Loop Contributions Research Articles

DNA Hairpin Hybridization under Extreme Pressures: A Single-Molecule FRET Study.

Organisms have evolved to live in a variety of complex environments, which clearly has required cellular biology to accommodate to extreme conditions of hydraulic pressure and elevated temperature. In this work, we exploit single-molecule Forster resonance energy transfer (FRET) spectroscopy to probe structural changes in DNA hairpins as a function of pressure and temperature, which allows us to extract detailed thermodynamic information on changes in free energy (ΔG°), free volume (ΔV°), enthalpy (ΔH°), and entropy (ΔS°) associated with DNA loop formation and sequence-dependent stem hybridization. Specifically, time-correlated single-photon counting experiments on freely diffusing 40A DNA hairpin FRET constructs are performed in a 50 μm × 50 μm square quartz capillary cell pressurized from ambient pressure up to 3 kbar. By pressure-dependent van't Hoff analysis of the equilibrium constants, ΔV° for hybridization of the DNA hairpin can be determined as a function of stem length (nstem = 7-10) with single base-pair resolution, which further motivates a simple linear deconstruction into additive stem (ΔV°stem = ΔV°bp x nstem) and loop (ΔV°loop) contributions. We find that increasing pressure destabilizes the DNA hairpin stem region [ΔV°bp = +1.98(16) cm3/(mol bp)], with additional positive free volume changes [ΔV°loop = +7.0(14) cm3/mol] we ascribe to bending and base stacking disruption of the 40-dA loop. From a van't Hoff temperature-dependent analysis of the DNA 40A hairpin equilibria, the data support a similar additive loop/stem deconstruction of enthalpic (ΔH° = ΔH°loop + ΔH°stem) and entropic (ΔS° = ΔS°loop + ΔS°stem) contributions, which permits insightful comparison with predictions from nearest-neighbor thermodynamic models for DNA duplex formation. In particular, the stem thermodynamics is consistent with exothermically favored (ΔH°stem < 0) and entropically penalized (ΔS°stem < 0) hydrogen bonding but with additional enthalpic (ΔH°loop > 0) and entropic (ΔS°loop > 0) contributions due to loop bending effects consistent with distortion of dA base stacking in the 40-dA linker.

Predictions of transitions * * Supported in part by the Fundamental Research Funds for the Central Universities (FRF-BR-19-001A), and by the National Natural Science Foundation of China (11975028)

We study the contributions of intermediate bottomonium-like states and the bottom meson loops in the heavy quark spin flip transitions . Depending on the constructive or destructive interferences between the -exchange and the bottom meson loops mechanisms, we predict two possible branching ratios for each process: BR or , and or . The contribution of the bottom meson loops is found to be considerably larger than that of the -exchange in the transitions, while its decay rates are not comparable to those of heavy quark spin conserved processes. We also predict the contribution of the charm meson loops in the branch fractions of .

Two-loop triangle integrals with 4 scales for the HZV vertex

We calculate analytically the two-loop triangle integrals entering the $\mathcal{O}(\alpha\alpha_s)$ corrections to the $HZV$ vertex with $V=Z^*,\gamma^*$ using the method of differential equations. Our result provides a prototype to study the analytic properties of multi-loop multi-scale Feynman integrals, and also allows fast numeric evaluation for phenomenological studies. We apply our results to the leptonic decay of the Higgs boson and to $ZH$ production at electron-positron colliders. Besides the top quark loop, we include also the bottom quark loop contributions, whose evaluation takes a lot of time using purely numeric methods, but is very efficient with our analytic results.

