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In this work, we show how Gibbs or thermal states appear dynamically in closed quantum many-body systems, building on the program of dynamical typicality. We introduce a novel perturbation theorem for physically relevant weak system-bath couplings that is applicable even in the thermodynamic limit. We identify conditions under which thermalization happens and discuss the underlying physics. Based on these results, we also present a fully general quantum algorithm for preparing Gibbs states on a quantum computer with a certified runtime and error bound. This complements quantum Metropolis algorithms, which are expected to be efficient but have no known runtime estimates and only work for local Hamiltonians.
A Bose-Hubbard model on a dynamical lattice was introduced in previous work as a spin system analogue of emergent geometry and gravity. Graphs with regions of high connectivity in the lattice were identified as candidate analogues of spacetime geometries that contain trapped surfaces. We carry out a detailed study of these systems and show explicitly that the highly connected subgraphs trap matter. We do this by solving the model in the limit of no back-reaction of the matter on the lattice, and for states with certain symmetries that are natural for our problem. We find that in this case the problem reduces to a one-dimensional Hubbard model on a lattice with variable vertex degree and multiple edges between the same two vertices. In addition, we obtain a (discrete) differential equation for the evolution of the probability density of particles which is closed in the classical regime. This is a wave equation in which the vertex degree is related to the local speed of propagation of probability. This allows an interpretation of the probability density of particles similar to that in analogue gravity systems: matter inside this analogue system sees a curved spacetime. We verify our analytic results by numerical simulations. Finally, we analyze the dependence of localization on a gradual, rather than abrupt, falloff of the vertex degree on the boundary of the highly connected region and find that matter is localized in and around that region.
We study phase synchronization in a network motif with a starlike structure in which the central node's (the hub's) frequency is strongly detuned against the other peripheral nodes. We find numerically and experimentally a regime of remote synchronization (RS), where the peripheral nodes form a phase synchronized cluster, while the hub remains free with its own dynamics and serves just as a transmitter for the other nodes. We explain the mechanism for this RS by the existence of a free amplitude and also show that systems with a fixed or constant amplitude, such as the classic Kuramoto phase oscillator, are not able to generate this phenomenon. Further, we derive an analytic expression which supports our explanation of the mechanism.
On 27 February 2010 the M-w 8.8 Maule earthquake in Central Chile ruptured a seismic gap where significant strain had accumulated since 1835. Shortly after the mainshock a dense network of temporary seismic stations was installed along the whole rupture zone in order to capture the aftershock activity. Here, we present the aftershock distribution and first motion polarity focal mechanisms based on automatic detection algorithms and picking engines. By processing the seismic data between 15 March and 30 September 2010 from stations from IRIS, IPGP, GFZ and University of Liverpool we determined 20,205 hypocentres with magnitudes M-w between 1 and 5.5. Seismic activity occurs in six groups: 1.) Normal faulting outer rise events 2.) A shallow group of plate interface seismicity apparent at 25-35 km depth and 50-120 km distance to the trench with some variations between profiles. Along strike, the aftershocks occur largely within the zone of coseismic slip but extend similar to 50 km further north, and with predominantly shallowly dipping thrust mechanisms. Along dip, the events are either within the zone of coseismic slip, or downdip from it, depending on the coseismic slip model used. 3.) A third band of seismicity is observed further downdip at 40-50 km depth and further inland at 150-160 km trench perpendicular distance, with mostly shallow dipping (similar to 28 degrees) thrust focal mechanisms indicating rupture of the plate interface significantly downdip of the coseismic rupture, and presumably above the intersection of the continental Moho with the plate interface. 4.) A deep group of intermediate depth events between 80 and 120 km depth is present north of 36 degrees S. Within the Maule segment, a large portion of events during the inter-seismic phase originated from this depth range. 5.) The magmatic arc exhibits a small amount of crustal seismicity but does not appear to show significantly enhanced activity after the M-w 8.8 Maule 2010 earthquake. 6.) Pronounced crustal aftershock activity with mainly normal faulting mechanisms is found in the region of Pichilemu (similar to 34.5 degrees S). These crustal events occur in a similar to 30 km wide region with sharp inclined boundaries and oriented oblique to the trench. The best-located events describe a plane dipping to the southwest, consistent with one of the focal planes of the large normal-faulting aftershock (M-w = 6.9) on 11 March 2010.
