Unpaired State Research Articles

Arsenene nanotubes adsorbed with various non-metallic atoms: Chemical bonding, odd-even effect, and electronic transport

The recently experimental fabricated arsenene has attracted extensive research interest due to its excellent physical and chemical properties. To further explore new physics and extend its realistic applications, we here theoretically study the chemical bonding and electronic properties for its 1D derivatives, zigzag arsenene nanotubes, adsorbed with various non-metal atoms in main groups. The calculated adsorption energy and molecular dynamics simulation suggest that these hybrid tubes are very stable with different adsorption sites. Importantly, our investigations reveal many novel interesting physical regularities. For example, for the atom adsorption from the same main-group, the higher the atomic number is, the lower (shorter/less) the corresponding adsorption energy (minimum bond length/charge transfer) is, and the amount of charge transfer closely related to the electronegativity of the adsorbent atoms relative to As atom. More interestingly, we find that the electronic phase (a metal or semiconductor) of the hybrid tubes changes alternately with the elemental group order, that is, the electron phase holds a significant odd-even effect with non-metal atomic outer-shell electron number, closely related to the unpaired electronic state. The mechano-electronic coupling effect can tune the indirect band gap to a smaller direct band gap under higher tensile strain for these hybrid tubes, more beneficially for light absorption and developing photoelectric devices, and the different non-metal atom adsorptions can regulate the carrier mobility and the carrier polarity to two and one orders of magnitude difference, respectively.

Studying sparsely populated conformational states in RNA combining chemical synthesis and solution NMR spectroscopy.

Using chemical synthesis and solution NMR spectroscopy, RNA structural ensembles including a major ground state and minor populated excited states can be studied at atomic resolution. In this work, atom-specific 13C labeled RNA building blocks - a 5-13C-uridine and a 2,8-13C2-adenosine building block - are used to introduce isolated 13C-1H-spin topologies into a target RNA to probe such structural ensembles via NMR spectroscopy. First, the 5-13C-uridine 2'-O-TBDMS-phosphoramidite building block was introduced into a 21 nucleotide (nt) tP5c stem construct of the tP5abc subdomain of the Tetrahymena group I ribozyme. Then, the 2,8-13C2-adenosine 2'-O-TBDMS-phosphoramidite building block was incorporated into a 9 kDa and a 15 kD construct derived from the epsilon (ε) RNA element of the duck Hepatitis B virus. The 2,8-13C2-adenosine resonances of the 9 kDa 28 nt sequence could be mapped to the full-length 53 nt construct. The isolated NMR active nuclei pairs were used to probe for low populated excited states (<10%) via 13C-Carr-Purcell-Meiboom-Gill (CPMG)-relaxation dispersion NMR spectroscopy. The 13C-CPMG relaxation dispersion experiment recapitulated a secondary structure switching event in the P5c hairpin of the group I intron construct previously revealed by 15N relaxation dispersion experiments. In the ε-HBV RNA an unfolding event occurring on the millisecond time scale was found in the upper stem in-line with earlier observations. This unpaired conformational state is presumed to be important for the binding of the epsilon reverse transcriptase (RT) enzyme. Thus, a full description of an RNA's folding landscape helps to obtain a deeper understanding of its function, as these high energy conformational states often represent functionally important intermediates involved in (un)folding or ribozyme catalysis.

Second-order tunneling under the dynamic localization condition of two particles in driven one-dimensional lattices with an impurity

We investigate the effect of the interplay between the interatomic interaction and impurity on dynamic localization for two interacting bosons held in driven one-dimensional lattices with an impurity. We find that the interplay of the interatomic interaction and impurity can induce second-order tunneling under the dynamic localization condition. In the resonant regime, where the impurity potential is equal to a multiple of the driving frequency, two bosons form a stable bound pair and the dominant tunneling of the doublon in the paired state is a second-order process. In the non-resonant regime, the tunneling dynamics of the single boson in the unpaired state can also be a second-order process between the two nearest-neighbor sites of the impurity with the negligible impurity site population, and the other boson is localized in the initial site all the time. Our results provide a promising approach for controlling transport of realistic systems.

