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We present a method that enables the identification and analysis of conformational Markovian transition states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented by using both analytical models and examples from MD simulations of the benchmark system helix-forming peptide Ala5, and of larger, biomedically important systems: the 15-lipoxygenase-2 enzyme (15-LOX-2), the epidermal growth factor receptor (EGFR) protein, and the Mga2 fungal transcription factor. The analysis of 15-LOX-2 uses data generated exclusively from biased umbrella sampling simulations carried out at the hybrid ab initio density functional theory (DFT) quantum mechanics/molecular mechanics (QM/MM) level of theory. In all cases, our method automatically identifies the corresponding transition states and metastable conformations in a variationally optimal way, with the input of a set of relevant coordinates, by accurately reproducing the intrinsic slowest relaxation rate of each system. Our approach offers a general yet easy-to-implement analysis method that provides unique insight into the molecular mechanism and the rare but crucial (i.e., rate-limiting) transition states occurring along conformational transition paths in complex dynamical systems such as molecular trajectories.
Walter Greiner: in memoriam
(2017)
Walter Greiner (29 October 1935 - 6 October 2016) was a German theoretical physicist. His scientific research interests include the thematic areas of atomic physics, heavy ion physics, nuclear physics, elementary particle physics (particularly quantum electrodynamics and quantum chromodynamics). He is most known in Germany for his series of books in theoretical physics, but he is also well known around the world. Greiner was born on October 29, 1935, in Neuenbau, Sonnenberg, Germany. He studied physics at the University of Frankfurt (Goethe University in Frankfurt Am Main), receiving in this institution a BSci in physics and a Master’s degree in 1960 with a thesis on plasma-reactors, and a PhD in 1961 at the University of Freiburg under Hans Marshal, with a thesis on the nuclear polarization in μμ-mesic atoms. During the period of 1962 to 1964 he was assistant professor at the University of Maryland, followed by a position as research associate at the University of Freiburg, in 1964. Starting in 1965, he became a full professor at the Institute for Theoretical Physics at Goethe University until 2003. Greiner has been a visiting professor to many universities and laboratories, including Florida State University, the University of Virginia, the University of California, the University of Melbourne, Vanderbilt University, Yale University, Oak Ridge National Laboratory and Los Alamos National Laboratory. In 2003, with Wolf Singer, he was the founding Director of the Frankfurt Institute for Advanced Studies (FIAS), and gave lectures and seminars in elementary particle physics. He died on October 6, 2016 at the age of 80.
Walter Greiner was an excellent teacher, researcher, friend. And he was a great supporter of the series of events known by the acronyms IWARA - International Workshop on Astronomy and Relativistic Astrophysics, STARS - Caribbean Symposium on Cosmology, Gravitation, Nuclear and Astroparticle Physics, and SMFNS - International Symposium on Strong Electromagnetic Fields and Neutron Stars. Walter Greiner left us. But his memory will remain always alive among us who have had the privilege of knowing him and enjoy his wisdom and joy of living.
The KER for electron capture of vibrational cooled HeH+ and H3 + ions at 20 keV from residual gas atoms has been measured in the Frankfurt Low Energy Storage Ring (FLSR). At a vacuum in the order of few 10-11 mbar, this residual gas consists to 99% of H2 molecules. For the identification of the recoil products of this reaction, a recoil spectrometer (with an MCP-detector with position and time sensitive read out) was installed at one of the focus points (IP) in the FLSR. The planned extension of this set up by a gas target to a full COLTRIMS reaction microscope will be discussed.
According to a proposal by 't Hooft, information loss introduced by constraints in certain classical dissipative systems may lead to quantization. This scheme can be realized within the Bateman model of two coupled oscillators, one damped and one accelerated. In this paper we analyze the links of this approach to effective Hamiltonians where the environmental degrees of freedom do not appear explicitly but their effect leads to the same friction force appearing in the Bateman model. In particular, it is shown that by imposing constraints, the Bateman Hamiltonian can be transformed into an effective one expressed in expanding coordinates. This one can be transformed via a canonical transformation into Caldirola and Kanai's effective Hamiltonian that can be linked to the conventional system-plus-reservoir approach, for example, in a form used by Caldeira and Leggett.
In this work we present, for the first time, the non-perturbative renormalization for the unpolarized, helicity and transversity quasi-PDFs, in an RI′ scheme. The proposed prescription addresses simultaneously all aspects of renormalization: logarithmic divergences, finite renormalization as well as the linear divergence which is present in the matrix elements of fermion operators with Wilson lines. Furthermore, for the case of the unpolarized quasi-PDF, we describe how to eliminate the unwanted mixing with the twist-3 scalar operator.
We utilize perturbation theory for the one-loop conversion factor that brings the renormalization functions to the MS-scheme at a scale of 2 GeV. We also explain how to improve the estimates on the renormalization functions by eliminating lattice artifacts. The latter can be computed in one-loop perturbation theory and to all orders in the lattice spacing.