Contemporary cosmological conceptions suggest that the dark matter in haloes of galaxies and galaxy clusters has most likely a clumpy structure. If a stream of gas penetrates through it, a small-scale gravitational field created by the clumps disturbs the flow resulting in momentum exchange between the stream and the dark matter. In this article, we perform an analysis of this effect, based on the hierarchical halo model of the dark matter structure and Navarro-Frenk-White density profiles. We consider the clumps of various masses, from the smallest up to the highest ones M = 10(9) M circle dot. It has been found that in any event the effect grows with the mass of the clump: not only the drag force F acting on the clump but also its acceleration w = F/M increases.
We discuss various astrophysical systems. The mechanism proved to be ineffective in the case of galaxy or galaxy cluster collisions. On the other hand, it played an important role during the process of galaxy formation. As a result, the dark matter should have formed a more compact, oblate and faster rotating substructure in the halo of our Galaxy. We have shown that this thick disc should be more clumpy than the halo. This fact is very important for the indirect detection experiments since it is the clumps that give the main contribution to the annihilation signal. Our calculations show that the mechanism of momentum exchange between the dark and baryon matter is ineffective on the outskirts of the galactic halo. It means that the clumps from there were not transported to the thick disc, and this region should be more clumpy than the halo on the average.
To explore the ionization conditions in highly-ionized absorbers at high redshift, we study in detail two intervening O vi absorbers at z approximate to 2 toward the quasar PKS 1448-232, based on high (R approximate to 75 000) and intermediate (R approximate to 45 000) resolution optical VLT/UVES spectra. We find that both absorption systems are composed of several narrow subcomponents with typical Civ/O VI Doppler-parameters of b < 10 km s(-1). This implies that the gas temperatures are T < 10(5) K and that the absorbers are photoionized by the UV background. The system at z = 2.1098 represents a simple, isolated O VI absorber that has only two absorption components and is relatively metal-rich (Z similar to 0.6 solar). Ioinization modeling implies that the system is photoionized with O VI, C IV, and H I coexisting in the same gas phase. The second system at z = 2.1660 represents a complicated, multi-component absorption system with eight O VI components spanning almost 300 km s(-1) in radial velocity. The photoionization modeling implies that the metallicity is non-uniform and relatively low (<= 0.1 solar) and that the O VI absorption must arise in a gas phase that differs from that traced by C IV, C III, and H I. Our detailed study of the two O VI systems towards PKS 1448-232 shows that multi-phase, multi-component high-ion absorbers similar to the one at z = 2.1660 can be described by applying a detailed ionization modeling of the various subcomponents to obtain reliable measurements of the physical conditions and the metal abundances in the gas.
Completely positive, trace preserving (CPT) maps and Lindblad master equations are both widely used to describe the dynamics of open quantum systems. The connection between these two descriptions is a classic topic in mathematical physics. One direction was solved by the now famous result due to Lindblad, Kossakowski, Gorini and Sudarshan, who gave a complete characterisation of the master equations that generate completely positive semi-groups. However, the other direction has remained open: given a CPT map, is there a Lindblad master equation that generates it (and if so, can we find its form)? This is sometimes known as the Markovianity problem. Physically, it is asking how one can deduce underlying physical processes from experimental observations.
We give a complexity theoretic answer to this problem: it is NP-hard. We also give an explicit algorithm that reduces the problem to integer semi-definite programming, a well-known NP problem. Together, these results imply that resolving the question of which CPT maps can be generated by master equations is tantamount to solving P = NP: any efficiently computable criterion for Markovianity would imply P = NP; whereas a proof that P = NP would imply that our algorithm already gives an efficiently computable criterion. Thus, unless P does equal NP, there cannot exist any simple criterion for determining when a CPT map has a master equation description.
