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Motivated by a recent finding of an exact solution of the relativistic Boltzmann equation in a Friedmann–Robertson–Walker spacetime, we implement this metric into the newly developed transport approach Simulating Many Accelerated Strongly-interacting Hadrons (SMASH). We study the numerical solution of the transport equation and compare it to this exact solution for massless particles. We also compare a different initial condition, for which the transport equation can be independently solved numerically. Very nice agreement is observed in both cases. Having passed these checks for the SMASH code, we study a gas of massive particles within the same spacetime, where the particle decoupling is forced by the Hubble expansion. In this simple scenario we present an analysis of the freeze-out times, as function of the masses and cross sections of the particles. The results might be of interest for their potential application to relativistic heavy-ion collisions, for the characterization of the freeze-out process in terms of hadron properties.
Background: Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies for overlapping peak clusters. For example, NOESY-type spectra have considerable overlaps leading to significant peak-picking intensity errors, which can result in erroneous structural restraints. Precise frequencies are critical for unambiguous resonance assignments.
Results: To alleviate this problem, a more sophisticated peaks decomposition algorithm, based on non-negative matrix factorization (NMF), was developed. We produce peak shapes from Fourier-transformed NMR spectra. Apart from its main goal of deriving components from spectra and producing peak lists automatically, the NMF approach can also be applied if the positions of some peaks are known a priori, e.g. from consistently referenced spectral dimensions of other experiments.
Conclusions: Application of the NMF algorithm to a three-dimensional peak list of the 23 kDa bi-domain section of the RcsD protein (RcsD-ABL-HPt, residues 688-890) as well as to synthetic HSQC data shows that peaks can be picked accurately also in spectral regions with strong overlap.
Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.
The pion-to-proton ratio is identified as a potential signal for a non-equilibrium first-order chiral phase transition in heavy-ion collisions, as the pion multiplicity is directly related to entropy production. To showcase this effect, a non-equilibrium Bjorken expansion starting from realistic initial conditions along a Taub adiabat is used to simulate the entropy production. Different dynamical criteria to determine the final entropy-per-baryon number are investigated and matched to a hadron resonance gas model along the chemical freeze out curve to obtain the final pion and proton numbers. We detect a strong enhancement of their multiplicity ratio at the energies where the system experiences a strong phase transition as compared to a smooth crossover which shows almost no enhancement.
We construct a new equation of state for the baryonic matter under an intense magnetic field within the framework of covariant density functional theory. The composition of matter includes hyperons as well as Δ-resonances. The extension of the nucleonic functional to the hypernuclear sector is constrained by the experimental data on Λ and Ξ-hypernuclei. We find that the equation of state stiffens with the inclusion of the magnetic field, which increases the maximum mass of neutron star compared to the non-magnetic case. In addition, the strangeness fraction in the matter is enhanced. Several observables, like the Dirac effective mass, particle abundances, etc. show typical oscillatory behavior as a function of the magnetic field and/or density which is traced back to the occupation pattern of Landau levels.
Radiation damage following the ionising radiation of tissue has different scenarios and mechanisms depending on the projectiles or radiation modality. We investigate the radiation damage effects due to shock waves produced by ions. We analyse the strength of the shock wave capable of directly producing DNA strand breaks and, depending on the ion's linear energy transfer, estimate the radius from the ion's path, within which DNA damage by the shock wave mechanism is dominant. At much smaller values of linear energy transfer, the shock waves turn out to be instrumental in propagating reactive species formed close to the ion's path to large distances, successfully competing with diffusion.
