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The pT-differential inclusive production cross section of the prompt charm-strange meson Ds+ in the rapidity range |y|<0.5 was measured in proton–proton collisions at s=7 TeV at the LHC using the ALICE detector. The analysis was performed on a data sample of 2.98×108 events collected with a minimum-bias trigger. The corresponding integrated luminosity is Lint=4.8 nb−1. Reconstructing the decay Ds+→ϕπ+, with ϕ→K−K+, and its charge conjugate, about 480 Ds± mesons were counted, after selection cuts, in the transverse momentum range 2<pT<12 GeV/c. The results are compared with predictions from models based on perturbative QCD. The ratios of the cross sections of four D meson species (namely D0, D+, D⁎+ and Ds+) were determined both as a function of pT and integrated over pT after extrapolating to full pT range, together with the strangeness suppression factor in charm fragmentation. The obtained values are found to be compatible within uncertainties with those measured by other experiments in e+e−, ep and pp interactions at various centre-of-mass energies.
Inclusive transverse momentum spectra of primary charged particles in Pb–Pb collisions at √sNN=2.76 TeV have been measured by the ALICE Collaboration at the LHC. The data are presented for central and peripheral collisions, corresponding to 0–5% and 70–80% of the hadronic Pb–Pb cross section. The measured charged particle spectra in |η|<0.8 and 0.3<pT<20 GeV/c are compared to the expectation in pp collisions at the same sNN, scaled by the number of underlying nucleon–nucleon collisions. The comparison is expressed in terms of the nuclear modification factor RAA. The result indicates only weak medium effects (RAA≈0.7) in peripheral collisions. In central collisions, RAA reaches a minimum of about 0.14 at pT=6–7 GeV/c and increases significantly at larger pT. The measured suppression of high-pT particles is stronger than that observed at lower collision energies, indicating that a very dense medium is formed in central Pb–Pb collisions at the LHC.
The first measurement of two-pion Bose–Einstein correlations in central Pb–Pb collisions at √sNN=2.76 TeV at the Large Hadron Collider is presented. We observe a growing trend with energy now not only for the longitudinal and the outward but also for the sideward pion source radius. The pion homogeneity volume and the decoupling time are significantly larger than those measured at RHIC.
The inclusive charged particle transverse momentum distribution is measured in proton–proton collisions at s=900 GeV at the LHC using the ALICE detector. The measurement is performed in the central pseudorapidity region (|η|<0.8) over the transverse momentum range 0.15<pT<10 GeV/c. The correlation between transverse momentum and particle multiplicity is also studied. Results are presented for inelastic (INEL) and non-single-diffractive (NSD) events. The average transverse momentum for |η|<0.8 is 〈pT〉INEL=0.483±0.001 (stat.)±0.007 (syst.) GeV/c and 〈pT〉NSD=0.489±0.001 (stat.)±0.007 (syst.) GeV/c, respectively. The data exhibit a slightly larger 〈pT〉 than measurements in wider pseudorapidity intervals. The results are compared to simulations with the Monte Carlo event generators PYTHIA and PHOJET.
In this paper, we present an overview of some of the existing issues of the research in quantum gravity. We also introduce the basic ideas that led Padmanabhan to consider a duality property in path integrals. Such a duality is consistent with the T-duality in string theory. More importantly, the path integral duality discloses a universal feature of any quantum geometry, namely the existence of a zero point length L0. We also comment about recent developments aiming to expose effects of the zero point length in strong electrodynamics and black holes. There are reasons to believe that the main characters of the phenomenology of quantum gravity may be described by means of a single parameter like L0.
In this Letter we derive the gravity field equations by varying the action for an ultraviolet complete quantum gravity. Then we consider the case of a static source term and we determine an exact black hole solution. As a result we find a regular spacetime geometry: in place of the conventional curvature singularity extreme energy fluctuations of the gravitational field at small length scales provide an effective cosmological constant in a region locally described in terms of a de Sitter space. We show that the new metric coincides with the noncommutative geometry inspired Schwarzschild black hole. Indeed, we show that the ultraviolet complete quantum gravity, generated by ordinary matter is the dual theory of ordinary Einstein gravity coupled to a noncommutative smeared matter. In other words we obtain further insights about that quantum gravity mechanism which improves Einstein gravity in the vicinity of curvature singularities. This corroborates all the existing literature in the physics and phenomenology of noncommutative black holes.