However, we also show that if the system dimension is fixed (relevant for current quantum process tomography experiments), then our algorithm scales efficiently in the required precision, allowing an underlying Lindblad master equation to be determined efficiently from even a single snapshot in this case.
Our work also leads to similar complexity-theoretic answers to a related long-standing open problem in probability theory.
If a one-dimensional quantum lattice system is subject to one step of a reversible discrete-time dynamics, it is intuitive that as much "quantum information" as moves into any given block of cells from the left, has to exit that block to the right. For two types of such systems - namely quantum walks and cellular automata - we make this intuition precise by defining an index, a quantity that measures the "net flow of quantum information" through the system. The index supplies a complete characterization of two properties of the discrete dynamics. First, two systems S-1, S-2 can be "pieced together", in the sense that there is a system S which acts like S-1 in one region and like S-2 in some other region, if and only if S-1 and S-2 have the same index. Second, the index labels connected components of such systems: equality of the index is necessary and sufficient for the existence of a continuous deformation of S-1 into S-2. In the case of quantum walks, the index is integer-valued, whereas for cellular automata, it takes values in the group of positive rationals. In both cases, the map S bar right arrow. ind S is a group homomorphism if composition of the discrete dynamics is taken as the group law of the quantum systems. Systems with trivial index are precisely those which can be realized by partitioned unitaries, and the prototypes of systems with non-trivial index are shifts.
We propose a simple theoretical model for aggregative and fragmentative collisions in Saturn's dense rings. In this model the ring matter consists of a bimodal size distribution: large (meter sized) boulders and a population of smaller particles (tens of centimeters down to dust). The small particles can adhesively stick to the boulders and can be released as debris in binary collisions of their carriers. To quantify the adhesion force we use the JKR theory (Johnson, K., Kendall, K., Roberts, A. [1971]. Proc. R. Soc. Lond. A 324, 301-313). The rates of release and adsorption of particles are calculated, depending on material parameters, sizes, and plausible velocity dispersions of carriers and debris particles. In steady state we obtain an expression for the amount of free debris relative to the fraction still attached to the carriers. In terms of this conceptually simple model a paucity of subcentimeter particles in Saturn's rings (French, R.G., Nicholson, P.D. [2000]. Icarus 145, 502-523; Marouf, E. et al. [2008]. Abstracts for "Saturn after Cassini-Huygens" Symposium, Imperial College London, UK, July 28 to August 1, p. 113) can be understood as a consequence of the increasing strength of adhesion (relative to inertial forces) for decreasing particle size. In this case particles smaller than a certain critical radius remain tightly attached to the surfaces of larger boulders, even when the boulders collide at their typical speed. Furthermore, we find that already a mildly increased velocity dispersion of the carrier-particles may significantly enhance the fraction of free debris particles, in this way increasing the optical depth of the system.
We consider the mean first-passage time of a random walker moving in a potential landscape on a finite interval, the starting and end points being at different potentials. From analytical calculations and Monte Carlo simulations we demonstrate that the mean first-passage time for a piecewise linear curve between these two points is minimized by the introduction of a potential barrier. Due to thermal fluctuations, this barrier may be crossed. It turns out that the corresponding expense for this activation is less severe than the gain from an increased slope towards the end point. In particular, the resulting mean first-passage time is shorter than for a linear potential drop between the two points.
