Positive Binding Energy Research Articles

Disruption of dark matter substructure: fact or fiction?

Accurately predicting the demographics of dark matter (DM) substructure is of paramount importance for many fields of astrophysics, including gravitational lensing, galaxy evolution, halo occupation modeling, and constraining the nature of dark matter. Because of its strongly non-linear nature, DM substructure is typically modeled using N-body simulations, which reveal that large fractions of DM subhaloes undergo complete disruption. In this paper we use both analytical estimates and idealized numerical simulations to investigate whether this disruption is mainly physical, due to tidal heating and stripping, or numerical (i.e., artificial). We show that, contrary to naive expectation, subhaloes that experience a tidal shock $\Delta E$ that exceeds the subhalo's binding energy, $|E_{\rm b}|$, do not undergo disruption, even when $\Delta E/|E_{\rm b}|$ is as large as 100. Along the same line, and contrary to existing claims in the literature, instantaneously stripping matter from the outskirts of a DM subhalo also does not result in its complete disruption, even when the instantaneous remnant has positive binding energy. In addition, we show that tidal heating due to high-speed (impulsive) encounters with other subhaloes (`harassment'), is negligible compared to the tidal effects due to the host halo. Hence, we conclude that, in the absence of baryonic processes, the complete, physical disruption of CDM substructure is extremely rare, and that most disruption in numerical simulations therefore must be artificial. We discuss various processes that have been associated with numerical overmerging, and conclude that inadequate force-softening is the most likely culprit.

Non-equilibrium effects in chaperone-assisted translocation of a stiff polymer

Chaperone-assisted biopolymer translocation is the main model proposed for translocation in vivo. A dynamical Monte Carlo method is used to simulate the translocation of a stiff homopolymer through a nanopore driven by chaperones. Chaperones are proteins that bind to the polymer near the wall and prevent its backsliding through Cis side. The important parameters include binding energy, size and the local concentration of the chaperones. The profile of these local concentrations, build up the chaperones distribution. Here we investigate the effects of binding energy, size and the exponential distribution of chaperones in their equilibration in each step of the polymer translocation needed for stable translocation time. The simulation results show that in case of chaperones with the size of a monomer (λ=1) and/or positive effective binding energy and/or uniform distribution, the chaperones binding equilibration rate/frequency is less than 5 times per monomer. However, in some special cases in the exponential distribution of chaperones with size λ>1 and negative effective binding energy the equilibration rate will diverge to more than 20 times per monomer. We show that this non-equilibrium effect results in supper diffusion, seen before. Moreover, we confirm the equilibration process theoretically.

Dielectric environment and/or random disorder effects on free, charged and localized excitonic states in monolayer WS2

Excitonic effects play an important role on the optoelectronic behavior of atomically thin two-dimensional (2D) crystals of the WS2 transition metal dichalcogenide. In this paper, neutral and charged exciton behaviors in monolayer WS2 are handled within effective-mass approximation for which the critical parameters are ensured from our ab initio calculations. Firstly, we reveal an exciton series with a novel energy dependence on the orbital angular momentum. Considerable control of the dielectric environment on neutral and charged excitons binding energies is elucidated. We demonstrate that for accepted values of effective masses, the negative and positive trion binding energies should be identical. Secondly, localization of neutral exciton center of mass motion by random potential arising from monolayer defects is also studied. The results obtained are in agreement with available experimental work.

Primary radiation damage of Zr-0.5%Nb binary alloy: atomistic simulation by molecular dynamics method

Ab initio calculations predict high positive binding energy (∼1 eV) between niobium atoms and self-interstitial configurations in hcp zirconium. It allows the expectation of increased niobium fraction in self-interstitials formed under neutron irradiation in atomic displacement cascades. In this paper, we report the results of molecular dynamics simulation of atomic displacement cascades in Zr-0.5%Nb binary alloy and pure Zr at the temperature of 300 K. Two sets of n-body interatomic potentials have been used for the Zr-Nb system. We consider a cascade energy range of 2–20 keV. Calculations show close estimations of the average number of produced Frenkel pairs in the alloy and pure Zr. A high fraction of Nb is observed in the self-interstitial configurations. Nb is mainly detected in single self-interstitial configurations, where its fraction reaches tens of percent, i.e. more than its tenfold concentration in the matrix. The basic mechanism of this phenomenon is the trapping of mobile self-interstitial configurations by niobium. The diffusion of pure zirconium and mixed zirconium-niobium self-interstitial configurations in the zirconium matrix at 300 K has been simulated. We observe a strong dependence of the estimated diffusion coefficients and fractions of Nb in self-interstitials produced in displacement cascades on the potential.