In this Letter we study the radiation measured by an accelerated detector, coupled to a scalar field, in the presence of a fundamental minimal length. The latter is implemented by means of a modified momentum space Green's function. After calibrating the detector, we find that the net flux of field quanta is negligible, and that there is no Planckian spectrum. We discuss possible interpretations of this result, and we comment on experimental implications in heavy ion collisions and atomic systems.
Fuzziness at the horizon
(2010)
We study the stability of the noncommutative Schwarzschild black hole interior by analysing the propagation of a massless scalar field between the two horizons. We show that the spacetime fuzziness triggered by the field higher momenta can cure the classical exponential blue-shift divergence, suppressing the emergence of infinite energy density in a region nearby the Cauchy horizon.
In this Letter, we propose a new scenario emerging from the conjectured presence of a minimal length ℓ in the spacetime fabric, on the one side, and the existence of a new scale invariant, continuous mass spectrum, of un-particles on the other side. We introduce the concept of un-spectral dimension DU of a d-dimensional, euclidean (quantum) spacetime, as the spectral dimension measured by an “un-particle” probe. We find a general expression for the un-spectral dimension DU labelling different spacetime phases: a semi-classical phase, where ordinary spectral dimension gets contribution from the scaling dimension dU of the un-particle probe; a critical “Planckian phase”, where four-dimensional spacetime can be effectively considered two-dimensional when dU=1; a “Trans-Planckian phase”, which is accessible to un-particle probes only, where spacetime as we currently understand it looses its physical meaning.
Quarkyonic or baryquark matter? On the dynamical generation of momentum space shell structure
(2023)
We study the equation of state of a mixture of (quasi-)free constituent quarks and nucleons with hard-core repulsion at zero temperature. Two opposite scenarios for the realization of the Pauli exclusion principle are considered: (i) a Fermi sea of quarks surrounded by a shell of baryons – the quarkyonic matter, and (ii) a Fermi sea of nucleons surrounded by a shell of quarks which we call baryquark matter. In both scenarios, the sizes of the Fermi sea and shell are fixed through energy minimization at fixed baryon number density. While both cases yield a qualitatively similar transition from hadronic to quark matter, we find that baryquark matter is energetically favored in this setup and yields a physically acceptable behavior of the speed of sound without the need to introduce an infrared regulator. In order to retain the theoretically more appealing quarkyonic matter as the preferred form of dense QCD matter will thus require modifications to the existing dynamical generation mechanisms, such as, for example, the introduction of momentum-dependent nuclear interactions.
The production of the hypertriton nuclei HΛ3 and H‾Λ¯3 has been measured for the first time in Pb–Pb collisions at sNN=2.76 TeV with the ALICE experiment at LHC. The pT-integrated HΛ3 yield in one unity of rapidity, dN/dy×B.R.(HΛ3→He3,π−)=(3.86±0.77(stat.)±0.68(syst.))×10−5 in the 0–10% most central collisions, is consistent with the predictions from a statistical thermal model using the same temperature as for the light hadrons. The coalescence parameter B3 shows a dependence on the transverse momentum, similar to the B2 of deuterons and the B3 of 3He nuclei. The ratio of yields S3=HΛ3/(He3×Λ/p) was measured to be S3=0.60±0.13(stat.)±0.21(syst.) in 0–10% centrality events; this value is compared to different theoretical models. The measured S3 is compatible with thermal model predictions. The measured HΛ3 lifetime, τ=181−39+54(stat.)±33(syst.)ps is in agreement within 1σ with the world average value.
The ALICE Collaboration has made the first measurement at the LHC of J/ψ photoproduction in ultra-peripheral Pb–Pb collisions at sNN=2.76 TeV. The J/ψ is identified via its dimuon decay in the forward rapidity region with the muon spectrometer for events where the hadronic activity is required to be minimal. The analysis is based on an event sample corresponding to an integrated luminosity of about 55 μb−1. The cross section for coherent J/ψ production in the rapidity interval −3.6<y<−2.6 is measured to be dσJ/ψcoh/dy=1.00±0.18(stat)−0.26+0.24(syst) mb. The result is compared to theoretical models for coherent J/ψ production and found to be in good agreement with those models which include nuclear gluon shadowing.