We present the results of a joint observational campaign between the Green Bank radio telescope and the VERITAS gamma-ray telescope, which searched for a correlation between the emission of very-high-energy (VHE) gamma rays (E-gamma > 150 GeV) and giant radio pulses (GRPs) from the Crab pulsar at 8.9 GHz. A total of 15,366 GRPs were recorded during 11.6 hr of simultaneous observations, which were made across four nights in 2008 December and in 2009 November and December. We searched for an enhancement of the pulsed gamma-ray emission within time windows placed around the arrival time of the GRP events. In total, eight different time windows with durations ranging from 0.033 ms to 72 s were positioned at three different locations relative to the GRP to search for enhanced gamma-ray emission which lagged, led, or was concurrent with, the GRP event. Furthermore, we performed separate searches on main pulse GRPs and interpulse GRPs and on the most energetic GRPs in our data sample. No significant enhancement of pulsed VHE emission was found in any of the preformed searches. We set upper limits of 5-10 times the average VHE flux of the Crab pulsar on the flux simultaneous with interpulse GRPs on single-rotation-period timescales. On similar to 8 s timescales around interpulse GRPs, we set an upper limit of 2-3 times the average VHE flux. Within the framework of recent models for pulsed VHE emission from the Crab pulsar, the expected VHE-GRP emission correlations are below the derived limits.
We present a toy-model for an ensemble of adhering mesoscopic constituents in order to estimate the effect of the granular temperature on the sizes of embedded aggregates. The major goal is to illustrate the relation between the mean aggregate size and the granular temperature in dense planetary rings. For sake of simplicity we describe the collective behavior of the ensemble by means of equilibrium statistical mechanics, motivated by the stationary temperature established by the balance between a Kepler-shear driven viscous heating and inelastic cooling in these cosmic granular disks. The ensemble consists of N' equal constituents which can form cluster(s) or move like a gas-or both phases may coexist-depending on the (granular) temperature of the system. We assume the binding energy levels of a cluster E-c = -N-c gamma a to be determined by a certain contact number N-c, given by the configuration of N constituents of the aggregate (energy per contact: -gamma a). By applying canonical and grand-canonical ensembles, we show that the granular temperature T of a gas of constituents (their mean kinetic energy) controls the size distribution of the aggregates. They are the smaller the higher the granular temperature T is. A mere gas of single constituents is sustained for T >> gamma a. In the case of large clusters (low temperatures T << gamma a) the size distribution becomes a Poissonian.
In this paper we analyze correlated continuous-time random walks introduced recently by Tejedor and Metzler (2010 J. Phys. A: Math. Theor. 43 082002). We obtain the Langevin equations associated with this process and the corresponding scaling limits of their solutions. We prove that the limit processes are self-similar and display anomalous dynamics. Moreover, we extend the model to include external forces. Our results are confirmed by Monte Carlo simulations.
Naturally occurring lipid granules diffuse in the cytoplasm and can be used as tracers to map out the viscoelastic landscape inside living cells. Using optical trapping and single particle tracking we found that lipid granules exhibit anomalous diffusion inside human umbilical vein endothelial cells. For these cells the exact diffusional pattern of a particular granule depends on the physiological state of the cell and on the localization of the granule within the cytoplasm. Granules located close to the actin rich periphery of the cell move less than those located towards to the center of the cell or within the nucleus. Also, granules in cells which are stressed by intense laser illumination or which have attached to a surface for a long period of time move in a more restricted fashion than those within healthy cells. For granules diffusing in healthy cells, in regions away from the cell periphery, occurrences of weak ergodicity breaking are observed, similar to the recent observations inside living fission yeast cells [1].
We study a disordered nonlinear Schrodinger equation with an additional relaxation process having a finite response time tau. Without the relaxation term, tau = 0, this model has been widely studied in the past and numerical simulations showed subdiffusive spreading of initially localized excitations. However, recently Caetano et al. [Eur. Phys. J. B 80, 321 (2011)] found that by introducing a response time tau > 0, spreading is suppressed and any initially localized excitation will remain localized. Here, we explain the lack of subdiffusive spreading for tau > 0 by numerically analyzing the energy evolution. We find that in the presence of a relaxation process the energy drifts towards the band edge, which enforces the population of fewer and fewer localized modes and hence leads to re-localization. The explanation presented here relies on former findings by Mulansky et al. [Phys. Rev. E 80, 056212 (2009)] on the energy dependence of thermalized states.