Mitochondria form a dynamic tubular reticulum within eukaryotic cells. Currently, quantitative understanding of its morphological characteristics is largely absent, despite major progress in deciphering the molecular fission and fusion machineries shaping its structure. Here we address the principles of formation and the large-scale organization of the cell-wide network of mitochondria. On the basis of experimentally determined structural features we establish the tip-to-tip and tip-to-side fission and fusion events as dominant reactions in the motility of this organelle. Subsequently, we introduce a graph-based model of the chondriome able to encompass its inherent variability in a single framework. Using both mean-field deterministic and explicit stochastic mathematical methods we establish a relationship between the chondriome structural network characteristics and underlying kinetic rate parameters. The computational analysis indicates that mitochondrial networks exhibit a percolation threshold. Intrinsic morphological instability of the mitochondrial reticulum resulting from its vicinity to the percolation transition is proposed as a novel mechanism that can be utilized by cells for optimizing their functional competence via dynamic remodeling of the chondriome. The detailed size distribution of the network components predicted by the dynamic graph representation introduces a relationship between chondriome characteristics and cell function. It forms a basis for understanding the architecture of mitochondria as a cell-wide but inhomogeneous organelle. Analysis of the reticulum adaptive configuration offers a direct clarification for its impact on numerous physiological processes strongly dependent on mitochondrial dynamics and organization, such as efficiency of cellular metabolism, tissue differentiation and aging.
p53 regulates the cellular response to genotoxic damage and prevents carcinogenic events. Theoretical and experimental studies state that the p53-Mdm2 network constitutes the core module of regulatory interactions activated by cellular stress induced by a variety of signaling pathways. In this paper, a strategy to control the p53-Mdm2 network regulated by p14ARF is developed, based on the pinning control technique, which consists into applying local feedback controllers to a small number of nodes (pinned ones) in the network. Pinned nodes are selected on the basis of their importance level in a topological hierarchy, their degree of connectivity within the network, and the biological role they perform. In this paper, two cases are considered. For the first case, the oscillatory pattern under gamma-radiation is recovered; afterward, as the second case, increased expression of p53 level is taken into account. For both cases, the control law is applied to p14ARF (pinned node based on a virtual leader methodology), and overexpressed Mdm2-mediated p53 degradation condition is considered as carcinogenic initial behavior. The approach in this paper uses a computational algorithm, which opens an alternative path to understand the cellular responses to stress, doing it possible to model and control the gene regulatory network dynamics in two different biological contexts. As the main result of the proposed control technique, the two mentioned desired behaviors are obtained.
I summarize recent developments in the hard-thermal-loop approach to QCD. I first discuss a finite-temperature and -density calculation of QCD thermodynamics at NNLO from the hard-thermal-loop perturbation theory. I then discuss a generalization of the hard-thermal-loop framework to the magnetic scale g2T, from which a novel non-Abelian massless mode is uncovered.
The Gribov mode in hot QCD
(2017)
The cytoskeleton is crucial for defining neuronal-type-specific dendrite morphologies. To explore how the complex interplay of actin-modulatory proteins (AMPs) can define neuronal types in vivo, we focused on the class III dendritic arborization (c3da) neuron of Drosophila larvae. Using computational modeling, we reveal that the main branches (MBs) of c3da neurons follow general models based on optimal wiring principles, while the actin-enriched short terminal branches (STBs) require an additional growth program. To clarify the cellular mechanisms that define this second step, we thus concentrated on STBs for an in-depth quantitative description of dendrite morphology and dynamics. Applying these methods systematically to mutants of six known and novel AMPs, we revealed the complementary roles of these individual AMPs in defining STB properties. Our data suggest that diverse dendrite arbors result from a combination of optimal-wiring-related growth and individualized growth programs that are neuron-type specific.
Relying on the existing estimates for the production cross sections of mini black holes in models with large extra dimensions, we review strategies for identifying those objects at collider experiments. We further consider a possible stable final state of such black holes and discuss their characteristic signatures. Keywords: Black holes
To be published in J. Phys. G - Proceedings of SQM 2004 : We review the results from the various hydrodynamical and transport models on the collective flow observables from AGS to RHIC energies. A critical discussion of the present status of the CERN experiments on hadron collective flow is given. We emphasize the importance of the flow excitation function from 1 to 50 A.GeV: here the hydrodynamic model has predicted the collapse of the v2-flow ~ 10 A.GeV; at 40 A.GeV it has been recently observed by the NA49 collaboration. Since hadronic rescattering models predict much larger flow than observed at this energy we interpret this observation as evidence for a first order phase transition at high baryon density r b. Moreover, the connection of the elliptic flow v2 to jet suppression is examined. It is proven experimentally that the collective flow is not faked by minijet fragmentation. Additionally, detailed transport studies show that the away-side jet suppression can only partially (< 50%) be due to hadronic rescattering. Furthermore, the change in sign of v1, v2 closer to beam rapidity is related to the occurence of a high density first order phase transition in the RHIC data at 62.5, 130 and 200 A.GeV.