Some quantitative data about the carbon-metabolism in Saccharomyces-cells of different ploidy were determined. The amount of carbon, necessary for the formation of a cell, proved to be proportional to the degree of ploidy of the cells. For the duplication of a diploid cell 6,7·10-11g glucose were used. In comparison with respiratory deficient cells the simultaneous utilization of fermentation and respiration metabolism in respiration sufficient cells leads to a decrease of the cell cycle duration, however, the energy needed for the formation of a cell is not decreased. The rate of cell multiplication has a maximum at about 30 °C for all classes of ploidy. Certain assumptions about the utilization of the carbon source were confirmed by experiments with 14C marked glucose.
The nuclear stopping, the elliptic flow, and the HBT interferometry are calculated by the UrQMD transport model, in which potentials for “pre-formed” particles (string fragments) from color fluxtube fragmentation as well as for confined particles are considered. This description provides stronger pressure at the early stage and describes these observables better than the default cascade mode (where the “pre-formed” particles from string fragmentation are treated to be free-streaming). It should be stressed that the inclusion of potential interactions pushes down the calculated HBT radius RO and pulls up the RS so that the HBT time-related puzzle disappears throughout the energies from AGS, SPS, to RHIC.
Based on the microscopic transport model UrQMD in which hadronic and string degrees of freedom are employed, the HBT parameters in the longitudinal co-moving system are investigated for charged pion and kaon, and Λ sources in heavy ion collisions (HICs) at SPS and RHIC energies. In the Cascade mode, RO and the RL at high SPS and RHIC energies do not follow the mT-scaling, however, after considering a soft equation of state with momentum dependence (SM-EoS) for formed baryons and a density-dependent Skyrme-like potential for “pre-formed” particles, the HBT radii of pions and kaons and even those of Λs with large transverse momenta follow the mT-scaling function R=3/mT fairly well.
We propose a method to experimentally study the equation of state of strongly interacting matter created at the early stage of nucleus–nucleus collisions. The method exploits the relation between relative entropy and energy fluctuations and equation of state. As a measurable quantity, the ratio of properly filtered multiplicity to energy fluctuations is proposed. Within a statistical approach to the early stage of nucleus–nucleus collisions, the fluctuation ratio manifests a non-monotonic collision energy dependence with a maximum in the domain where the onset of deconfinement occurs.
Modifications of the gyromagnetic moment of electrons and muons due to a minimal length scale combined with a modified fundamental scale Mf are explored. First-order deviations from the theoretical SM value for g−2 due to these string theory-motivated effects are derived. Constraints for the fundamental scale Mf are given.
Large extra dimensions could lower the Planck scale to experimentally accessible values. Not only is the Planck scale the energy scale at which effects of modified gravity become important. The Planck length also acts as a minimal length in nature, providing a natural ultraviolet cutoff and a limit to the possible resolution of spacetime.
In this Letter we examine the influence of the minimal length on the Casimir energy between two plates.
We determine the hard-loop resummed propagator in an anisotropic QCD plasma in general covariant gauges and define a potential between heavy quarks from the Fourier transform of its static limit. We find that there is stronger attraction on distance scales on the order of the inverse Debye mass for quark pairs aligned along the direction of anisotropy than for transverse alignment.
We suggest that the fluctuations of strange hadron multiplicity could be sensitive to the equation of state and microscopic structure of strongly interacting matter created at the early stage of high energy nucleus–nucleus collisions. They may serve as an important tool in the study of the deconfinement phase transition. We predict, within the statistical model of the early stage, that the ratio of properly filtered fluctuations of strange to non-strange hadron multiplicities should have a non-monotonic energy dependence with a minimum in the mixed phase region.
We propose to use the hadron number fluctuations in the limited momentum regions to study the evolution of initial flows in high energy nuclear collisions. In this method by a proper preparation of a collision sample the projectile and target initial flows are marked in fluctuations in the number of colliding nucleons. We discuss three limiting cases of the evolution of flows, transparency, mixing and reflection, and present for them quantitative predictions obtained within several models. Finally, we apply the method to the NA49 results on fluctuations of the negatively charged hadron multiplicity in Pb+Pb interactions at 158A GeV and conclude that the data favor a hydrodynamical model with a significant degree of mixing of the initial flows at the early stage of collisions.