Trapped imbalanced fermionic superfluids in one dimension: A variational approach

We propose and analyze a variational wave function for a population-imbalanced one-dimensional Fermi gas that allows for Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) type pairing correlations among the two fermion species, while also accounting for the harmonic confining potential. In the strongly interacting regime, we find large spatial oscillations of the order parameter, indicative of an FFLO state. The obtained density profiles versus imbalance are consistent with recent experimental results as well as with theoretical calculations based on combining Bethe ansatz with the local density approximation. Although we find no signature of the FFLO state in the densities of the two fermion species, we show that the oscillations of the order parameter appear in density-density correlations, both in-situ and after free expansion. Furthermore, above a critical polarization, the value of which depends on the interaction, we find the unpaired Fermi-gas state to be energetically more favorable.

Strong enhancement of third-harmonic generation in a double layer graphene system caused by electron-hole pairing

A manifestation of electron-hole pairing in nonlinear electromagnetic response of a double layer graphene system is studied. It is shown that the pairing causes the appearance of a number of peaks in the frequency dependence of the intensity of the third-harmonic generation (THG). The highest peak corresponds to , where ω is the incident wave frequency, and Δ is the order parameter of the electron-hole pairing. The absolute value of the THG intensity in the systems with electron-hole pairing is of several orders of magnitude greater than the THG intensity in the unpaired state. It is shown that huge enhancement of the THG intensity occurs both in the double monolayer and double bilayer graphene systems.

Probing-directed identification of novel structured RNAs

ABSTRACTTranscripts often harbor RNA elements, which regulate cell processes co- or post-transcriptionally. The functions of many regulatory RNA elements depend on their structure, thus it is important to determine the structure as well as to scan genomes for structured elements. State of the art ab initio approaches to predict structured RNAs rely on DNA sequence analysis. They use 2 major types of information inferred from a sequence: thermodynamic stability of an RNA structure and evolutionary footprints of base-pair interactions. In recent years, chemical probing of RNA has arisen as an alternative source of structural information. RNA probing experiments detect positions accessible to specific types of chemicals or enzymes indicating their propensity to be in a paired or unpaired state. There exist several strategies to integrate probing data into RNA secondary structure prediction algorithms that substantially improve the prediction quality. However, whether and how probing data could contribute to detection of structured RNAs remains an open question. We previously developed the energy-based approach RNASurface to detect locally optimal structured RNA elements. Here, we integrate probing data into the RNASurface energy model using a general framework. We show that the use of experimental data allows for better discrimination of ncRNAs from other transcripts. Application of RNASurface to genome-wide analysis of the human transcriptome with PARS data identifies previously undetectable segments, with evidence of functionality for some of them.

Xist imprinting is promoted by the hemizygous (unpaired) state in the male germ line

The long noncoding X-inactivation-specific transcript (Xist gene) is responsible for mammalian X-chromosome dosage compensation between the sexes, the process by which one of the two X chromosomes is inactivated in the female soma. Xist is essential for both the random and imprinted forms of X-chromosome inactivation. In the imprinted form, Xist is paternally marked to be expressed in female embryos. To investigate the mechanism of Xist imprinting, we introduce Xist transgenes (Tg) into the male germ line. Although ectopic high-level Xist expression on autosomes can be compatible with viability, transgenic animals demonstrate reduced fitness, subfertility, defective meiotic pairing, and other germ-cell abnormalities. In the progeny, paternal-specific expression is recapitulated by the 200-kb Xist Tg. However, Xist imprinting occurs efficiently only when it is in an unpaired or unpartnered state during male meiosis. When transmitted from a hemizygous father (+/Tg), the Xist Tg demonstrates paternal-specific expression in the early embryo. When transmitted by a homozygous father (Tg/Tg), the Tg fails to show imprinted expression. Thus, Xist imprinting is directed by sequences within a 200-kb X-linked region, and the hemizygous (unpaired) state of the Xist region promotes its imprinting in the male germ line.