We apply the methodology for the renormalization to an ensemble of twisted mass fermions with Nf = 2 + 1 + 1 dynamical quarks, and a pion mass of around 375 MeV.
Motivated by recent experimental suggestions of charge-order-driven ferroelectricity in organic charge-transfer salts, such as κ-(BEDT-TTF)2Cu[N(CN)2]Cl, we investigate magnetic and charge-ordered phases that emerge in an extended two-orbital Hubbard model on the anisotropic triangular lattice at 3/4 filling. This model takes into account the presence of two organic BEDT-TTF molecules, which form a dimer on each site of the lattice, and includes short-range intramolecular and intermolecular interactions and hoppings. By using variational wave functions and quantum Monte Carlo techniques, we find two polar states with charge disproportionation inside the dimer, hinting to ferroelectricity. These charge-ordered insulating phases are stabilized in the strongly correlated limit and their actual charge pattern is determined by the relative strength of intradimer to interdimer couplings. Our results suggest that ferroelectricity is not driven by magnetism, since these polar phases can be stabilized also without antiferromagnetic order and provide a possible microscopic explanation of the experimental observations. In addition, a conventional dimer-Mott state (with uniform density and antiferromagnetic order) and a nonpolar charge-ordered state (with charge-rich and charge-poor dimers forming a checkerboard pattern) can be stabilized in the strong-coupling regime. Finally, when electron–electron interactions are weak, metallic states appear, with either uniform charge distribution or a peculiar 12-site periodicity that generates honeycomb-like charge order.
Transition path sampling is a powerful tool in the study of rare events. Shooting trial trajectories from configurations along existing transition paths proved particularly efficient in the sampling of reactive trajectories. However, most shooting attempts tend not to result in transition paths, in particular in cases where the transition dynamics has diffusive character. To overcome the resulting efficiency problem, we developed an algorithm for “shooting from the top.” We first define a shooting range through which all paths have to pass and then shoot off trial trajectories only from within this range. For a well chosen shooting range, nearly every shot is successful, resulting in an accepted transition path. To deal with multiple mechanisms, weighted shooting ranges can be used. To cope with the problem of unsuitably placed shooting ranges, we developed an algorithm that iteratively improves the location of the shooting range. The transition path sampling procedure is illustrated for models of diffusive and Langevin dynamics. The method should be particularly useful in cases where the transition paths are long so that only relatively few shots are possible, yet reasonable order parameters are known.
We have developed and characterized the novel PTR3, a proton transfer reaction-time-of-flight mass spectrometer (PTR-TOF) using a new gas inlet and an innovative reaction chamber design. The reaction chamber consists of a tripole operated with rf voltages generating an electric field only in the radial direction. An elevated electrical field is necessary to reduce clustering of primary hydronium (H3O+) and product ions with water molecules present in the sample gas. The axial movement of the ions is achieved by the sample gas flow only. Therefore, the new design allows a 30-fold longer reaction time and a 40-fold increase in pressure compared to standard PTR-TOF-MS. First calibration tests show sensitivities of up to 18000 counts per second/parts per billion and volume (cps/ppbv) at a mass resolution of >8000 m/Δm (fwhm). The new inlet using center-sampling through a critical orifice reduces wall losses of low volatility compounds. Therefore, the new PTR3 instrument is sensitive to VOC typically present in the ppbv range as well as to semivolatile organic compounds (SVOC) and even highly oxidized organic molecules (HOMs) present in the parts per quadrillion per volume (ppqv) range in the atmosphere.
We present a calculation of the global polarization of Λ hyperons in relativistic Au–Au collisions at RHIC Beam Energy Scan range sNN−−−√=7.7−200 GeV with a 3+1-dimensional cascade+viscous hydro model, UrQMD+vHLLE. Within this model, the mean polarization of Λ in the out-of-plane direction is predicted to decrease rapidly with collision energy from a top value of about 2% at the lowest energy examined. We explore the connection between the polarization signal and thermal vorticity and estimate the feed-down contribution to Λ polarization due to the decay of higher mass hyperons.
We present results on transverse momentum (pT) and rapidity (y) differential production cross sections, mean transverse momentum and mean transverse momentum square of inclusive J/ψ and ψ(2S) at forward rapidity (2.5 < y < 4) as well as ψ(2S)-to-J/ψ cross section ratios. These quantities are measured in pp collisions at center of mass energies s√=5.02 and 13 TeV with the ALICE detector. Both charmonium states are reconstructed in the dimuon decay channel, using the muon spectrometer. A comprehensive comparison to inclusive charmonium cross sections measured at s√=2.76, 7 and 8 TeV is performed. A comparison to non-relativistic quantum chromodynamics and fixed-order next-to-leading logarithm calculations, which describe prompt and non-prompt charmonium production respectively, is also presented. A good description of the data is obtained over the full pT range, provided that both contributions are summed. In particular, it is found that for pT > 15 GeV/c the non-prompt contribution reaches up to 50% of the total charmonium yield.