Nitrogen Trapping Ability of Hydrogen-Induced Vacancy and the Effect on the Formation of AlN in Aluminum

This paper presents the ternary interaction of N, H, and vacancy point defects and the nitrogen trapping ability of aluminum vacancies induced by hydrogen by means of DFT methods employed in VASP (Vienna Ab initio Simulation Package) and Abinit packages. The obtained vacancy formation energy of 0.65 eV is close to experimental values. Although the N–vacancy complex is unstable with the negative binding energy of −0.51 eV, the stability of H–vacancy–N is proved by the positive binding energy of 0.59 eV and the appearance of the orbital hybridization in the density of state (DOS) of atoms connecting to this complex. Moreover, Al vacancies can trap more than 4 N atoms, which prevents the formation of aluminum nitride and subsequently affects not only the hardness of the Al surface but also many practical applications of AlN coating.

Nanoparticle formation of deposited Agn-clusters on free-standing graphene

Size-selected Agn-clusters on unsupported graphene of a commercial Quantifoil sample have been investigated by surface and element-specific techniques such as transmission electron microscopy (TEM), spatially-resolved inner-shell X-ray photoelectron spectroscopy (XPS) and Auger electron spectroscopy (AES). An agglomeration of the highly mobile clusters into nm-sized Ag-nanodots of 2–3 nm is observed. Moreover, crystalline as well as non-periodic fivefold symmetric structures of the Ag-nanoparticles are evident by high-resolution TEM. Using a lognormal size-distribution as revealed by TEM, the measured positive binding energy shift of the air-exposed Ag-nanodots can be explained by the size-dependent dynamical liquid-drop model.

Effective Atomic Displacements in Fe-9at.%Cr Alloy

A computer simulation of atomic displacement cascades in Fe-9at.%Cr binary alloy has been performed by molecular dynamics method for temperature of 300 K and cascade energies from 100 eV to 20 keV. The average number of Frenkel pairs produced in cascade has been calculated. The data on point defect clusterization have been obtained. Obtained evaluations of effective fraction of surviving defects are well approximated by the sum of power and linear functions of cascade energy. Increased chromium fraction in the self-interstitial (SIA) configurations has been observed and has been explained by combination of two factors: positive binding energy of Cr atom with SIAs and mobility of SIA configuration. The diffusion coefficient of single SIA configuration in the matrix of pure bcc Fe has been evaluated for the temperature range of 300 – 1000 K. We have prepared 100 group neutron cross-sections of effective displacement generation in Fe-9at.%Cr binary alloy. It has been shown that effective dpa generation rate can be 2-3 times lower than corresponding rates of conventional dpa generation rate.

N-Terminus Binding Preference for Either Tanshinone or Analogue in Both Inhibition of Amyloid Aggregation and Disaggregation of Preformed Amyloid Fibrils-Toward Introducing a Kind of Novel Anti-Alzheimer Compounds.