Inflaton portal to a highly decoupled EeV dark matter particle

We explore the possibility that the dark-matter relic abundance is generated in a context where the inflaton is the only mediator between the visible and the hidden sectors of our universe. Due to the relatively large mass of the inflaton field, such a portal leads to an extremely feeble interaction between the dark and the visible sectors suggesting that the dark sector cannot reach any thermal equilibrium with the visible sector. After the two sectors are populated by the decay of the inflaton, a heavy dark-matter particle thermally decouples within the dark sector. Later, a lighter dark particle, whose decay width is naturally suppressed by the inflaton propagator, decays into the visible sector after it dominates the energy density of universe. This process dilutes the dark-matter relic density by injecting entropy in the visible sector. We show that an inflaton mass of $\mathcal{O}(10^{13})$ GeV together with couplings of order one are fully compatible with a dark-matter relic abundance $\Omega h^2\sim 0.1$. As a general feature of the model, the entropy dilution mechanism is accompanied by a period of early matter domination, which modifies the amount of e-folds of inflation necessary to accommodate Planck data. Moreover, the coupling of the inflaton to the dark and visible sectors brings loop contributions to the inflationary potential which can destabilize the inflation trajectory. Considering all these complementary constraints, we show that, in the context of a plateau-inflation scenario such as the $\alpha$-attractor model, the inflaton can constitute a viable mediator between the visible sector and a $\sim 10$ EeV dark-matter candidate. Furthermore, we show that improved constraints on the tensor-to-scalar ratio and spectral index could potentially rule out dark-matter scenarios of this sort in the future.

NNLO classical solution for Lipatov’s effective action for reggeized gluons

We consider the formalism of small-[Formula: see text] effective action for reggeized gluons[Formula: see text] and, following the approach developed in Refs. 11–17, calculate the classical gluon field to NNLO precision with fermion loops included. It is demonstrated that for each perturbative order, the self-consistency of the equations of motion is equivalent to the transversality conditions applied to the solution of the equations, these conditions allow to construct the general recursive scheme for the solution’s calculation. The one fermion loop contribution to the classical solutions and application of the obtained results are also discussed.

Precise prediction for the W boson mass in the MRSSM

The mass of the W boson, MW, plays a central role for high-precision tests of the electroweak theory. Confronting precise theoretical predictions with the accurately measured experimental value provides a high sensitivity to quantum effects of the theory entering via loop contributions. The currently most accurate prediction for the W boson mass in the Minimal R-symmetric Supersymmetric Standard Model (MRSSM) is presented. Employing the on-shell scheme, it combines all numerically relevant contributions that are known in the Standard Model (SM) in a consistent way with all MRSSM one-loop corrections. Special care is taken in the treatment of the triplet scalar vacuum expectation value vT that enters the prediction for MW already at lowest order. In the numerical analysis the decoupling properties of the supersymmetric loop contributions and the comparison with the MSSM are investigated. Potentially large numerical effects of the MRSSM-specific Λ superpotential couplings are highlighted. The comparison with existing results in the literature is discussed.

BFKL Pomeron loop contribution in diffractive photoproduction and inclusive hadroproduction of J/\u03c8 and \u03d2

We analyze contributions to the heavy vector meson production with large transverse momentum in proton-proton and diffractive photon-proton scattering driven by an exchange of two Balitsky-Fadin-Kuraev-Lipatov Pomerons in the squared amplitudes. The Pomerons couple to a single parton and form a Pomeron loop closed by the vector meson impact factors. For the photon-proton case the diffractive cut of the Pomeron loop contributes, and for the inclusive hadroproduction one finds the loop with two cut Pomerons. We compute both of these Pomeron loop contributions and study in detail their properties. The results are then used to calculate the cross sections for diffractive J/ψ photoproduction with large transverse momentum at HERA and the correlated two Pomeron contribution for inclusive J/ψ and ϒ production cross sections at the LHC. Within a unified approach a good description of the photoproduction data is found, but correlated two Pomeron mechanism gives only a small contribution to hadroproduction of the vector mesons at the LHC.

Ecosystem contribution by microbial loop in Bohai Bay, China,a numerical study

The contributions of the microbial loop to the ecosystem in the Bohai Bay, China was studied in this paper. An eco-hydrodynamic model coupled with pelagic and benthic systems was developed, and the comparison between the numerical results and the field survey data shows that the model is able to reproduce the growth curves for ecological variables in the Bohai Bay. The contributions of the microbial loop and new production of nitrogen (new nitrogen) on other ecological variables were investigated using the coupled model. The results demonstrate that the average contributions of the microbial loop to zooplankton growth were 0.0644, 0.134, 0.0873, 0.0590 mmol C m−3 for spring, summer, autumn and winter in pelagic ecosystem of the Bohai Bay, respectively, with the annual mean value being 372.28 mg⋅m−3⋅a−1 in the Bohai Bay. The contribution rate of new production of nitrogen through the sediment–water interface ranges from 17.2% to 56.0%, with the average value being 41.1%.

