the dark radiation corresponds to massless dark gluons.
Fragility of ferromagnetic double exchange interactions and pressure tuning of magnetism in 3 d - 5 d double perovskite Sr 2 FeOsO 6
The ability to tune exchange (magnetic) interactions between 3d transition metals in perovskite structures has proven to be a powerful route to discovery of novel properties. Here we demonstrate that the introduction of 3d-5d exchange pathways in double perovskites enables additional tunability, a result of the large spatial extent of 5d wave functions. Using x-ray probes of magnetism and structure at high pressure, we show that compression of Sr2FeOsO6 drives an unexpected continuous change in the sign of Fe-Os exchange interactions and a transition from antiferromagnetic to ferrimagnetic order. We analyze the relevant electron-electron interactions, shedding light into fundamental differences with the more thoroughly studied 3d-3d systems.
XYLEM NAC DOMAIN1, an angiosperm NAC transcription factor, inhibits xylem differentiation through conserved motifs that interact with RETINOBLASTOMA‐RELATED
Summary The Arabidopsis thaliana gene XYLEM NAC DOMAIN1 ( XND1 ) is upregulated in xylem tracheary elements. Yet overexpression of XND1 blocks differentiation of tracheary elements. The molecular mechanism of XND1 action was investigated. Phylogenetic and motif analyses indicated that XND1 and its homologs are present only in angiosperms and possess a highly conserved C‐terminal region containing linear motifs (CKII‐acidic, LXCXE, E2F TD ‐like and LXCXE‐mimic) predicted to interact with the cell cycle and differentiation regulator RETINOBLASTOMA‐RELATED (RBR). Protein–protein interaction and functional analyses of XND1 deletion mutants were used to test the importance of RBR‐interaction motifs. Deletion of either the LXCXE or the LXCXE‐mimic motif reduced both the XND1–RBR interaction and XND1 efficacy as a repressor of differentiation, with loss of the LXCXE motif having the strongest negative impacts. The function of the XND1 C‐terminal domain could be partially replaced by RBR fused to the N‐terminal domain of XND1. XND1 also transactivated gene expression in yeast and plants. The properties of XND1, a transactivator that depends on multiple linear RBR‐interaction motifs to inhibit differentiation, have not previously been described for a plant protein. XND1 harbors an apparently angiosperm‐specific combination of interaction motifs potentially linking the general differentiation regulator RBR with a xylem‐specific pathway for inhibition of differentiation.
Repopulation of interacting tumor cells during fractionated radiotherapy: Stochastic modeling of the tumor control probability
Purpose: Optimal treatment planning for fractionated external beam radiation therapy requires inputs from radiobiology based on recent thinking about the “five Rs” (repopulation, radiosensitivity, reoxygenation, redistribution, and repair). The need is especially acute for the newer, often individualized, protocols made feasible by progress in image guided radiation therapy and dose conformity. Current stochastic tumor control probability (TCP) models incorporating tumor repopulation effects consider “stem-like cancer cells” (SLCC) to be independent, but the authors here propose that SLCC-SLCC interactions may be significant. The authors present a new stochastic TCP model for repopulating SLCC interacting within microenvironmental niches. Our approach is meant mainly for comparing similar protocols. It aims at practical generalizations of previous mathematical models. Methods: The authors consider protocols with complete sublethal damage repair between fractions. The authors use customized open-source software and recent mathematical approaches from stochastic process theory for calculating the time-dependent SLCC number and thereby estimating SLCC eradication probabilities. As specific numerical examples, the authors consider predicted TCP results for a 2 Gy per fraction, 60 Gy protocol compared to 64 Gy protocols involving early or late boosts in a limited volume to some fractions. Results: In sample calculations with linear quadratic parameters α = 0.3 per Gy, α/β = 10 Gy, boosting is predicted to raise TCP from a dismal 14.5% observed in some older protocols for advanced NSCLC to above 70%. This prediction is robust as regards: (a) the assumed values of parameters other than α and (b) the choice of models for intraniche SLCC-SLCC interactions. However, α = 0.03 per Gy leads to a prediction of almost no improvement when boosting. Conclusions: The predicted efficacy of moderate boosts depends sensitively on α. Presumably, the larger values of α are the ones appropriate for individualized treatment protocols, with the smaller values relevant only to protocols for a heterogeneous patient population. On that assumption, boosting is predicted to be highly effective. Front boosting, apart from practical advantages and a possible advantage as regards iatrogenic second cancers, also probably gives a slightly higher TCP than back boosting. If the total number of SLCC at the start of treatment can be measured even roughly, it will provide a highly sensitive way of discriminating between various models and parameter choices. Updated mathematical methods for calculating repopulation allow credible generalizations of earlier results.
Metabolic Interactions between Brachypodium and Pseudomonas fluorescens under Controlled Iron-Limited Conditions
Plant iron (Fe) nutritional status has a significant impact on rhizosphere microbial communities. While this effect has been attributed to alterations in the composition of root exudates, the underlying mechanisms are not known. Here, we investigated the effect of Fe deficiency on the interactions between the grass Brachypodium distachyon and the common soil bacteria Pseudomonas fluorescens SBW25. Increased phytosiderophore production was the most significant response of Brachypodium root exudation to Fe deficiency. We observed upregulated expression of phytosiderophore biosynthesis genes but lower accumulated exudate concentrations in the presence of Pseudomonas, indicating that the bacteria degrade these phytosiderophores. Pseudomonas did not produce endogenous siderophores under the low Fe conditions. Rather, the bacterial transcriptome revealed upregulation of four genes in response to Fe deficiency that contain motifs associated with cellular uptake of small molecules. Collectively, these results suggest that rhizosphere Pseudomonas fluorescens may take up phytosiderophores produced by grasses in response to Fe deficiency, and we propose target genes that may be involved. Our findings provide insight into the molecular basis for the exchange of C, N, and Fe between plants and bacteria under Fe deficient conditions. These interactions may contribute to differences in the rhizosphere microbial community structure across soil pH regimes.