Amyloid-β (Aβ40/Aβ42) peptide with a length of 40 or 42 residues is naturally secreted as cleavage product of the amyloid precursor protein, and formation of Aβ aggregates in a patient's brain is a hallmark of Alzheimer's disease (AD). Therefore, disaggregation and disruption provide potential therapeutic approaches to reduce, inhibit, and even reverse Aβ aggregation. The disaggregation/inhibition effect of the inhibitors applies generally to both Aβ40 and Aβ42 aggregations. Here we capture the atomic-level details of the interaction between Aβ40/Aβ42 and either natural tanshinone compound TS1 or its derivative TS0, and observe novel results by using molecular dynamics simulations. We observe that the natural TS1 indeed inhibits the monomolecular Aβ42 (mAβ42) aggregation and disaggregates Aβ42 amyloid fibrils, being in good agreement with the experimental results. TS1 is favorable to stabilize mAβ40 and even Aβ40 fibril, playing an opposite role to that in the Aβ42 counterpart, however. TS0 can inhibit the misfolding of either mAβ40 or mAβ42 and disaggregate Aβ42 fibril but stabilize the Aβ40 fibril. Using a combination of secondary structural analysis, MM-PBSA binding energy calculations, and radial distribution functions computations, we find that both TS0 and TS1, especially the former, prefer to bind at the charged residues within disordered N-terminus with a scarce positive binding energy and disappear the characteristic C-terminal bend region of Aβ42 fibril, as well as twist the Aβ42 fibril seriously. It turns out to destabilize the Aβ42 fibril and enable the conversion of U-shaped Aβ42 fibril from the onefold to the twofold morphologies. The N-terminal binding preference helps us to identify N-terminal region as the specific epitope for specific inhibitors/drugs (such as TS0 and analogues), heralding unusual inhibition/disaggregation or stabilization mechanisms, and offering an alternative direction in engineering new inhibitors to treat AD.

First principles study of inert-gas (helium, neon, and argon) interactions with hydrogen in tungsten

We have systematically evaluated binding energies of hydrogen with inert-gas (helium, neon, and argon) defects, including interstitial clusters and vacancy-inert-gas complexes, and their stable configurations using first-principles calculations. Our calculations show that these inert-gas defects have large positive binding energies with hydrogen, 0.4–1.1 eV, 0.7–1.0 eV, and 0.6–0.8 eV for helium, neon, and argon, respectively. This indicates that these inert-gas defects can act as traps for hydrogen in tungsten, and impede or interrupt the diffusion of hydrogen in tungsten, which supports the discussion on the influence of inert-gas on hydrogen retention in recent experimental literature. The interaction between these inert-gas defects and hydrogen can be understood by the attractive interaction due to the distortion of the lattice structure induced by inert-gas defects, the intrinsic repulsive interaction between inert-gas atoms and hydrogen, and the hydrogen-hydrogen repelling in tungsten lattice.

Theoretical insights into kesterite and stannite phases of Cu2(Sn1–XGeX)ZnSe4 based alloys: A prospective photovoltaic material

A comparative study of kesterite (KS) and stannite (ST) phases of Cu2(Sn1−xGex)ZnSe4 (CTGZSe) alloys has been carried out using a hybrid functional within the framework of density functional theory (DFT). Our calculations suggest that KS phase is energetically more stable. We find that the total energy of the KS phase decreases with increasing concentration (x) of Ge. The calculated positive binding energies suggest that the alloy systems are stable. The formation enthalpy clearly indicates that CTGZSe alloys are thermodynamically stable and its growth can be achieved by following the route of an exothermic reaction. The calculated energy band gaps of the alloys agree well with the experimental data for the KS phase. The band offsets of KS and ST phases as a function of Ge concentration (x) can be explained on the basis of the calculated energy band gaps. We find a slight upshift in the conduction band edges while the valence band edges remain almost the same on varying the concentration (x) of Ge. Our results could be useful for the development of CTGZSe alloys based solar cells.

Preparation of Pt–Ru/C as an Oxygen-Reduction Electrocatalyst in Microbial Fuel Cells for Wastewater Treatment

Carbon-supported Pt–Ru alloys with a Pt/Ru ratio of 1:1 were prepared by NaBH4 reduction at room temperature. X-ray diffraction (XRD) measurements indicate that the as-prepared Pt–Ru nanoparticles had a face-centered cubic (fcc) structure. X-ray photoelectron spectroscopy (XPS) analyses demonstrate that alloying with Ru can decrease the 4f electron density of Pt, which results in a positive binding energy shift of 0.2 eV for the Pt 4f peaks. The catalytic properties of the synthesized Pt–Ru alloy catalysts were compared with those of commercial Pt/C catalysts by linear sweep voltammetry (LSV). The results show that the mass activity of the oxygen reduction reaction (ORR) is enhanced by 2.3 times as much mass activity of Pt relative to the commercial Pt/C catalyst. Single-chambered microbial fuel cell tests also confirm that the Pt–Ru alloys as cathode catalysts have better performance than that of commercial Pt/C catalysts.