We present an in-depth study of masses and decays of excited scalar and pseudoscalar q¯q states in the Extended Linear Sigma Model (eLSM). The model also contains ground-state scalar, pseudoscalar, vector and axial-vector mesons. The main objective is to study the consequences of the hypothesis that the f0(1790) resonance, observed a decade ago by the BES Collaboration and recently by LHCb, represents an excited scalar quarkonium. In addition we also analyse the possibility that the new a0(1950) resonance, observed recently by BABAR, may also be an excited scalar state. Both hypotheses receive justification in our approach although there appears to be some tension between the simultaneous interpretation of f0(1790)/a0(1950) and pseudoscalar mesons η(1295), π(1300), η(1440) and K(1460) as excited q¯q states.
The ability to learn sequential behaviors is a fundamental property of our brains. Yet a long stream of studies including recent experiments investigating motor sequence learning in adult human subjects have produced a number of puzzling and seemingly contradictory results. In particular, when subjects have to learn multiple action sequences, learning is sometimes impaired by proactive and retroactive interference effects. In other situations, however, learning is accelerated as reflected in facilitation and transfer effects. At present it is unclear what the underlying neural mechanism are that give rise to these diverse findings. Here we show that a recently developed recurrent neural network model readily reproduces this diverse set of findings. The self-organizing recurrent neural network (SORN) model is a network of recurrently connected threshold units that combines a simplified form of spike-timing dependent plasticity (STDP) with homeostatic plasticity mechanisms ensuring network stability, namely intrinsic plasticity (IP) and synaptic normalization (SN). When trained on sequence learning tasks modeled after recent experiments we find that it reproduces the full range of interference, facilitation, and transfer effects. We show how these effects are rooted in the network’s changing internal representation of the different sequences across learning and how they depend on an interaction of training schedule and task similarity. Furthermore, since learning in the model is based on fundamental neuronal plasticity mechanisms, the model reveals how these plasticity mechanisms are ultimately responsible for the network’s sequence learning abilities. In particular, we find that all three plasticity mechanisms are essential for the network to learn effective internal models of the different training sequences. This ability to form effective internal models is also the basis for the observed interference and facilitation effects. This suggests that STDP, IP, and SN may be the driving forces behind our ability to learn complex action sequences.
The crossbar H-mode (CH) cavity is an accelerating structure operated in the H21(0) mode. The robustness of the crossbar geometry allows one to realize room temperature as well as superconducting linac cavities. The shunt impedance characteristics of this structure are attractive to develop proton and heavy ion linacs in the low and medium beta range. A first room temperature eight-cell prototype has proven the feasibility of the crossbar design in terms of mechanical construction, copper plating, and cooling. An innovative rf coupling concept has been developed where two CH cavities are connected by a two gap E010-mode resonator which, at the same time, provides transverse focusing by a quadrupole triplet. The concept has been applied in the design of the new FAIR proton linac and a scaled model of the second cavity of this injector has been built and tested too. The full scale prototype is now under construction at the University of Frankfurt. In this paper, the room temperature CH cavity development as well as the general layout of the FAIR proton injector (70 MeV, 325 MHz, 70 mA) is presented and discussed.
The crossbar-H-mode (CH) structure is the first superconducting multicell drift tube cavity for the low and medium energy range operated in the H21 mode. Because of the large energy gain per cavity, which leads to high real estate gradients, it is an excellent candidate for the efficient acceleration in high power proton and ion accelerators with fixed velocity profile. A prototype cavity has been developed and tested successfully with a gradient of 7MV/m. A few new superconducting CH cavities with improved geometries for different high power applications are under development at present. One cavity (f=325 MHz, β=0.16, seven cells) is currently under construction and studied with respect to a possible upgrade option for the GSI UNILAC. Another cavity (f=217 MHz, β=0.059, 15 cells) is designed for a cw operated energy variable heavy ion linac application. Furthermore, the EUROTRANS project (European research program for the transmutation of high level nuclear waste in an accelerator driven system, 600 MeV protons, 352 MHz) is one of many possible applications for this kind of superconducting rf cavity. In this context a layout of the 17 MeV EUROTRANS injector containing four superconducting CH cavities was proposed by the Institute for Applied Physics (IAP) Frankfurt. The status of the cavity development related to the EUROTRANS injector is presented.
Recent STAR data for the directed flow of protons, antiprotons and charged pions obtained within the beam energy scan program are analyzed within the Parton-Hadron-String-Dynamics (PHSD/HSD) transport models. Both versions of the kinetic approach are used to clarify the role of partonic degrees of freedom. The PHSD results, simulating a partonic phase and its coexistence with a hadronic one, are roughly consistent with the STAR data. Generally, the semi-qualitative agreement between the measured data and model results supports the idea of a crossover type of quark-hadron transition which softens the nuclear EoS but shows no indication of a first-order phase transition. Furthermore, the directed flow of kaons and antikaons is evaluated in the PHSD/HSD approachesfrom √sNN ≈ 3 - 200 GeV which shows a high sensitivity to hadronic potentials in the FAIR/NICA energy regime √sNN ≤ 8 GeV.