The electropolymerization of 3,4-(2,2-dibutylpropylenedioxy)thiophene (ProDOT-Bu-2) onto single carbon fiber microelectrode (SCFME) was conducted in acetonitrile (ACN) containing sodium perchlorate (NaClO4) as electrolyte and investigated by cyclic voltammetry (CV). The nanostructured films of poly[3,4-(2,2-dibutyl-propyleneclioxy)thiophene] (PProDOT-Bu-2) which were depositing showed complete reversible redox behavior in monomer-free electrolyte solution.
The capacitive behavior of the films was investigated by electrochemical impedance spectroscopy (EIS) at applied potentials from 0.1 V to 1.3 V. The analysis by equivalent circuit modeling revealed an applied potential around 0.4V to be most suitable for the system PProDOT-Bu-2/SCFME as a double layer supercapacitor component inducing a double layer capacitance C-d, value of 62 mFcm(-2).
The problem of how complex quantum systems eventually come to rest lies at the heart of statistical mechanics. The maximum-entropy principle describes which quantum states can be expected in equilibrium, but not how closed quantum many-body systems dynamically equilibrate. Here, we report the experimental observation of the non-equilibrium dynamics of a density wave of ultracold bosonic atoms in an optical lattice in the regime of strong correlations. Using an optical superlattice, we follow its dynamics in terms of quasi-local densities, currents and coherences-all showing a fast relaxation towards equilibrium values. Numerical calculations based on matrix-product states are in an excellent quantitative agreement with the experimental data. The system fulfills the promise of being a dynamical quantum simulator, in that the controlled dynamics runs for longer times than present classical algorithms can keep track of.
The use of nanoparticles in polymer composite dielectrics has promised great improvements, but useful results have been elusive. Here, the importance of the interfacial interactions between the nanoparticles and the polymer matrix are investigated in TiO2 nanocomposites for dielectric materials using surface functionalisation. The interface is observed to dominate the nanocomposite properties and leads to a threefold increase in permittivity at volume fractions as low as 10%. Surface functionalisation of the filler nanoparticles with silanes allows control of this interface, avoiding significant degradation of the other important material properties, particularly electrical breakdown strength, and resulting in a material that is demonstrated successfully as an active material in a dielectric elastomer actuator application with increased work output compared to the pure polymer. Although further permittivity increases are observed when the interface regions have formed a percolation network, the other material properties deteriorate. The observation of percolation behaviour allows the interface thickness to be estimated.
The solar outer atmosphere is an extremely dynamic environment characterized by the continuous interplay between the plasma and the magnetic field that generates and permeates it. Such interactions play a fundamental role in hugely diverse astrophysical systems, but occur at scales that cannot be studied outside the solar system. Understanding this complex system requires concerted, simultaneous solar observations from the visible to the vacuum ultraviolet (VUV) and soft X-rays, at high spatial resolution (between 0.1'' and 0.3''), at high temporal resolution (on the order of 10 s, i.e., the time scale of chromospheric dynamics), with a wide temperature coverage (0.01 MK to 20 MK, from the chromosphere to the flaring corona), and the capability of measuring magnetic fields through spectropolarimetry at visible and near-infrared wavelengths. Simultaneous spectroscopic measurements sampling the entire temperature range are particularly important. These requirements are fulfilled by the Japanese Solar-C mission (Plan B), composed of a spacecraft in a geosynchronous orbit with a payload providing a significant improvement of imaging and spectropolarimetric capabilities in the UV, visible, and near-infrared with respect to what is available today and foreseen in the near future. The Large European Module for solar Ultraviolet Research (LEMUR), described in this paper, is a large VUV telescope feeding a scientific payload of high-resolution imaging spectrographs and cameras. LEMUR consists of two major components: a VUV solar telescope with a 30 cm diameter mirror and a focal length of 3.6 m, and a focal-plane package composed of VUV spectrometers covering six carefully chosen wavelength ranges between 170 and 1270 . The LEMUR slit covers 280'' on the Sun with 0.14'' per pixel sampling. In addition, LEMUR is capable of measuring mass flows velocities (line shifts) down to 2 km s (-aEuro parts per thousand 1) or better. LEMUR has been proposed to ESA as the European contribution to the Solar C mission.