Ab-Initio Studies of Acceptor Impurities and Stability of Complexes in Ge

The application of germanium (Ge) as a promising material for complementary metal-oxide semiconductors (CMOS) technology is attracting attention due to its narrow band gap, high carrier mobility and low voltage operations. Recent experimental and theoretical studies revealed that dopants in Ge cluster with vacancies forms with lower energies and contribute to low activation of dopants impurity in Ge. DFT electronic simulation have been used to provide concise information about the formation of defect clusters and complexes that influence diffusion mechanisms in Ge. Our main objective in this study is to use simulations based on ͑DFT to calculate the structural, electronic properties and interactions between acceptors and Ge in different configurations with a view to finding the most energetically stable configuration of various defect complexes in Ge. By means of density functional theory (DFT), we present ab-initio calculation of interactions between A (A: Be,Mg, Ca, Sr, Ba, Ga, In) vacancy complexes (A-VGe) and vacancy-interstitial complexes (A-VGeIA) in two configurations of the hexagonal (H) and tetrahedral (T) in Ge. These calculations employed a projector augmented wave (PAW) pseudopotentials within the generalized gradient approximation (GGA). The geometric structures and formation energies of A-VGe and A-VGeIA in both the T and H configurations for the neutral charge state were obtained. The formation energies of A-VGe were low and energectically favourable with Ga-VGe and Ca-VGe forming with the lowest formation energies at -1.24 and -0.38 eV respectively. For the A-VGeIA, the results of the H configuration were more energetically favourable and forms with lower formation energies than the T configuration. The Ca-VGeICa and Be-VGeIBe forms with the lowest formation energies of -2.59 and -1.49 eV respectively. The stability of the A-VGeIA and A-VGe complexes in Ge were obtained from their binding energies. The binding energies (Eb ) which are defined as the energy required to split up the defects cluster into well separated non-interacting defect is given as Eb = E(formation)(VGe) + E(formation)(AGe) - E(formation){defect-complex}, where E(formation)(VGe), E(formation)(AGe) and E(formation)(defect-complex) are the formation energies of the neutral charge state of the germanium vacancy, interstitials and defect-complexes. The above equation could be interpreted as the energy gain of the bonded structure with respect to the isolated components. Positive binding energies suggest that the defect complexes are stable and cannot easily dissociate. The calculated binding energies of both the A-VGe and the A-VGeIA displayed the ability of these complexes to form without dissociation. For the A-VGeIA, the H configuration forms with more favourable binding energies than the T configuration. In summary the detailed calculated results we have presented are expect to be useful in the process modeling of Ge-based devices.

A first principle hybrid functional calculation of [formula omitted]-[formula omitted] defect complexes in germanium

By means of density functional theory (DFT), using the screened Heyd, Scuseria, and Ernzerhof (HSE06) hybrid functional we present results of the TmGe3+-VGe defect complexes in germanium (Ge). The formation energies of the first (fnn), second (snn), third (tnn) and fourth (ftnn) nearest neighbour configurations of VGe-VGe were examined. The charge state transition levels for all these configurations were examined as well. The TmGe3+-VGe complexes were found to have a positive binding energies for the neutral charge state in the fnn and ftnn configurations. The thermodynamic transition levels revealed that the TmGe3+-VGe induced shallow levels in the band gap for the fnn, tnn and ftnn configurations and deep level for the tnn configuration. The snn configuration showed no charge state transition level, the − 2 charge state was stable for all Fermi energies in the band gap. The TmGe3+-VGe displayed evidence of a single donor level (+1/0) and an acceptor level (−1/−2) within the band gap. Charge state controlled metastability was exhibited by the TmGe3+-VGe.