Loop-induced direct detection signatures from CP-violating scalar mediators

We investigate direct detection signatures of dark matter particles interacting with quarks via a light spin-0 mediator with general CP phases. Since tree-level scattering may be strongly suppressed in the non-relativistic limit, loop contributions play an important role and can lead to observable signals in near-future experiments. We study the phenomenology of different mediator masses and CP phases with an emphasis on scenarios with maximal CP violation and Higgs portal models. Intriguingly, the sum of the rates obtained at tree- and loop-level can give a characteristic recoil spectrum not obtainable from a single type of interaction. We furthermore develop a novel method for decomposing the two-loop contribution to effective interactions between dark matter and gluons into two separate one-loop diagrams, which in our case substantially simplifies the calculation of the important top-quark contribution.

Proton decay at one loop

Proton decay is usually discussed in the context of grand unified theories. However, as is well-known, in the standard model effective theory proton decay appears in the form of higher dimensional non-renormalizable operators. Here, we study systematically the 1-loop decomposition of the $d=6$ $B+L$ violating operators. We exhaustively list the possible 1-loop ultra-violet completions of these operators and discuss that, in general, two distinct classes of models appear. Models in the first class need an additional symmetry in order to avoid tree-level proton decay. These models necessarily contain a neutral particle, which could act as a dark matter candidate. For models in the second class the loop contribution dominates automatically over the tree-level proton decay, without the need for additional symmetries. We also discuss possible phenomenology of two example models, one from each class, and their possible connections to neutrino masses, LHC searches and dark matter.

Leading loop effects in pseudoscalar-Higgs portal dark matter

We examine a model with a fermionic dark matter candidate having pseudoscalar interaction with the standard model particles where its direct detection elastic scattering cross section at tree level is highly suppressed. We then calculate analytically the leading loop contribution to the spin independent scattering cross section. It turns out that these loop effects are sizable over a large region of the parameter space. Taking constraints from direct detection experiments, the invisible Higgs decay measurements, observed DM relic density, we find viable regions which are within reach in the future direct detection experiments such as XENONnT.

Exogenous Peptide Replacement of Three Loops in Domain II of Cry1Ab Toxin Reduces Its Toxicity against Helicoverpa armigera (Lepidoptera: Noctuidae)

To investigate the contribution of surface-exposed loops (loops 1, 2 and 3) in the toxicity of Cry1Ab against Helicoverpa armigera larvae, three loop-replaced Cry1Ab mutants were prokaryotically expressed in Escherichia coli BL21 (DE3). Proteolytic processing of Cry1Ab toxins with trypsin indicated that the replacement of each surface-exposed loop caused no damage to toxin stability. Results of in vitro binding and competition assay indicated that, similarly to the native Cry1Ab toxin, the mutants retained almost the same binding affinity and specificity with brush border membrane vesicles (BBMV) of H. armigera. Nevertheless, H. armigera larvae fed with each loop-replaced Cry1Ab mutant showed less growth inhibition in comparison with those fed with native Cry1Ab toxin. The most significant decrease in toxicity was observed from larvae fed with loop 2-replaced Cry1Ab mutant, with a c. 12-fold increase in the weight of tested larvae relative to that of larvae fed native Cry1Ab toxin. The results demonstrate that the replacement of three surface-exposed loops located in domain II of Cry1Ab toxin may result in a certain reduction in the toxicity. Relative to loop 1 and loop 3, loop 2 seem to play a more important role in generating toxicity of Cry1Ab against H. armigera larvae.

Note on the conjectured breakdown of QED perturbation theory in strong fields

Strong background fields require a non-perturbative treatment, which is afforded in QED by the Furry expansion of scattering amplitudes. It has been conjectured that this expansion breaks down for sufficiently strong fields, based on the asymptotic growth of loop corrections with increasing "quantum nonlinearity", essentially the product of field strength and particle energy. However, calculations to date have assumed that the background is constant. We show here, using general plane waves of finite duration, that observables at high quantum nonlinearity scale differently depending on whether intensity or energy is large. We find that, at high energy, loop contributions to observables tend to fall with increasing quantum nonlinearity, rather than grow.