We address the problem of recognizing alpha-stable Levy distribution with Levy index close to 2 from experimental data. We are interested in the case when the sample size of available data is not large, thus the power law asymptotics of the distribution is not clearly detectable, and the shape of the empirical probability density function is close to a Gaussian. We propose a testing procedure combining a simple visual test based on empirical fourth moment with the Anderson-Darling and Jarque-Bera statistical tests and we check the efficiency of the method on simulated data. Furthermore, we apply our method to the analysis of turbulent plasma density and potential fluctuations measured in the stellarator-type fusion device and demonstrate that the phenomenon of the L-H transition from low confinement, L mode, to a high confinement, H mode, which occurs in this device is accompanied by the transition from Levy to Gaussian fluctuation statistics.
We compare the growth dynamics of the three n-alkanes C36H74, C40H82, and C44H90 on SiO2 using real-time and in situ energy-dispersive x-ray reflectivity. All molecules investigated align in an upright-standing orientation on the substrate and exhibit a transition from layer-by-layer growth to island growth after about 4 monolayers under the conditions employed. Simultaneous fits of the reflected intensity at five distinct points in reciprocal space show that films formed by longer n-alkanes roughen faster during growth. This behavior can be explained by a chain-length dependent height of the Ehrlich-Schwoebel barrier. Further x-ray diffraction measurements after growth indicate that films consisting of longer n-alkanes also incorporate more lying-down molecules in the top region. While the results reveal behavior typical for chain-like molecules, the findings can also be useful for the optimization of organic field effect transistors where smooth interlayers of n-alkanes without coexistence of two or more molecular orientations are required.
Cold gas accretion by high-velocity clouds and their connection to QSO Absorption-line systems
(2012)
We combine H I 21 cm observations of the Milky Way, M31, and the local galaxy population with QSO absorption-line measurements to geometrically model the three-dimensional distribution of infalling neutral-gas clouds ("high-velocity clouds" (HVCs)) in the extended halos of low-redshift galaxies. We demonstrate that the observed distribution of HVCs around the Milky Way and M31 can be modeled by a radial exponential decline of the mean H I volume-filling factor in their halos. Our model suggests a characteristic radial extent of HVCs of R-halo similar to 50 kpc, a total H I mass in HVCs of similar to 10(8) M-circle dot, and a neutral-gas accretion rate of similar to 0.7 M-circle dot yr(-1) for M31/Milky-Way-type galaxies. Using a Holmberg-like luminosity scaling of the halo size of galaxies we estimate R-halo similar to 110 kpc for the most massive galaxies. The total absorption cross-section of HVCs at z approximate to 0 most likely is dominated by galaxies with total H I masses between 10(8.5) and 10(10) M-circle dot. Our model indicates that the H I disks of galaxies and their surrounding HVC population can account for 30%-100% of intervening QSO absorption-line systems with log N(H I) >= 17.5 at z approximate to 0. We estimate that the neutral-gas accretion rate density of galaxies at low redshift from infalling HVCs is dM(H) (I)/dt/dV approximate to 0.022 M-circle dot yr(-1) Mpc(-3), which is close to the measured star formation rate density in the local universe. HVCs thus may play an important role in the ongoing formation and evolution of galaxies.
A combination of experiment and theory shows that dielectric elastomers exhibit complex interplay of nonlinear processes. Membranes of a dielectric elastomer are prepared in various states of prestretches by using rigid clamps and mechanical forces. Upon actuation by voltage, some membranes form wrinkles followed by snap-through instability, others form wrinkles without the snap-through instability, and still others fail by local instability without forming wrinkles. Membranes surviving these nonlinear processes are found to attain a constant dielectric strength, independent of the state of prestretches. Giant voltage-induced stretch of 3.6 is attained.