We study the sensitivities of the directed flow in Au+Au collisions on the equation of state (EoS), employing the transport theoretical model JAM. The EoS is modified by introducing a new collision term in order to control the pressure of a system by appropriately selecting an azimuthal angle in two-body collisions according to a given EoS. It is shown that this approach is an efficient method to modify the EoS in a transport model. The beam energy dependence of the directed flow of protons is examined with two different EoS, a first-order phase transition and crossover. It is found that our approach yields quite similar results as hydrodynamical predictions on the beam energy dependence of the directed flow; Transport theory predicts a minimum in the excitation function of the slope of proton directed flow and does indeed yield negative directed flow, if the EoS with a first-order phase transition is employed. Our result strongly suggests that the highest sensitivity for the critical point can be seen in the beam energy range of 4.7 ≤√sNN≤11.5GeV.
We investigate the properties of the QCD matter across the deconfinement phase transition in the scope of the parton-hadron string dynamics (PHSD) transport approach. We present here in particular the results on the electromagnetic radiation, i.e. photon and dilepton production, in relativistic heavy-ion collisions. By comparing our calculations for the heavy-ion collisions to the available data, we determine the relative importance of the various production sources and address the possible origin of the observed strong elliptic flow v2 of direct photons. We argue that the different centrality dependence of the hadronic and partonic sources for direct photon production in nucleusnucleus collisions can be employed to shed some more light on the origin of the photon v2 “puzzle”. While the dilepton spectra at low invariant mass show in-medium effects like an enhancement from multiple baryonic resonance formation or a collisional broadening of the vector meson spectral functions, the dilepton yield at high invariant masses (above 1.1 GeV) is dominated by QGP contributions for central heavy-ion collisions at ultra-relativistic energies. This allows to have an independent view on the parton dynamics via their electromagnetic massive radiation.
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.
We study a random matrix model for QCD at finite density via complex Langevin dynamics. This model has a phase transition to a phase with nonzero baryon density. We study the convergence of the algorithm as a function of the quark mass and the chemical potential and focus on two main observables: the baryon density and the chiral condensate. For simulations close to the chiral limit, the algorithm has wrong convergence properties when the quark mass is in the spectral domain of the Dirac operator. A possible solution of this problem is discussed.
The high collision energies reached at the LHC lead to significant production yields of light (anti-)nuclei and (hyper-)nuclei in proton–proton, proton–lead and, in particular, lead–lead collisions. The excellent particle identification capabilities of the ALICE apparatus, based on the specific energy loss in the Time Projection Chamber and the velocity information in the Time-Of-Flight detector, allow for the detection of these rarely produced particles. Further, the Inner Tracking System gives the possibility to separate primary nuclei from those coming from weak decay of heavier systems. One example of such a weak decay is the measurement of the (anti-)hypertriton decay to 3He + π− (3H̅e̅ + π+). The aforementioned capabilities of the ALICE apparatus offer the unique opportunity to search for exotica, like the bound state of a Λ and a neutron which would decay into a deuteron and a pion, or the bound state of two Λ’s. Results on the production of stable nuclei in Pb–Pb collisions at √sNN = 2.76 TeV are presented, and compared with thermal model predictions. We further present the current status of the searches, by their upper limits on the production yields, and compare the results to thermal and coalescence model expectations.
The pA system is typically regarded in heavy ion collisions as a “cold” nuclear matter environment and thought to isolate and identify initial state effects due to the presence of multiple nucleons in the incoming nucleus. Moreover, pA collisions bridge the gap between peripheral AA collisions and the pp baseline to create a more complete understanding of underlying production mechanisms and how they evolve with multiplicity. Recent measurements at both RHIC and the LHC provide an indication, however, that the “cold” nuclear matter picture may be somewhat naïve.
Recent LHC results from the 2013 p–Pb run at √sNN = 5.02 TeV will be discussed.
Time resolved measurements of the biased disk effect at an Electron Cyclotron Resonance Ion Source
(1999)
First results are reported from time resolved measurements of ion currents extracted from the Frankfurt 14 GHz Electron Cyclotron Resonance Ion Source with pulsed biased-disk voltage. It was found that the ion currents react promptly to changes of the bias. From the experimental results it is concluded that the biased disk effect is mainly due to improvements of the extraction conditions for the source and/or an enhanced transport of ions into the extraction area. By pulsing the disk voltage, short current pulses of highly charged ions can be generated with amplitudes significantly higher than the currents obtained in continuous mode.