Dissecting structure/function relationship of Streptococcus mutans membrane protein chaperones/insertases, YidC1 and YidC2

BackgroundApproximately, one third of most bacterial open reading frames encode membrane proteins; therefore, understanding the machinery that translocates these proteins to their functional location is of great interest. Most membrane proteins are translocated co‐translationally by the signal recognition particle (SRP) pathway via the SecYEG translocon. Additionally the Oxa/Alb/YidC (mitochondria/chloroplast/bacteria) family of membrane‐localized protein chaperone/insertases assists in membrane protein translocation in a Sec‐dependent manner, or independently if the proteins are small with two or fewer transmembrane (TM) domains. Most gram‐negative bacteria contain a single yidC whose deletion is lethal. Most gram‐positive bacteria contain two or more YidCs. The cariogenic bacterium S. mutans encodes YidC1 and YidC2, each with similar 5 TM domain topologies. Deletion of yidC2 results in a severe phenotype similar to disruption of the SRP pathway including impaired growth, sensitivity to acid, osmotic, and oxidative stresses, and loss of competence and mutacin production. Deletion of DyidC1 leads to increased localization of surface proteins and hyperadherence. The goal of this study is to better understand the structure and function of YidC1 and YidC2 as related to their known phenotypes.MethodsThe significance of the two cytoplasmic loops, C1 and C2, of YidC1 and YidC2 were evaluated in domain swapping experiments in which DNA segments encoding one or both C1 and C2 domains of yidC1 were incorporated into yidC2 and vice versa. Chimeric genes were integrated into the non‐essential gtfA locus of the DyidC1 and DyidC2 strains. Next the residual endogenous yidC was deleted, thus generating strains with a sole chimeric YidC for phenotypic analyses. In addition, a naturally‐acquired W138R point mutation within yidC1 was identified in a phenotypically‐reverted DyidC2 mutant; therefore, the significance of this residue was evaluated as well.Results and ConclusionsAn S. mutans strain producing a chimeric YidC2 harboring the C1 loop of YidC1 was similar to the DyidC2 strain with respect to sensitivity to acid and osmotic stress suggesting a functional contribution of YidC2's C1 loop to stress tolerance. Transfer of YidC2 C1 into YidC1 enabled YidC1 to rescue acid and osmotic stress sensitivity. Also, a deliberately engineered W138R point mutation within YidC1 enabled it to rescue growth and stress phenotypes of the DyidC2 mutant. Sequence comparison revealed that the YidC1 tryptophan 138 residue corresponds to serine 152 in YidC2, the only polar residue within its TM3. Additionally, engineered W138K/S mutations within YidC1 also enabled rescue of DyidC2‐associated phenotypes. These data reveal that functional activities unique to YidC2 reside within both its C1 domain and TM3 that can be transferred to YidC1.Support or Funding InformationNIH grant: R01 DE08007This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Bounds on rare decays of η and η′ mesons from the neutron EDM

We provide model-independent bounds on the rates of rare decays $\eta (\eta^\prime) \to \pi\pi$ based on experimental limits on the neutron electric dipole moment (nEDM). Starting from phenomenological $\eta(\eta^\prime) \pi\pi$ couplings, the nEDM arises at two loop level. The leading-order relativistic ChPT calculation with the minimal photon coupling to charged pions and a proton inside the loops leads to a finite, counter term-free result. This is an improvement upon previous estimates which used approximations in evaluating the two loop contribution and were plagued by divergences. While constraints on the $\eta(\eta^\prime) \pi\pi$ couplings in our phenomenological approach are somewhat milder than in the picture with the QCD $\theta$-term, our calculation means that whatever the origin of these couplings, The decays $\eta (\eta') \to 2 \pi$ will remain unobservable in the near future.

Production of the Zb(′) states from the ϒ(5S,6S) decays

In the present work, we investigate the production mechanism of the $Z_b(10610)$ and $Z_b(10650)$ states from the $\Upsilon(5S,6S)$ decays. Two types of bottom-meson loops are discussed. We show that the loop contributions with all intermediate states being the $S$-wave ground state bottom mesons are negligible, while the loops with one bottom meson being the broad $B_0^\ast$ or $B_1^\prime$ resonance could provide the dominant contributions to the $\Upsilon(5S) \to Z_b^{(\prime)} \pi$. It is found that such a mechanism is not suppressed by the large width of the $B_0/B_1'$ resonance. In addition, we also estimate the branching ratios for the $\Upsilon(6S) \to Z_b^{(\prime)} \pi$ which could be tested by future precise measurements at Belle-II.