We study the anomalous diffusion of a particle in an external force field whose motion is governed by nonrenewal continuous time random walks with correlated waiting times. In this model the current waiting time T-i is equal to the previous waiting time Ti-1 plus a small increment. Based on the associated coupled Langevin equations the force field is systematically introduced. We show that in a confining potential the relaxation dynamics follows power-law or stretched exponential pattern, depending on the model parameters. The process obeys a generalized Einstein-Stokes-Smoluchowski relation and observes the second Einstein relation. The stationary solution is of Boltzmann-Gibbs form. The case of an harmonic potential is discussed in some detail. We also show that the process exhibits aging and ergodicity breaking.
Chemotaxis, the directed motion of a cell toward a chemical source, plays a key role in many essential biological processes. Here, we derive a statistical model that quantitatively describes the chemotactic motion of eukaryotic cells in a chemical gradient. Our model is based on observations of the chemotactic motion of the social ameba Dictyostelium discoideum, a model organism for eukaryotic chemotaxis. A large number of cell trajectories in stationary, linear chemoattractant gradients is measured, using microfluidic tools in combination with automated cell tracking. We describe the directional motion as the interplay between deterministic and stochastic contributions based on a Langevin equation. The functional form of this equation is directly extracted from experimental data by angle-resolved conditional averages. It contains quadratic deterministic damping and multiplicative noise. In the presence of an external gradient, the deterministic part shows a clear angular dependence that takes the form of a force pointing in gradient direction. With increasing gradient steepness, this force passes through a maximum that coincides with maxima in both speed and directionality of the cells. The stochastic part, on the other hand, does not depend on the orientation of the directional cue and remains independent of the gradient magnitude. Numerical simulations of our probabilistic model yield quantitative agreement with the experimental distribution functions. Thus our model captures well the dynamics of chemotactic cells and can serve to quantify differences and similarities of different chemotactic eukaryotes. Finally, on the basis of our model, we can characterize the heterogeneity within a population of chemotactic cells.
Generalized facilitated diffusion model for DNA-binding proteins with search and recognition states
(2012)
Transcription factors (TFs) such as the lac repressor find their target sequence on DNA at remarkably high rates. In the established Berg-von Hippel model for this search process, the TF alternates between three-dimensional diffusion in the bulk solution and one-dimensional sliding along the DNA chain. To overcome the so-called speed-stability paradox, in similar models the TF was considered as being present in two conformations (search state and recognition state) between which it switches stochastically. Combining both the facilitated diffusion model and alternating states, we obtain a generalized model. We explicitly treat bulk excursions for rodlike chains arranged in parallel and consider a simplified model for coiled DNA. Compared to previously considered facilitated diffusion models, corresponding to limiting cases of our generalized model, we surprisingly find a reduced target search rate. Moreover, at optimal conditions there is no longer an equipartition between the time spent by the protein on and off the DNA chain.
Label-free electrical detection of consecutive deoxyribonucleic acid (DNA) hybridization/denaturation by means of an array of individually addressable field-effect-based nanoplate silicon-on-insulator (SOI) capacitors modified with gold nanoparticles (Au-NP) is investigated. The proposed device detects charge changes on Au-NP/DNA hybrids induced by the hybridization or denaturation event. DNA hybridization was performed in a high ionic-strength solution to provide a high hybridization efficiency. On the other hand, to reduce the screening of the DNA charge by counter ions and to achieve a high sensitivity, the sensor signal induced by the hybridization and denaturation events was measured in a low ionic-strength solution. High sensor signals of about 120, 90, and 80 mV were registered after the DNA hybridization, denaturation, and re-hybridization events, respectively. Fluorescence microscopy has been applied as reference method to verify the DNA immobilization, hybridization, and denaturation processes. An electrostatic charge-plane model for potential changes at the gate surface of a nanoplate field-effect sensor induced by the DNA hybridization has been developed taking into account both the Debye length and the distance of the DNA charge from the gate surface.