We point out that during the supernova II type explosion the thermodynamical conditions of stellar matter between the protoneutron star and the shock front correspond to the nuclear liquid–gas coexistence region, which can be investigated in nuclear multifragmentation reactions. We have demonstrated, that neutron-rich hot heavy nuclei can be produced in this region. The production of these nuclei may influence dynamics of the explosion and contribute to the synthesis of heavy elements.
It has been suggested that the existence of a non-Gaussian fixed point in general relativity might cure the ultraviolet problems of this theory. Such a fixed point is connected to an effective running of the gravitational coupling. We calculate the effect of the running gravitational coupling on the black hole production cross section in models with large extra dimensions.
Phosphorylation of the sarcoplasmic reticulum Ca(2+)-ATPase (SERCA1a) was studied with time-resolved Fourier transform infrared spectroscopy. ATP and ATP analogs (ITP, 2'- and 3'-dATP) were used to study the effect of the adenine ring and the ribose hydroxyl groups on ATPase phosphorylation. All modifications of ATP altered conformational changes and phosphorylation kinetics. The differences compared with ATP increased in the following order: 3'-dATP > ITP > 2'-dATP. Enzyme phosphorylation with ITP results in larger absorbance changes in the amide I region, indicating larger conformational changes of the Ca(2+)-ATPase. The respective absorbance changes obtained with 3'-dATP are significantly different from the others with different band positions and amplitudes in the amide I region, indicating different conformational changes of the protein backbone. ATPase phosphorylation with 3'-dATP is also much ( approximately 30 times) slower than with ATP. Our results indicate that modifications to functional groups of ATP (the ribose 2'- and 3'-OH and the amino group in the adenine ring) affect gamma-phosphate transfer to the phosphorylation site of the Ca(2+)-ATPase by changing the extent of conformational change and the phosphorylation rate. ADP binding to the ADP-sensitive phosphoenzyme (Ca(2)E1P) stabilizes the closed conformation of Ca(2)E1P.
Time-resolved Fourier transform infrared difference spectra of the phosphoenzyme conversion and Ca(2+) release reaction (Ca(2)E(1)-P --> E(2)-P) of the sarcoplasmic reticulum Ca(2+)-ATPase were recorded at pH 7 and 1 degrees C in H(2)O and (2)H(2)O. In the amide I spectral region, the spectra indicate backbone conformational changes preserving conformational changes of the preceding phosphorylation step. beta-sheet or turn structures (band at 1685 cm(-1)) and alpha-helical structures (band at 1653 cm(-1)) seem to be involved. Spectra of the model compound EDTA for Ca(2+) chelation indicate the assignment of bands at 1570, 1554, 1411 and 1399 cm(-1) to Ca(2+) chelating Asp and Glu carboxylate groups partially shielded from the aqueous environment. In addition, an E(2)-P band at 1638 cm(-1) has been tentatively assigned to a carboxylate group in a special environment. A Tyr residue seems to be involved in the reaction (band at 1517 cm(-1) in H(2)O and 1515 cm(-1) in (2)H(2)O). A band at 1192 cm(-1) was shown by isotopic replacement in the gamma-phosphate of ATP to originate from the E(2)-P phosphate group. This is a clear indication that the immediate environment of the phosphoenzyme phosphate group changes in the conversion reaction, altering phosphate geometry and/or electron distribution.
P-O bond destabilization accelerates phosphoenzyme hydrolysis of sarcoplasmic reticulum Ca2+-ATPase
(2004)
The phosphate group of the ADP-insensitive phosphoenzyme (E2-P) of sarcoplasmic reticulum Ca2+-ATPase (SERCA1a) was studied with infrared spectroscopy to understand the high hydrolysis rate of E2-P. By monitoring an autocatalyzed isotope exchange reaction, three stretching vibrations of the transiently bound phosphate group were selectively observed against a background of 50,000 protein vibrations. They were found at 1194, 1137, and 1115 cm–1. This information was evaluated using the bond valence model and empirical correlations. Compared with the model compound acetyl phosphate, structure and charge distribution of the E2-P aspartyl phosphate resemble somewhat the transition state in a dissociative phosphate transfer reaction; the aspartyl phosphate of E2-P has 0.02 Å shorter terminal P–O bonds and a 0.09 Å longer bridging P–O bond that is ∼20% weaker, the angle between the terminal P–O bonds is wider, and –0.2 formal charges are shifted from the phosphate group to the aspartyl moiety. The weaker bridging P–O bond of E2-P accounts for a 1011–1015-fold hydrolysis rate enhancement, implying that P–O bond destabilization facilitates phosphoenzyme hydrolysis. P–O bond destabilization is caused by a shift of noncovalent interactions from the phosphate oxygens to the aspartyl oxygens. We suggest that the relative positioning of Mg2+ and Lys684 between phosphate and aspartyl oxygens controls the hydrolysis rate of the ATPase phosphoenzymes and related phosphoproteins.