A small electrostatic storage ring is the central machine of the Frankfurt Ion Storage Experiments (FIRE) which will be built at the new Stern-Gerlach Center of Frankfurt University. As a true multiuser, multipurpose facility with ion energies up to 50 keV, it will allow new methods to analyze complex many-particle systems from atoms to very large biomolecules. With envisaged storage times of some seconds and beam emittances in the order of a few mm mrad, measurements with up to 6 orders of magnitude better resolutions as compared to single-pass experiments become possible. In comparison to earlier designs, the ring lattice was modified in many details: Problems in earlier designs were related to, e.g., the detection of light particles and highly charged ions with different charge states. Therefore, the deflectors were redesigned completely, allowing a more flexible positioning of the diagnostics. Here, after an introduction to the concept of electrostatic machines, an overview of the planned FIRE is given and the ring lattice and elements are described in detail.
We report on the results on the dynamical modelling of cluster formation with the new combined PHSD+FRIGA model at Nuclotron and NICA energies. The FRIGA clusterization algorithm, which can be applied to the transport models, is based on the simulated annealing technique to obtain the most bound configuration of fragments and nucleons. The PHSD+FRIGA model is able to predict isotope yields as well as hypernucleus production. Based on present predictions of the combined model we study the possibility to detect such clusters and hypernuclei in the BM@N and MPD/NICA detectors.
The properties of matter at finite baryon densities play an important role for the astrophysics of compact stars as well as for heavy ion collisions or the description of nuclear matter. Because of the sign problem of the quark determinant, lattice QCD cannot be simulated by standard Monte Carlo at finite baryon densities. I review alternative attempts to treat dense QCD with an effective lattice theory derived by analytic strong coupling and hopping expansions, which close to the continuum is valid for heavy quarks only, but shows all qualitative features of nuclear physics emerging from QCD. In particular, the nuclear liquid gas transition and an equation of state for baryons can be calculated directly from QCD. A second effective theory based on strong coupling methods permits studies of the phase diagram in the chiral limit on coarse lattices.
The production of 77,79,85,85mKr and 77Br via the reaction Se(a, x) was investigated between Ea = 11 and 15 MeV using the activation technique. The irradiation of natural selenium targets on aluminum backings was conducted at the Physikalisch-Technische Bundesanstalt (PTB) in Braunschweig, Germany. The spectroscopic analysis of the reaction products was performed using a high-purity germanium detector located at PTB and a low energy photon spectrometer detector at the Goethe University Frankfurt, Germany. Thicktarget yields were determined. The corresponding energy-dependent production cross sections of 77,79,85,85mKr and 77Br were calculated from the thicktarget yields. Good agreement between experimental data and theoretical predictions using the TALYS-1.6 code was found.
Overrepresentation of bidirectional connections in local cortical networks has been repeatedly reported and is a focus of the ongoing discussion of nonrandom connectivity. Here we show in a brief mathematical analysis that in a network in which connection probabilities are symmetric in pairs, Pij = Pji, the occurrences of bidirectional connections and nonrandom structures are inherently linked; an overabundance of reciprocally connected pairs emerges necessarily when some pairs of neurons are more likely to be connected than others. Our numerical results imply that such overrepresentation can also be sustained when connection probabilities are only approximately symmetric.
Criticality meets learning : criticality signatures in a self-organizing recurrent neural network
(2017)
Many experiments have suggested that the brain operates close to a critical state, based on signatures of criticality such as power-law distributed neuronal avalanches. In neural network models, criticality is a dynamical state that maximizes information processing capacities, e.g. sensitivity to input, dynamical range and storage capacity, which makes it a favorable candidate state for brain function. Although models that self-organize towards a critical state have been proposed, the relation between criticality signatures and learning is still unclear. Here, we investigate signatures of criticality in a self-organizing recurrent neural network (SORN). Investigating criticality in the SORN is of particular interest because it has not been developed to show criticality. Instead, the SORN has been shown to exhibit spatio-temporal pattern learning through a combination of neural plasticity mechanisms and it reproduces a number of biological findings on neural variability and the statistics and fluctuations of synaptic efficacies. We show that, after a transient, the SORN spontaneously self-organizes into a dynamical state that shows criticality signatures comparable to those found in experiments. The plasticity mechanisms are necessary to attain that dynamical state, but not to maintain it. Furthermore, onset of external input transiently changes the slope of the avalanche distributions – matching recent experimental findings. Interestingly, the membrane noise level necessary for the occurrence of the criticality signatures reduces the model’s performance in simple learning tasks. Overall, our work shows that the biologically inspired plasticity and homeostasis mechanisms responsible for the SORN’s spatio-temporal learning abilities can give rise to criticality signatures in its activity when driven by random input, but these break down under the structured input of short repeating sequences.