A theory of reparameterizations for AdS3 gravity

We rewrite the Chern-Simons description of pure gravity on global AdS3 and on Euclidean BTZ black holes as a quantum field theory on the AdS boundary. The resulting theory is (two copies of) the path integral quantization of a certain coadjoint orbit of the Virasoro group, and it should be regarded as the quantum field theory of the boundary gravitons. This theory respects all of the conformal field theory axioms except one: it is not modular invariant. The coupling constant is 1/c with c the central charge, and perturbation theory in 1/c encodes loop contributions in the gravity dual. The QFT is a theory of reparametrizations analogous to the Schwarzian description of nearly AdS2 gravity, and has several features including: (i) it is ultraviolet-complete; (ii) the torus partition function is the vacuum Virasoro character, which is one-loop exact by a localization argument; (iii) it reduces to the Schwarzian theory upon compactification; (iv) it provides a powerful new tool for computing Virasoro blocks at large c via a diagrammatic expansion. We use the theory to compute several observables to one-loop order in the bulk, including the “heavy-light” limit of the identity block. We also work out some generalizations of this theory, including the boundary theory which describes fluctuations around two-sided eternal black holes.

Backreaction of superhorizon scalar field fluctuations on a de Sitter geometry: A renormalization group perspective

We study the backreaction of gravitationally amplified quantum fluctuations of scalar fields on a classical de Sitter geometry. We formulate the problem in the framework of the Wilsonian renormalisation group, which allows us to treat the scalar field fluctuations in a nonperturbative manner and to follow the renormalisation flow of the spacetime curvature as long wavelength, superhorizon fluctuations are progressively integrated out. For light fields in units of the spacetime curvature, these are described by an effective zero-dimensional field theory and can essentially be computed analytically. A nontrivial flow of the spacetime curvature is induced either by a nonminimal coupling to gravity or by self-interactions. The latter leads to a decrease of the spacetime curvature through loop effects, which, for minimally coupled, massless fields, grow unbounded in the infrared. However, such large loop contributions are eventually screened by the dynamical generation of a nonperturbative, gravitationally induced mass and the renormalisation of the spacetime curvature saturates to a nonzero value. Finally, we show that, in the case of spontaneously broken continuous symmetries, the Goldstone modes do not contribute to the infrared flow of the spacetime curvature, despite being strongly amplified by the gravitational field.

Asymptotic behavior of the heavy quark form factors at higher order

In the asymptotic limit $Q^2 \gg m^2$, the heavy quark form factors exhibit Sudakov behavior. We study the corresponding renormalization group equations of the heavy quark form factors which do not only govern the structure of infrared divergences, but also control the high energy logarithms. This enables us to obtain the complete logarithmic three--loop and partial four--loop contributions to the heavy quark form factors in perturbative Quantum Chromodynamics.

Loop dynamics behind the affinity of DARPins towards ERK2: Molecular dynamics simulations (MDs) and elastic network model (ENM)

The binding affinity and dynamics profiles of non-phosphorylated extracellular regulated kinase 2 (ERK2), in complex with DARPins (designed ankyrin repeat proteins) as a phosphorylation inhibitor, has been investigated using molecular dynamics simulations (MDs) and elastic network model (ENM). The study investigates the effect of ERK2 loop dynamics on its specificity, upon binding with DARPins. From experiments, DARPin E40 has been found as a specific binder (E40/ERK2) with higher binding affinity while DARPin pE59 has lower binding affinity towards ERK2 (pE59/ERK2). Theoretical binding affinities along the 100 ns molecular dynamics simulations between DARPins and ERK2 were analyzed and found in good agreement with the experiments, where BFE (binding free energy) of E40/ERK was found to be much lower (more favorable) as compared to that of pE59/ERK2 with the contribution of activation loop and αG loops. Moreover, elastic network model (ENM) studies successfully delineate the dynamics of four loops of ERK2 (activation, αG, MAPK and L16) along the trajectories. Slow eigenvectors from global mode shapes and dynamic cross correlation indicate the responsible regions for the binding. The specificity of DARPins can be discriminated by the binding free energy of the activation and αG loop, which indicated the stronger interaction of these region in E40/ERK2. Robustness of the average properties (mean-square fluctuations, eigenvectors from global mode shapes, dynamic cross-correlations) controlled by the low frequency motions, which are reproduced in both MDs and ENM suggested that GNM based on a coarsegrained single-site-per-residue model can be used as a complimentary and fast analytical approach to investigate the structural dynamics.