Orbital-free density functional theory study of the energetics of vacancy clustering and prismatic dislocation loop nucleation in aluminium

In the present work, we conduct large-scale orbital-free density functional theory calculations to study the energetics of vacancy clustering in aluminium from electronic structure calculations by accurately accounting for both the electronic structure and long-ranged elastic fields. Our results show positive binding energies for a range of vacancy clusters considered. However, the binding energies for the various quad-vacancy clusters considered in this study are vastly different, and only some of these clusters are found to be stable with respect to dissociation into divacancies. This suggests that, while vacancy clustering is an energetically feasible mechanism, this happens preferentially through the formation of certain vacancy clusters. Among the vacancy clusters considered in this study, the 19 vacancy hexagonal cluster lying in plane has a very large binding energy with the relaxed atomic structure representative of a prismatic dislocation loop. This suggests that vacancy prismatic loops as small as those formed from 19 vacancies are stable, thus providing insights into the nucleation sizes of these defects in aluminium.

Deciphering the mechanism behind the varied binding activities of COXIBs through Molecular Dynamic Simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies

COX-2 is a well-known drug target in inflammatory disorders. COX-1/COX-2 selectivity of NSAIDs is crucial in assessing the gastrointestinal side effects associated with COX-1 inhibition. Celecoxib, rofecoxib, and valdecoxib are well-known specific COX-2 inhibiting drugs. Recently, polmacoxib, a COX-2/CA-II dual inhibitor has been approved by the Korean FDA. These COXIBs have similar structure with diverse activity range. Present study focuses on unraveling the mechanism behind the 10-fold difference in the activities of these sulfonamide-containing COXIBs. In order to obtain insights into their binding with COX-2 at molecular level, molecular dynamics simulations studies, and MM-PBSA approaches were employed. Further, per-residue decomposition of these energies led to the identification of crucial amino acids and interactions contributing to the differential binding of COXIBs. The results clearly indicated that Leu338, Ser339, Arg499, Ile503, Phe504, Val509, and Ser516 (Leu352, Ser353, Arg513, Ile517, Phe518, Val523, and Ser530 in PGHS-1 numbering) were imperative in determining the activity of these COXIBs. The binding energies and energy contribution of various residues were similar in all the three simulations. The results suggest that hydrogen bond interaction between the hydroxyl group of Ser516 and five-membered ring of diarylheterocycles augments the affinity in COXIBs. The SAR of the inhibitors studied and the per-residue energy decomposition values suggested the importance of Ser516. Additionally, the positive binding energy obtained with Arg106 explains the binding of COXIBs in hydrophobic channel deep in the COX-2 active site. The findings of the present work would aid in the development of potent COX-2 inhibitors.

On the search of stable, aromatic and ionic endohedral compounds of C28: A theoretical study

The X@C28 compounds form the family of the smallest endohedral fullerenes. Currently, they consist of C28, which is endohedrally doped with group-4 elements (Ti, Zr, Hf) and U. We have studied the electronic properties, equilibrium geometries, binding energies and other properties of several X@C28 at the PBE/def2-TZVP level. These were compared with the tetraanion C284−. For this study we have chosen elements from groups 4, 14 and Sc as endohedral dopants for being many of them tetravalent. In addition, we studied by the first time the entire group-10 (Ni, Pd and Pt) as endohedral dopant of C28. To elucidate the stability of these ionic compounds, we have studied their binding energies. Our results show that a big positive binding energy is necessary but not enough to determine the stability of these endohedral fullerenes. We propose that a HOMO–LUMO gap around 2eV results in less reactive compounds, property only shown by group-4 compounds. Some compounds have aromatic character in all rings according with their NICS(0)iso and reparametrized HOMA indexes. In addition, the charge distribution have been studied with NBO and Hirshfeld population analysis as well as electrostatic potential maps in order to find similarities between them and that shown by the tetraanion C284−. The most stable compounds are the group-4 X@C28 which form compounds: energetically favorable, less reactive, ionic and aromatic. Our results are compared with available experimental information about the formation of these compounds.