For a chaotic system pairs of initially close-by trajectories become eventually fully uncorrelated on the attracting set. This process of decorrelation can split into an initial exponential decrease and a subsequent diffusive process on the chaotic attractor causing the final loss of predictability. Both processes can be either of the same or of very different time scales. In the latter case the two trajectories linger within a finite but small distance (with respect to the overall extent of the attractor) for exceedingly long times and remain partially predictable. Standard tests for chaos widely use inter-orbital correlations as an indicator. However, testing partially predictable chaos yields mostly ambiguous results, as this type of chaos is characterized by attractors of fractally broadened braids. For a resolution we introduce a novel 0-1 indicator for chaos based on the cross-distance scaling of pairs of initially close trajectories. This test robustly discriminates chaos, including partially predictable chaos, from laminar flow. Additionally using the finite time cross-correlation of pairs of initially close trajectories, we are able to identify laminar flow as well as strong and partially predictable chaos in a 0-1 manner solely from the properties of pairs of trajectories.
The detailed biophysical mechanisms through which transcranial magnetic stimulation (TMS) activates cortical circuits are still not fully understood. Here we present a multi-scale computational model to describe and explain the activation of different pyramidal cell types in motor cortex due to TMS. Our model determines precise electric fields based on an individual head model derived from magnetic resonance imaging and calculates how these electric fields activate morphologically detailed models of different neuron types. We predict neural activation patterns for different coil orientations consistent with experimental findings. Beyond this, our model allows us to calculate activation thresholds for individual neurons and precise initiation sites of individual action potentials on the neurons’ complex morphologies. Specifically, our model predicts that cortical layer 3 pyramidal neurons are generally easier to stimulate than layer 5 pyramidal neurons, thereby explaining the lower stimulation thresholds observed for I-waves compared to D-waves. It also shows differences in the regions of activated cortical layer 5 and layer 3 pyramidal cells depending on coil orientation. Finally, it predicts that under standard stimulation conditions, action potentials are mostly generated at the axon initial segment of cortical pyramidal cells, with a much less important activation site being the part of a layer 5 pyramidal cell axon where it crosses the boundary between grey matter and white matter. In conclusion, our computational model offers a detailed account of the mechanisms through which TMS activates different cortical pyramidal cell types, paving the way for more targeted application of TMS based on individual brain morphology in clinical and basic research settings.
Electronic states with non-trivial topology host a number of novel phenomena with potential for revolutionizing information technology. The quantum anomalous Hall effect provides spin-polarized dissipation-free transport of electrons, while the quantum spin Hall effect in combination with superconductivity has been proposed as the basis for realizing decoherence-free quantum computing. We introduce a new strategy for realizing these effects, namely by hole and electron doping kagome lattice Mott insulators through, for instance, chemical substitution. As an example, we apply this new approach to the natural mineral herbertsmithite. We prove the feasibility of the proposed modifications by performing ab-initio density functional theory calculations and demonstrate the occurrence of the predicted effects using realistic models. Our results herald a new family of quantum anomalous Hall and quantum spin Hall insulators at affordable energy/temperature scales based on kagome lattices of transition metal ions.
Study of hard core repulsive interactions in an hadronic gas from a comparison with lattice QCD
(2016)
We study the influence of hard-core repulsive interactions within the Hadron-Resonace Gas model in comparison to first principle calculation performed on a lattice. We check the effect of a bag-like parametrization for particle eigenvolume on flavor correlators, looking for an extension of the agreement with lattice simulations up to higher temperatures, as was yet pointed out in an analysis of hadron yields measured by the ALICE experiment. Hints for a flavor depending eigenvolume are present.
It is proposed to install an experimental setup in the fixed-target hall of the Nuclotron with the final goal to perform a research program focused on the production of strange matter in heavyion collisions at beam energies between 2 and 6 A GeV. The basic setup will comprise a large acceptance dipole magnet with inner tracking detector modules based on double-sided Silicon micro-strip sensors and GEMs. The outer tracking will be based on the drift chambers and straw tube detector. Particle identification will be based on the time-of-flight measurements. This setup will be sufficient perform a comprehensive study of strangeness production in heavy-ion collisions, including multi-strange hyperons, multi-strange hypernuclei, and exotic multi-strange heavy objects. These pioneering measurements would provide the first data on the production of these particles in heavy-ion collisions at Nuclotron beam energies, and would open an avenue to explore the third (strangeness) axis of the nuclear chart. The extension of the experimental program is related with the study of in-medium effects for vector mesons decaying in hadronic modes. The studies of the NN and NA reactions for the reference is assumed.
Abstract We consider the phase structure of hadronic and hadron-quark models at finite temperature and density. The basis for the hadronic part is an extension of a flavor-SU(3) ? ? ? model. We study the effect on the phase diagram by adding additional hadronic resonances to the model. With the resulting equation of state we investigate heavy-ion c... collisions using hydrodynamical simulations. In a combined approach we include quarks and the Polyakov loop field in the calculation and study chiral symmetry restoration and the deconfinement transition.