String theory suggests the existence of a minimum length scale. An exciting quantum mechanical implication of this feature is a modification of the uncertainty principle. In contrast to the conventional approach, this generalised uncertainty principle does not allow to resolve space–time distances below the Planck length. In models with extra dimensions, which are also motivated by string theory, the Planck scale can be lowered to values accessible by ultra high energetic cosmic rays (UHECRs) and by future colliders, i.e., Mf≈ 1 TeV. It is demonstrated that in this novel scenario, short distance physics below 1/Mf is completely cloaked by the uncertainty principle. Therefore, Planckian effects could be the final physics discovery at future colliders and in UHECRs. As an application, we predict the modifications to the e+e−→f+f− cross-sections.
We calculate the antibaryon-to-baryon ratios, p̄/p,Λ̄/Λ,Ξ/Ξ, and Ω/Ω for Au+Au collisions at RHIC (sNN=200 GeV). The effects of strong color fields associated with an enhanced strangeness and diquark production probability and with an effective decrease of formation times are investigated. Antibaryon-to-baryon ratios increase with the color field strength. The ratios also increase with the strangeness content |S|. The netbaryon number at midrapidity considerably increases with the color field strength while the netproton number remains roughly the same. This shows that the enhanced baryon transport involves a conversion into the hyperon sector (hyperonization) which can be observed in the (Λ−Λ̄)/(p−p̄) ratio.
Production of J/ψ mesons in heavy ion collisions is considered within the statistical coalescence model. The model is in agreement with the experimental data of the NA50 Collaboration for Pb+Pb collisions at 158 AGeV in a wide centrality range, including the so-called “anomalous” suppression domain. The model description of the J/ψ data requires, however, strong enhancement of the open charm production in central Pb+Pb collisions. This model prediction may be checked in the future SPS runs.
The measured particle ratios in central heavy-ion collisions at RHIC-BNL are investigated within a chemical and thermal equilibrium chiral SU(3) σ–ω approach. The commonly adopted noninteracting gas calculations yield temperatures close to or above the critical temperature for the chiral phase transition, but without taking into account any interactions. Contrary, the chiral SU(3) model predicts temperature and density dependent effective hadron masses and effective chemical potentials in the medium and a transition to a chirally restored phase at high temperatures or chemical potentials. Three different parametrizations of the model, which show different types of phase transition behaviour, are investigated. We show that if a chiral phase transition occured in those collisions, “freezing” of the relative hadron abundances in the symmetric phase is excluded by the data. Therefore, either very rapid chemical equilibration must occur in the broken phase, or the measured hadron ratios are the outcome of the dynamical symmetry breaking. Furthermore, the extracted chemical freeze-out parameters differ considerably from those obtained in simple noninteracting gas calculations. In particular, the three models yield up to 35 MeV lower temperatures than the free gas approximation. The in-medium masses turn out to differ up to 150 MeV from their vacuum values.
We study properties of compact stars with the deconfinement phase transition in their interiors. The equation of state of cold baryon-rich matter is constructed by combining a relativistic mean-field model for the hadronic phase and the MIT Bag model for the deconfined phase. In a narrow parameter range two sequences of compact stars (twin stars), which differ by the size of the quark core, have been found. We demonstrate the possibility of a rapid transition between the twin stars with the energy release of about 1052 ergs. This transition should be accompanied by the prompt neutrino burst and the delayed gamma-ray burst.