First-principles calculations of transition metal solute interactions with hydrogen in tungsten

We have performed systematic first-principles calculations to predict the interaction between transition metal (TM) solutes and hydrogen in the interstitial site as well as the vacancy in tungsten. We showed that the site preference of the hydrogen atom is significantly influenced by the solute atoms, which can be traced to the charge density perturbation in the vicinity of the solute atom. The solute-H interactions are mostly attractive except for Re, which can be well understood in terms of the competition between the chemical and elastic interactions. The chemical interaction dominates the solute-H interaction for the TM solutes with a large atomic volume and small electronegativity compared to tungsten, while the elastic interaction is primarily responsible for the solute-H interaction for the TM solutes with a small atomic volume and large electronegativity relative to tungsten. The presence of a hydrogen atom near the solute atom has a negative effect on the binding of other hydrogen atoms. The large positive binding energies among the solute, vacancy and hydrogen suggest that they would easily form a defect cluster in tungsten, where the solute-vacancy and vacancy-H interaction contribute greatly while the solute-H interaction contributes a little. Our result provides a sound theoretical explanation for recent experimental phenomena of hydrogen retention in the tungsten alloy and further recommends a suitable W–Re–Ta ternary alloy for possible plasma-facing materials (PFMs) including the consideration of the hydrogen retention.

Spin States of 2D Nanocomposites of Ni and V Nanoclusters on Hexagonal h-BN, BC3 and Graphene

Atomic and electronic structures of adsorbed nickel and vanadium atoms and nanoclusters (Nin and Vn, n = 1–10) on hexagonal h-BN and BC3 lattices were studied using DFT PBE/PBC/PW (Perdew–Burke–Ernzerhof potential of density functional theory/periodic boundary conditions/plane wave basis set) technique. For the sake of comparison the structure and properties of the same nanoclusters deposited on pristine graphene were calculated as well. It was found that for all types of supports an increase of n from 1 to 10 leaded to decrease of coordination types from η6 to η2 and η1. The h-BN- and BC3-based nanocomposites were characterized by high (up to 18 µ for Ni10/BC3) magnetic moments of the nanoclusters and featured by positive binding energies. The graphene-based nanocomposites revealed energetic stability and, in general, lower magnetic moments per unit cell. The direct potential energy barriers for migration of Ni η2/η2 and η6/η6 types of dimers on graphene were low (10.9–28.9 kJ/mol) with high reverse barriers for η6/η6 dimers, which favored dynamically equilibrated Ni clusterization on graphene.

State identification and tunable Kondo effect of MnPc on Ag(001)

We present a detailed investigation of spectroscopic features located at the central metal ion of MnPc (where Pc represents phthalocyanine) on Ag(001) by means of scanning tunneling spectroscopy (STS) and first-principles theory. STS data taken close to the Fermi level reveal an asymmetric feature that cannot be fitted with a single Fano function representing a one-channel Kondo effect. Instead, our data indicate the existence of a second superimposed feature. Two potential physical origins, a second Kondo channel related to the ${d}_{xz/yz}$ orbitals, and a spectral feature of the ${d}_{{z}^{2}}$ orbital itself, are discussed. A systematic experimental and theoretical comparison of MnPc with CoPc and FePc indicates that the second feature observed on MnPc is caused by the ${d}_{{z}^{2}}$ orbital. This conclusion is corroborated by STM-induced dehydrogenation experiments on FePc and MnPc which in both cases result in a gradual shift towards more positive binding energies and a narrowing of the Kondo resonance. Theoretical analysis reveals that the latter is caused by the reduced hybridization between the $d$ orbital and the substrate. Spatially resolved differential conductivity maps taken close to the respective peak positions show that the intensity of both features is highest over the central Mn ion, thereby providing further evidence against a second Kondo channel originating from the ${d}_{xz/yz}$ orbital of the central Mn ion.

Nanoisland formation of small Ag -clusters on HOPG as determined by inner-shell photoionisation spectroscopy

Abstract XPS (3d) and Auger spectra (MNN) of deposited Ag n -clusters on a non-sputtered HOPG surface have been measured. Most of the XPS and Auger spectra appear very similar to the corresponding bulk spectrum, caused by a high mobility and agglomeration of the clusters on the inert carbon surface, independent of the initial cluster size. The metallic fingerprint of the cluster-agglomerated islands is sustained under UHV conditions for several days. Oxidised Ag-islands reveal a positive binding energy shift in distinct contrast to the negative XPS shift usually observed for silver oxide bulk compounds. The XPS binding energy shift has been used for estimation of the diameter of the cluster-assembled nanoislands (6–9 nm) using an electrostatic model.