The Fisher information constitutes a natural measure for the sensitivity of a probability distribution with respect to a set of parameters. An implementation of the stationarity principle for synaptic learning in terms of the Fisher information results in a Hebbian self-limiting learning rule for synaptic plasticity. In the present work, we study the dependence of the solutions to this rule in terms of the moments of the input probability distribution and find a preference for non-Gaussian directions, making it a suitable candidate for independent component analysis (ICA). We confirm in a numerical experiment that a neuron trained under these rules is able to find the independent components in the non-linear bars problem. The specific form of the plasticity rule depends on the transfer function used, becoming a simple cubic polynomial of the membrane potential for the case of the rescaled error function. The cubic learning rule is also an excellent approximation for other transfer functions, as the standard sigmoidal, and can be used to show analytically that the proposed plasticity rules are selective for directions in the space of presynaptic neural activities characterized by a negative excess kurtosis.
We present an effective model for timing-dependent synaptic plasticity (STDP) in terms of two interacting traces, corresponding to the fraction of activated NMDA receptors and the concentration in the dendritic spine of the postsynaptic neuron. This model intends to bridge the worlds of existing simplistic phenomenological rules and highly detailed models, thus constituting a practical tool for the study of the interplay of neural activity and synaptic plasticity in extended spiking neural networks. For isolated pairs of pre- and postsynaptic spikes, the standard pairwise STDP rule is reproduced, with appropriate parameters determining the respective weights and timescales for the causal and the anticausal contributions. The model contains otherwise only three free parameters, which can be adjusted to reproduce triplet nonlinearities in hippocampal culture and cortical slices. We also investigate the transition from time-dependent to rate-dependent plasticity occurring for both correlated and uncorrelated spike patterns.
Generating functionals may guide the evolution of a dynamical system and constitute a possible route for handling the complexity of neural networks as relevant for computational intelligence.We propose and explore a new objective function, which allows to obtain plasticity rules for the afferent synaptic weights. The adaption rules are Hebbian, self-limiting, and result from the minimization of the Fisher information with respect to the synaptic flux. We perform a series of simulations examining the behavior of the new learning rules in various circumstances.The vector of synaptic weights aligns with the principal direction of input activities, whenever one is present. A linear discrimination is performed when there are two or more principal directions; directions having bimodal firing-rate distributions, being characterized by a negative excess kurtosis, are preferred. We find robust performance and full homeostatic adaption of the synaptic weights results as a by-product of the synaptic flux minimization. This self-limiting behavior allows for stable online learning for arbitrary durations.The neuron acquires new information when the statistics of input activities is changed at a certain point of the simulation, showing however, a distinct resilience to unlearn previously acquired knowledge. Learning is fast when starting with randomly drawn synaptic weights and substantially slower when the synaptic weights are already fully adapted.
Ein Laserblitz von unvorstellbarer Intensität pulverisiert im Labor ein Molekül. Wachsam zeichnen die Instrumente die Flugbahn und Geschwindigkeit jedes Bruchstücks auf. Physiker gewinnen daraus hochpräzise Informationen über die Molekülstruktur. Auch links- und rechtshändige Formen lassen sich unterscheiden.
Oscillations play a critical role in cognitive phenomena and have been observed in many brain regions. Experimental evidence indicates that classes of neurons exhibit properties that could promote oscillations, such as subthreshold resonance and electrical gap junctions. Typically, these two properties are studied separately but it is not clear which is the dominant determinant of global network rhythms. Our aim is to provide an analytical understanding of how these two effects destabilize the fluctuation-driven state, in which neurons fire irregularly, and lead to an emergence of global synchronous oscillations. Here we show how the oscillation frequency is shaped by single neuron resonance, electrical and chemical synapses.The presence of both gap junctions and subthreshold resonance are necessary for the emergence of oscillations. Our results are in agreement with several experimental observations such as network responses to oscillatory inputs and offer a much-needed conceptual link connecting a collection of disparate effects observed in networks.
A measurement of the transverse momentum spectra of jets in Pb-Pb collisions at sNN−−−√=2.76 TeV is reported. Jets are reconstructed from charged particles using the anti-kT jet algorithm with jet resolution parameters R of 0.2 and 0.3 in pseudo-rapidity |η|<0.5. The transverse momentum pT of charged particles is measured down to 0.15 GeV/c which gives access to the low pT fragments of the jet. Jets found in heavy-ion collisions are corrected event-by-event for average background density and on an inclusive basis (via unfolding) for residual background fluctuations and detector effects. A strong suppression of jet production in central events with respect to peripheral events is observed. The suppression is found to be similar to the suppression of charged hadrons, which suggests that substantial energy is radiated at angles larger than the jet resolution parameter R=0.3 considered in the analysis. The fragmentation bias introduced by selecting jets with a high pT leading particle, which rejects jets with a soft fragmentation pattern, has a similar effect on the jet yield for central and peripheral events. The ratio of jet spectra with R=0.2 and R=0.3 is found to be similar in Pb-Pb and simulated PYTHIA pp events, indicating no strong broadening of the radial jet structure in the reconstructed jets with R<0.3.