Cooperative effect in ion pairing of oligolysine with heptafluorobutyric acid in reversed-phase chromatography

The retention behavior of an oligolysine mixture, consisting of two to eight residues, was examined at different concentrations of heptafluorobutyric acid (HFBA) in the mobile phase using a C18 column. A single ion record (SIR) mode of the mass spectrometer produced a distinct retention time for each oligomer component. As the concentration of HFBA increased, the retention time of each oligomer increased. Furthermore, the increase in retention time is chain-length dependent such that, the longer the oligomer chain, the more rapid was the rate that retention time increased. A closed pairing model that presumes an equilibrium between the unpaired state and the paired state with a fixed number of HFBA molecules was used to analyze the retention factor as a function of [HFBA]. Curve fitting gave estimates of the ion-pairing equilibrium constant ( K ip,m), the distribution constant of paired oligolysine ( K D,ip), and the number of paired HFBA for each oligolysine ( n). The plot of the fraction of paired oligolysine in the mobile phase, estimated from K ip,m and n as a function of [HFBA], revealed a cooperative effect. In contrast, an open pairing model that assumes independent pairing of HFBA with each residue failed to describe the observed retention behavior.

Phase diagram of chiral quark matter: Color and electrically neutral Fulde-Ferrell phase

The phase diagram of charge and color neutral two-flavor color superconducting quark matter is studied including the homogeneous two-flavor superconductor (2SC) and the inhomogeneous Fulde-Ferrell (FF) phases within the Nambu-Jona-Lasinio model. The low-temperature domain T < 5 MeV of the phase diagram contains the FF phase, which borders at high temperatures to the 2SC phase. The critical temperature of phase transition from the 2SC to the unpaired state is in the range 20-30 MeV. We derive the equation of state of matter and its composition and show that matter in mature compact stars should be in the inhomogeneous FF-like superconducting state. We briefly discuss the astrophysical implications of such a phase in compact stars.

Ultrarelativistic electron-hole pairing in graphene bilayer

We consider ground state of electron-hole graphene bilayer composed of two independently doped graphene layers when a condensate of spatially separated electron-hole pairs is formed. In the weak coupling regime the pairing affects only conduction band of electron-doped layer and valence band of hole-doped layer, thus the ground state is similar to ordinary BCS condensate. At strong coupling, an ultrarelativistic character of electron dynamics reveals and the bands which are remote from Fermi surfaces (valence band of electron-doped layer and conduction band of hole-doped layer) are also affected by the pairing. The analysis of instability of unpaired state shows that s-wave pairing with band-diagonal condensate structure, described by two gaps, is preferable. A relative phase of the gaps is fixed, however at weak coupling this fixation diminishes allowing gapped and soliton-like excitations. The coupled self-consistent gap equations for these two gaps are solved at zero temperature in the constant-gap approximation and in the approximation of separable potential. It is shown that, if characteristic width of the pairing region is of the order of magnitude of chemical potential, then the value of the gap in the spectrum is not much different from the BCS estimation. However, if the pairing region is wider, then the gap value can be much larger and depends exponentially on its energy width.

Anomalous Specific-Heat Jump in a Two-Component Ultracold Fermi Gas

The thermodynamic functions of a Fermi gas with spin population imbalance are studied in the temperature-asymmetry plane in the BCS limit. The low-temperature domain is characterized by an anomalous enhancement of the entropy and the specific heat above their values in the unpaired state, decrease of the gap and eventual unpairing phase transition as the temperature is lowered. The unpairing phase transition induces a second jump in the specific heat, which can be measured in calorimetric experiments. While the superfluid is unstable against a supercurrent carrying state, it may sustain a metastable state if cooled adiabatically down from the stable high-temperature domain. In the latter domain the temperature dependence of the gap and related functions is analogous to the predictions of the BCS theory.

Dynamical selection in developing fermionic pairing

We consider the development of pairing in an ideal Fermi gas in the presence of a time-dependent BCS interaction. The pairing amplitude time evolution is controlled by the interplay of linear instability of the unpaired state and nonlinear interactions which limit the growth. This results in oscillatory time dependence with predictable characteristics, selecting periodic soliton trains of a specific form, described by a Jacobi elliptic function. While the parameters of the soliton train, such as the period, amplitude, and time lag, fluctuate among different realizations, the elliptic function form remains robust. The parameter fluctuations are accounted for by the randomness of particle distribution in the initial unpaired state.