We discuss the present collective flow signals for the phase transition to quark-gluon plasma (QGP) and the collective flow as a barometer for the equation of state (EoS). A study of Mach shocks induced by fast partonic jets propagating through the QGP is given. We predict a significant deformation of Mach shocks in central Au+Au collisions at RHIC and LHC energies as compared to the case of jet propagation in a static medium. Results of a hydrodynamical study of jet energy loss are presented.
We discuss the present collective flow signals for the phase transition to the quark-gluon plasma (QGP) and the collective flow as a barometer for the equation of state (EoS). We emphasize the importance of the flow excitation function from 1 to 50A GeV: here the hydrodynamicmodel has predicted the collapse of the v1-flow at ~ 10A GeV and of the v2-flow at ~ 40A GeV. In the latter case, this has recently been observed by the NA49 collaboration. Since hadronic rescattering models predict much larger flow than observed at this energy, we interpret this observation as potential evidence for a first order phase transition at high baryon density pB.
A critical discussion of the present status of the CERN experiments on charm dynamics and hadron collective flow is given. We emphasize the importance of the flow excitation function from 1 to 50 A·GeV: here the hydrodynamic model has predicted the collapse of the v1-flow and of the v2-flow at 10 A·GeV; at 40 A·GeV it has been recently observed by the NA49 collaboration. Since hadronic rescattering models predict much larger flow than observed at this energy we interpret this observation as potential evidence for a first order phase transition at high baryon density B. A detailed discussion of the collective flow as a barometer for the equation of state (EoS) of hot dense matter at RHIC follows. Here, hadronic rescattering models can explain < 30% of the observed elliptic flow, v2, for pT > 2 GeV/c. This is interpreted as evidence for the production of superdense matter at RHIC with initial pressure far above hadronic pressure, p > 1 GeV/fm3. We suggest that the fluctuations in the flow, v1 and v2, should be measured in future since ideal hydrodynamics predicts that they are larger than 50 % due to initial state fluctuations. Furthermore, the QGP coe cient of viscosity may be determined experimentally from the fluctuations observed. The connection of v2 to jet suppression is examined. It is proven experimentally that the collective flow is not faked by minijet fragmentation. Additionally, detailed transport studies show that the awayside jet suppression can only partially (< 50%) be due to hadronic rescattering. We, finally, propose upgrades and second generation experiments at RHIC which inspect the first order phase transition in the fragmentation region, i.e. at µB 400 MeV (y 4 5), where the collapse of the proton flow should be seen in analogy to the 40 A·GeV data. The study of Jet-Wake-riding potentials and Bow shocks caused by jets in the QGP formed at RHIC can give further information on the equation of state (EoS) and transport coe cients of the Quark Gluon Plasma (QGP).
Results from various theoretical approaches and ideas presented at this exciting meeting (summary talk at the 5th International Conference on Physics and Astrophysics of Quark Gluon Plasma (ICPAQGP - 2005)) are reviewed. I also point towards future directions, in particular hydrodynamic behaviour induced by jets traveling through the quark-gluon plasma, which might be worth looking at in more detail.
The experimental signatures of TeV-mass black hole (BH) formation in heavy ion collisions at the LHC is examined. We find that the black hole production results in a complete disappearance of all very high p_T (> 500 GeV) back-to-back correlated di-jets of total mass M > M_f ~ 1 TeV. We show that the subsequent Hawking-decay produces multiple hard mono-jets and discuss their detection. We study the possibility of cold black hole remnant (BHR) formation of mass ~ M_f and the experimental distinguishability of scenarios with BHRs and those with complete black hole decay. Due to the rather moderate luminosity in the first year of LHC running the least chance for the observation of BHs or BHRs at this early stage will be by ionizing tracks in the ALICE TPC. Finally we point out that stable BHRs would be interesting candidates for energy production by conversion of mass to Hawking radiation.