Conventional radar-based image reconstruction techniques fail when they are applied to heterogeneous breast tissue, since the underlying in-breast relative permittivity is unknown or assumed to be constant. This results in a systematic error during the process of image formation. A recent trend in microwave biomedical imaging is to extract the relative permittivity from the object under test to improve the image reconstruction quality and thereby to enhance the diagnostic assessment. In this paper, we present a novel radar-based methodology for microwave breast cancer detection in heterogeneous breast tissue integrating a 3D map of relative permittivity as a priori information. This leads to a novel image reconstruction formulation where the delay-and-sum focusing takes place in time rather than range domain. Results are shown for a heterogeneous dense (class-4) and a scattered fibroglandular (class-2) numerical breast phantom using Bristol's 31-element array configuration.
We enlarge the so-called extended linear Sigma model (eLSM) by including the charm quark according to the global U(4)r × U(4)l chiral symmetry. In the eLSM, besides scalar and pseudoscalar mesons, also vector and axial-vector mesons are present. Almost all the parameters of the model were fixed in a previous study of mesons below 2 GeV. In the extension to the four-flavor case, only three additional parameters (all of them related to the bare mass of the charm quark) appear.We compute the (OZI dominant) strong decays of open charmed mesons. The results are compatible with the experimental data, although the theoretical uncertainties are still large.
In the presence of a minimal length, physical objects cannot collapse to an infinite density, singular, matter point. In this paper, we consider the possible final stage of the gravitational collapse of "thick" matter layers. The energy momentum tensor we choose to model these shell-like objects is a proper modification of the source for "noncommutative geometry inspired," regular black holes. By using higher momenta of Gaussian distribution to localize matter at finite distance from the origin, we obtain new solutions of the Einstein equation which smoothly interpolates between Minkowski's geometry near the center of the shell and Schwarzschild’s spacetime far away from the matter layer. The metric is curvature singularity free. Black hole type solutions exist only for "heavy" shells; that is, M >= Me, where Me is the mass of the extremal configuration. We determine the Hawking temperature and a modified area law taking into account the extended nature of the source.
In the framework of an interference setup in which only two outcomes are possible (such as in the case of a Mach–Zehnder interferometer), we discuss in a simple and pedagogical way the difference between a standard, unitary quantum mechanical evolution and the existence of a real collapse of the wavefunction. This is a central and not-yet resolved question of quantum mechanics and indeed of quantum field theory as well. Moreover, we also present the Elitzur–Vaidman bomb, the delayed choice experiment, and the effect of decoherence. In the end, we propose two simple experiments to visualize decoherence and to test the role of an entangled particle.
EUROTRANS is a European research program for the transmutation of high level nuclear waste in an accelerator-driven system (ADS). As proposed, the driver linac needs to deliver a 2.5–4 mA, 600 MeV continuous-wave (CW) proton beam and later a 20 mA, 800 MeV one to the spallation target in the prototype-scale and industrial-scale demonstration phases, respectively. This paper is focusing on the conceptual studies performed with respect to the 17 MeV injector. First, the special beam dynamics strategies and methods, which have been developed and applied to design a current-variable injector up to 30 mA for allowing an easy upgrade without additional R&D costs, will be introduced. Then the error study made for evaluating the tolerance limits of the designed injector will be presented as well.
Focus on quantum efficiency
(2014)
Technologies which convert light into energy, and vice versa, rely on complex, microscopic transport processes in the condensed phase, which obey the laws of quantum mechanics, but hitherto lack systematic analysis and modeling. Given our much improved understanding of multicomponent, disordered, highly structured, open quantum systems, this ‘focus on’ collection collects cuttingedge research on theoretical and experimental aspects of quantum transport in truly complex systems as defined, e.g., by the macromolecular functional complexes at the heart of photosynthesis, by organic quantum wires, or even photovoltaic devices. To what extent microscopic quantum coherence effects can (be made to) impact on macroscopic transport behavior is an equally challenging and controversial question, and this "focus on" collection provides a setting for the present state of affairs, as well as for the "quantum opportunities" on the horizon.
We study the equilibrium properties of strongly-interacting infinite parton-hadron matter, characterized by the transport coefficients such as shear and bulk viscosity and electric conductivity, and the non-equilibrium dynamics of heavy-ion collisions within the Parton-Hadron-String Dynamics (PHSD) transport approach, which incorporates explicit partonic degrees of freedom in terms of strongly interacting quasiparticles (quarks and gluons) in line with an equation of state from lattice QCD as well as the dynamical hadronization and hadronic collision dynamics in the final reaction phase. We discuss in particular the possible origin for the strong elliptic flow v2 of direct photons observed at RHIC energies.