Pairing in a two-component ultracold Fermi gas: Phases with broken-space symmetries

We explore the phase diagram of a two-component ultracold atomic Fermi gas interacting with zero-range forces in the limit of weak coupling. We focus on the dependence of the pairing gap and the free energy on the variations in the number densities of the two species while the total density of the system is held fixed. As the density asymmetry is increased, the system exhibits a transition from a homogenous Bardeen-Cooper-Schrieffer (BCS) phase to phases with spontaneously broken global space symmetries. One such realization is the deformed Fermi surface superfluidity (DFS) which exploits the possibility of deforming the Fermi surfaces of the species into ellipsoidal form at zero total momentum of Cooper pairs. The critical asymmetries at which the transition from DFS to the unpaired state occurs are larger than those for the BCS phase. In this precritical region the DFS phase lowers the pairing energy of the asymmetric BCS state. We compare quantitatively the DFS phase to another realization of superconducting phases with broken translational symmetry: the single-plane-wave Larkin-Ovchinnikov-Fulde-Ferrell phase, which is characterized by a nonvanishing center-of-mass momentum of the Cooper pairs. The possibility of the detection of the DFS phase in the time-of-flight experiments is discussed and quantified for the case of $^{6}\mathrm{Li}$ atoms trapped in two different hyperfine states.

Superconducting high-temperature pairing–theoretical considerations on an unusual phenomenon

In the theoretical framework of a recently developed first-order mechanism for the superconducting pairing an inverted temperature dependence for the transition between the unpaired and a paired state has been observed. We suggest the existence of a paired state at high temperatures T emerging from an unpaired low-temperature state. The entropy driven stabilization of paired states is the outcome of a T-dependent competition between the electronic energy and the electronic configuration entropy. With increasing T the entropy admixtures to the free energy of a given quantum ensemble can exceed energetic effects. The unusual T-dependence of superconductivity has been derived by cluster calculations in the two-parameter Hubbard approximation. The clusters chosen are of the four-electron-four-center type.

Superconducting first‐order pairing: Finite‐temperature simulations

AbstractA recently developed first‐order mechanism for superconducting pairing has been extended from T = 0 K to finite temperatures. On the basis of quantum statistical considerations, we have suggested a direct pairing interaction that does not necessarily involve second‐order elements, such as the electron–phonon coupling or specific magnetic interactions submitted by spin fluctuations. The driving force for the (energy‐driven) first‐order pairing is an attenuation of the destabilizing influence of the Pauli antisymmetry principle (PAP). Only the moves of unpaired fermions are controlled by the PAP, while the moves of superconducting Cooper pairs are not. The quantum statistics of Cooper pairs is of a mixed type, as it combines fermionic on‐site and bosonic intersite properties. The strong correlation between the strength of PAP constraints and system topology in combination with the electron number has been discussed for some larger clusters. Detailed finite‐temperature simulations on first‐order pairing have been performed for four‐center–four‐electron clusters with different topologies. A canonical ensemble statistics has been employed to derive the electronic energy, the electronic configuration entropy, and the free energy of paired and unpaired states in thermal equilibrium. The simulations show that pairing can be caused by either the electronic energy or the electronic configuration entropy. The coexistence of two different sets of quantum particles in paired states (i.e., the Cooper pairs and the unpaired electrons) can lead to an enhanced configuration entropy. In this context, we discuss the possibility of an entropy‐driven high‐temperature superconductor emerging from a low‐temperature unpaired state. The charge and spin degrees of freedom of the four‐center–four‐electron systems have been studied with the help of the charge and spin fluctuations. The spin fluctuations are helpful in judging the validity of pairing theories based on magnetic interactions. The charge fluctuations are a measure for the carrier delocalization in unpaired and paired states. The well‐known proximity between Jahn–Teller activity and superconductivity is analyzed in the zero‐temperature limit. It is demonstrated that both processes compete in their ability to reduce PAP constraints. All theoretical results have been derived within the framework of the simple Hubbard Hamiltonian. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

Phases of asymmetric nuclear matter with broken space symmetries

Isoscalar Cooper pairing in isospin asymmetric nuclear matter occurs between states populating two distinct Fermi surfaces, each for neutrons and protons. The transition from a BCS-like to the normal (unpaired) state, as the isospin asymmetry is increased, is intervened by superconducting phases which spontaneously break translational and rotational symmetries. One possibility is the formation of a condensate with a periodic crystallinelike structure where Cooper pairs carry net momentum (the nuclear Larkin-Ovchinnikov-Fulde-Ferrell-phase). Alternatively, perturbations of the Fermi surfaces away from spherical symmetry allow for minima in the condensate free energy which correspond to a states with quadrupole deformations of Fermi surfaces and zero momentum of the Cooper pairs. In a combined treatment of these phases we show that, although the Cooper pairing with finite momentum might arise as a local minimum, the lowest energy state features are deformed Fermi surfaces and Cooper pairs with vanishing total momentum.