Recent calculations applying statistical mechanics indicate that in a setting with compactified large extra dimensions a black hole might evolve into a (quasi-)stable state with mass close to the new fundamental scale Mf. Black holes and therefore their relics might be produced at the LHC in the case of extra-dimensional topologies. In this energy regime, Hawking's evaporation scenario is modified due to energy conservation and quantum effects. We reanalyse the evaporation of small black holes including the quantisation of the emitted radiation due to the finite surface of the black hole. It is found that observable stable black hole relics with masses ∼1–3Mf would form which could be identified by a delayed single jet with a corresponding hard momentum kick to the relic and by ionisation, e.g., in a TPC.
We consider J/ψ production in heavy ion collisions at RHIC energies in the statistical coalescence model with exact (canonical ensemble) charm conservation. Charm quark–antiquark pairs are assumed to be created in primary hard parton collisions, but open and hidden charm particles are formed at the hadronization stage according to the laws of statistical mechanics. The dependence of the J/ψ production on both the number of nucleon participants and the collision energy is studied. The model predicts J/ψ suppression for low energies, whereas at the highest RHIC energy the model reveals J/ψ enhancement.
We study the production of transversely polarized Λ hyperons in high-energy collisions of protons with large nuclei. The large gluon density of the target at saturation provides an intrinsic semi-hard scale which should naturally allow for a weak-coupling QCD description of the process in terms of a convolution of the quark distribution of the proton with the elementary quark–nucleus scattering cross section (resummed to all twists) and a fragmentation function. In this case of transversely polarized Λ production we employ a so-called polarizing fragmentation function, which is an odd function of the transverse momentum of the Λ relative to the fragmenting quark. Due to this kt-odd nature, the resulting Λ polarization is essentially proportional to the derivative of the quark–nucleus cross section with respect to transverse momentum, which peaks near the saturation momentum scale. Such processes might therefore provide generic signatures for high parton density effects and for the approach to the “black-body” (unitarity) limit of hadronic scattering.
Transverse activity of kaons and deconfinement phase transition in nucleus–nucleus collisions
(2003)
We found that the experimental results on transverse mass spectrum of kaons produced in central Pb+Pb (Au+Au) collisions show an anomalous dependence on the colliding energy. The inverse slope of the spectrum increases with the energy in the low (AGS) and high (RHIC) energy domains, whereas it remains constant in the intermediate (SPS) energy range. We argue that this anomaly is probably caused by the modification of the equation of state in the transition region between confined and deconfined matter. This observation may be considered as a new signal, in addition to the previously reported anomalies in the pion and strangeness production, of the onset of deconfinement located in the low SPS energy domain.
For statistical multifragmentation model the critical indices α′,β,γ′,δ are calculated as functions of the Fisher parameter τ. It is found that these indices have different values than in Fisher's droplet model. Some peculiarities of the scaling relations are discussed. The basic model predicts for the index τ a narrow range of values, 1.799<τ<1.846, which is consistent with two experiments on nuclear multifragmentation.
In high energy p(p)+p interactions the mean multiplicity and transverse mass spectra of neutral mesons from η to ϒ (m≅0.5–10 GeV/c2) and the transverse mass spectra of pions (mT> 1 GeV/c2) reveal a remarkable behaviour: they follow, over more than 10 orders of magnitude, the power-law function: Cm(T)−P. The parameters C and P are energy dependent, but similar for all mesons produced at the same collision energy. This scaling resembles that expected in the statistical description of hadron production: the parameter P plays the role of a temperature and the normalisation constant C is analogous to the system volume. The fundamental difference is, however, in the form of the distribution function. In order to reproduce the experimental results and preserve the basic structure of the statistical approach the Boltzmann factor e−E∗/T appearing in standard statistical mechanics has to be substituted by a power-law factor (E∗/Λ)−P.
In this paper, we present a family of regular black hole solutions in the presence of charge and angular momentum. We also discuss the related thermodynamics and we comment about the black hole life cycle during the balding and spin down phases. Interestingly the static solution resembles the Ayón-Beato–García spacetime, provided the T-duality scale is redefined in terms of the electric charge, l0→Q. The key factor at the basis of our derivation is the employment of Padmanabhan's propagator to calculate static potentials. Such a propagator encodes string T-duality effects. This means that the regularity of the spacetimes here presented can open a new window on string theory phenomenology.
Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins. However, the requirement of having a VET donor and a VET sensor installed simultaneously limits the possible target proteins and sites; to increase their number we compare six IR labels regarding their utility as VET sensors. We compare these labels in terms of their FTIR, and VET signature in VET donor-sensor dipeptides in different solvents. Furthermore, we incorporated four of these labels in PDZ3 to assess their capabilities in more complex systems. Our results show that different IR labels can be used interchangeably, allowing for free choice of the right label depending on the system under investigation and the methods available.
We investigated the excitation of surface plasmon polaritons on gold films with the metallized probe tip of a scattering-type scanning near-field optical microscope (s-SNOM). The emission of the polaritons from the tip, illuminated by near-infrared laser radiation, was found to be anisotropic and not circularly symmetric as expected on the basis of literature data. We furthermore identified an additional excitation channel via light that was reflected off the tip and excited the plasmon polaritons at the edge of the metal film. Our results, while obtained for a non-rotationally-symmetric type of probe tip and thus specific for this situation, indicate that when an s-SNOM is employed for the investigation of plasmonic structures, the unintentional excitation of surface waves and anisotropic surface wave propagation must be considered in order to correctly interpret the signatures of plasmon polariton generation and propagation.
The deuteron coalescence parameter 𝐵2 in proton+proton and nucleus+nucleus collisions in the energy range of √s N N = 900–7000 GeV for proton + proton and √s N N = 2–2760 GeV for nucleus + nucleus collisions is analyzed with the Ultrarelativistic Quantum Molecular Dynamics (UrQMD) transport model, supplemented by an event-by-event phase space coalescence model for deuteron and anti-deuteron production. The results are compared to data by the E866, E877, PHENIX, STAR and ALICE experiments. The 𝐵2 values are calculated from the final spectra of protons and deuterons. At lower energies, √s N N ≤ 20 GeV, B2 drops drastically with increasing energy. The calculations confirm that this is due to the increasing freeze-out volume reflected in B2 ∼ 1/V . At higher energies, √s N N ≥ 20 GeV, B2 saturates at a constant level. This qualitative change and the vanishing of the volume suppression is shown to be due to the development of strong radial flow with increasing energy. The flow leads to strong space-momentum correlations which counteract the volume effect.
Cryo-electron tomography (CryoET) resolves individual macromolecules inside living cells. However, the complex composition and high density of cells challenge the faithful identification of features in tomograms. Here, we capitalize on recent advances in electron tomography and demonstrate that 3D template matching (TM) localizes a wide range of structures inside crowded eukaryotic cells with confidence 10 to 100-fold above the noise level. We establish a TM pipeline with systematically tuned parameters for automated, objective and comprehensive feature identification. High-fidelity and high-confidence localizations of nuclear pore complexes, vaults, ribosomes, proteasomes, lipid membranes and microtubules, and individual subunits, demonstrate that TM is generic. We resolve ~100-kDa proteins, connect the functional states of complexes to their cellular localization, and capture vaults carrying ribosomal cargo in situ. By capturing individual molecular events inside living cells with defined statistical confidence, high-confidence TM greatly speeds up the CryoET workflow and sets the stage for visual proteomics.
Proton-powered c-ring rotation in mitochondrial ATP synthase is crucial to convert the transmembrane protonmotive force into torque to drive the synthesis of ATP. Capitalizing on recent cryo-EM structures, we aim at a structural and energetic understanding of how functional directional rotation is achieved. We performed multi-microsecond atomistic simulations to determine the free energy profiles along the c-ring rotation angle before and after the arrival of a new proton. Our results reveal that rotation proceeds by dynamic sliding of the ring over the a-subunit surface, during which interactions with conserved polar residues stabilize distinct intermediates. Ordered water chains line up for a Grotthuss-type proton transfer in one of these intermediates. After proton transfer, a high barrier prevents backward rotation and an overall drop in free energy favors forward rotation, ensuring the directionality of c-ring rotation required for the thermodynamically disfavored ATP synthesis. The essential arginine of the a-subunit stabilizes the rotated configuration through a salt-bridge with the c-ring. Overall, we describe a complete mechanism for the rotation step of the ATP synthase rotor, thereby illuminating a process critical to all life at atomic resolution.
Proton-powered c-ring rotation in mitochondrial ATP synthase is crucial to convert the transmembrane protonmotive force into torque to drive the synthesis of ATP. Capitalizing on recent cryo-EM structures, we aim at a structural and energetic understanding of how functional directional rotation is achieved. We performed multi-microsecond atomistic simulations to determine the free energy profiles along the c-ring rotation angle before and after the arrival of a new proton. Our results reveal that rotation proceeds by dynamic sliding of the ring over the a-subunit surface, during which interactions with conserved polar residues stabilize distinct intermediates. Ordered water chains line up for a Grotthuss-type proton transfer in one of these intermediates. After proton transfer, a high barrier prevents backward rotation and an overall drop in free energy favors forward rotation, ensuring the directionality of c-ring rotation required for the thermodynamically disfavored ATP synthesis. The essential arginine of the a-subunit stabilizes the rotated configuration through a salt-bridge with the c-ring. Overall, we describe a complete mechanism for the rotation step of the ATP synthase rotor, thereby illuminating a process critical to all life at atomic resolution.
Precise tune determination and split beam emittance reconstruction at the CERN PS synchrotron
(2023)
In accelerator physics, the need to improve the performance and better control the operating point of an accelerator has become, year after year, an increasingly important need in order to achieve higher energies and brightness, as well as point-like particle beams. If this involves increasingly advanced technological developments (in terms, for example, of materials for more intense superconducting magnets), it can not take place in the absence of targeted studies of linear and non-linear beam dynamics. In the context of this Ph.D. thesis in physics, linear and non-linear dynamics of charged particles in circular accelerators is the topic that will be discussed and treated in detail. In particular, the presentation and discussion of the results will be divided in two main topics: the need to know the physical properties of a proton beam; and the development of innovative methods to determine and study the accelerator’s working point. With regard to the first topic, an innovative procedure will be presented to determine the transverse size of the PS beam in the beam extraction phase. Among the different ways the extraction occurs at the PS, the analysed one is based on the transverse splitting of the beam by means of non-linear fields. Thus, the knowledge of the transverse beam size is not trivial since resonant linear and non-linear beam structures (namely, core and islands) arise and, for each of them, the beam size has to be quantified. This parameter is crucial for two main reasons: the accelerator that will receive the beam exiting the upstream accelerator may have restrictions (physical or magnetic) that involve a partial or total loss of the incoming beam; and any experiments located downstream of the considered accelerator may need a beam with a transversal size as constant as possible; consequently, its monitoring and control are essential. The second topic concerns the accurate determination of the working point of an accelerator, defined as the number of transverse oscillations the particle beam travels per unit of accelerator circumference, both horizontally and vertically. This quantity is called horizontal and vertical tune, respectively. Their knowledge is also crucial to understand whether the beam will be stable or unstable. In fact, not all tune values are acceptable, as there are particular values that bring the beam into resonance. In this configuration, the amplitude of the transverse oscillations of the particles increases in an uncontrolled manner and leads to the loss of all or part of the beam. Note that, in particular operating conditions, the resonant conditions are sought and desired to model, in a suitable way, the transversal shape of the beam, such as the above mentioned PS extraction scheme. It is even clearer how much the determination of the machine working point is essential to determine the operating conditions of an accelerator. In this context, several methods (also taken from the field of applied mathematics) to calculate the tune will be demonstrated and tested numerically on different types of synthetic signals. At the end of this description, the use of experimental data will allow to obtain the benchmark of a new method for the direct calculation of some characteristic quantities of non-linear beam dynamics (namely, the amplitude detuning, i.e. the variation of tune as a function of intensity of the perturbation provided to the beam.
The β-barrel assembly machinery (BAM) consisting of the central β-barrel BamA and four other lipoproteins mediates the folding of the majority of the outer membrane proteins. BamA is placed in an asymmetric bilayer and its lateral gate is suggested to be the functional hotspot. Here we used in situ pulsed electron-electron double resonance spectroscopy to characterize BamA in the native outer membrane. In the detergent micelles, the data is consistent with mainly an inward-open conformation of BamA. The native membrane considerably enhanced the conformational heterogeneity. The lateral gate and the extracellular loop 3 exist in an equilibrium between different conformations. The outer membrane provides a favorable environment for occupying multiple conformational states independent of the lipoproteins. Our results reveal a highly dynamic behavior of the lateral gate and other key structural elements and provide direct evidence for the conformational modulation of a membrane protein in situ.