Unpaired and spin-singlet paired states of a two-dimensional electron gas in a perpendicular magnetic field

We present a variational study of both unpaired and spin-singlet paired states induced in a two-dimensional electron gas at low density by a perpendicular magnetic field. It is based on an improved circular-cell approximation which leads to a number of closed analytical results. The ground-state energy of the Wigner crystal containing a single electron per cell in the lowest Landau level is obtained as a function of the filling factor $\ensuremath{\nu}:$ the results are in good agreement with those of earlier approaches and predict ${\ensuremath{\nu}}_{c}\ensuremath{\approx}0.25$ for the upper filling factor at which the solid-liquid transition occurs. A novel localized state of spin-singlet electron pairs is examined and found to be a competitor of the unpaired state for filling factor $\ensuremath{\nu}&gt;1.$ The corresponding phase boundary is quantitatively displayed in the magnetic field-electron density plane.

Electronic structure and hyperfine parameters of substitutional Al and P impurities in silica

The electronic structure of substitutional Al and P impurities in silica is investigated using supercell calculations within the framework of density functional theory (DFT). Evaluation of hyperfine matrices for the magnetic nuclei facilitates comparison to experimental data. It is found that the unpaired spin state of substitutional P is well described by the theory while the unpaired spin state found for substitutional Al is severely at variance with the experimental data. Cluster calculations using both the DFT and the Hartree-Fock approximation indicate that the problem is not caused by the supercell approach but rather by the residual self-interactions present in the DFT energy functionals. A simple model discussion serves to illustrate why DFT succeeds for P but fails for Al: First, it is argued that DFT self-interactions are larger for holes than for electrons. Second, there is an asymmetry between electrons and holes in the electronic states of the silica network: The hole present at the Al impurity goes into a nonbonding O orbital while the extra electron present at the P impurity goes into a P-O antibonding state.

Hydrogen in jellium: First-principles pair interactions

Ground-state pair potentials between protons immersed in jellium (interacting electrons plus a compensating background) and at densities corresponding to the range $1&lt;{r}_{s}&lt;4$ are calculated using first-principles density functional theory methods. While the results obtained for immersing a single H atom in an electron gas agree with previous calculations, it is discovered that molecular-type short-range binding becomes unstable at surprisingly low density (at about ${r}_{s}=3.2),$ and that at even lower density there is a bistability between a weakly bound molecule and an unpaired state. This behavior is a result of the possible pairing of hydrogen and itinerant jellium electrons with little electrostatic penalty, a consequence of the positive background filling the entire volume V. Another important finding is a density range $(1.5&lt;{r}_{s}&lt;2)$ where the pair potentials are insufficiently strong to bind the protons, suggesting the possibility of inducing hydrogen into a state of low-temperature quantum fluid at a critical density.

Scanning Force Microscopy Study on a Single-Stranded DNA: The Genome of Parvovirus B19

The genome of parvovirus B19 is a 5600-base-long single-stranded DNA molecule with peculiar sequence symmetries. Both complementary forms of this single-stranded DNA are contained in distinct virions and they hybridize intermolecularly to double-stranded DNA if extracted from the capsids with traditional methods, thus losing some of their native structural features. A scanning force microscopy analysis of these double-stranded DNA molecules after thermal denaturation and renaturation gave us the chance to study the possible states that this DNA can assume in both its single-stranded and double-stranded forms. A novel but still poorly reproducible in situ lysis experiment that we have conducted on single virions with the scanning force microscope made it possible to image the totally unpaired state that the single-stranded DNA molecule most likely assumes inside the viral particle. Structural considerations on single molecules offer the opportunity for the formulation of plausible hypotheses on the interaction between the DNA and the viral structural proteins that could prove important for the DNA packaging in the capsid and, possibly, the viral infection mechanisms.