The discovery of volcanic activity on Enceladus stands out amongst the long list of findings by the Cassini mission to Saturn. In particular the compositional analysis of Enceladus ice particles by Cassini's Cosmic Dust Analyser (CDA) (Srama et al., 2004) has proven to be a powerful technique for obtaining information about processes below the moon's ice crust. Small amounts of sodium salts embedded in the particles' ice matrices provide direct evidence for a subsurface liquid water reservoir, which is, or has been, in contact with the moon's rocky core (Postberg et al., 2009, 2011b).
Jupiter's Galilean satellites Ganymede, Europa, and Callisto are also believed to have subsurface oceans and are therefore prime targets for future NASA and ESA outer Solar System missions. The Galilean moons are engulfed in tenuous dust clouds consisting of tiny pieces of the moons' surfaces (Kruger et al., 1999), released by hypervelocity impacts of micrometeoroids, which steadily bombard the surfaces of the moons. In situ chemical analysis of these grains by a high resolution dust spectrometer will provide spatially resolved mapping of the surface composition of Europa. Ganymede, and Callisto, meeting key scientific objectives of the planned missions. However, novel high-resolution reflectron-type dust mass spectrometers (Sternovsky et al., 2007; Srama et al., 2007) developed for dust astronomy missions (Gran et al., 2009) are probably not robust enough to be operated in the energetic radiation environment of the inner Jovian system. In contrast, CDA's linear spectrometer is much less affected by harsh radiation conditions because its ion detector is not directly facing out into space. The instrument has been continuously operated on Cassini for 11 years. In this paper we investigate the possibility of operating a CDA-like instrument as a high resolution impact mass spectrometer. We show that such an instrument is capable of reliably identifying traces of organic and inorganic materials in the ice matrix of ejecta expected to be generated from the surfaces of the Galilean moons. These measurements are complementary, and in some cases superior, compared to other traditional techniques such as infrared remote sensing or in situ ion or neutral mass spectrometers.
Context. The variation of the dimensionless fundamental physical constant mu = m(p)/m(e) - the proton to electron mass ratio - can be constrained via observation of Lyman and Werner lines of molecular hydrogen in the spectra of damped Lyman alpha systems (DLAs) in the line of sight to distant QSOs.
Aims. Our intention is to maximize the possible precision of quasar absorption spectroscopy with regard to the investigation of the variation of the proton-to-electron mass-ratio mu. The demand for precision requires an understanding of the errors involved and effective techniques to handle present systematic errors.
Methods. An analysis based on UVES high resolution data sets of QSO 0347-383 and its DLA is put forward and new approaches to some of the steps involved in the data analysis are introduced. We apply corrections for the observed offsets between discrete spectra and for the first time we find indications for inter-order distortions.
Results. Drawing on VLT-UVES observations of QSO 0347-383 in 2009 our analysis yields Delta mu/mu = (4.3 +/- 7.2) x 10(-6) at z(abs) = 3.025.
Conclusions. Current analyzes tend to underestimate the impact of systematic errors. Based on the scatter of the measured redshifts and the corresponding low significance of the redshift-sensitivity correlation we estimate the limit of accuracy of line position measurements to similar to 220 m s (1), consisting of roughly 150 m s (1) due to the uncertainty of the absorption line fit and about 150 m s (1) allocated to systematics related to instrumentation and calibration.
We explore the properties of adsorption of flexible polyelectrolyte chains in confined spaces between the oppositely charged surfaces in three basic geometries. A method of approximate uniformly valid solutions for the Green function equation for the eigenfunctions of polymer density distributions is developed to rationalize the critical adsorption conditions. The same approach was implemented in our recent study for the inverse problem of polyelectrolyte adsorption onto a planar surface, and on the outer surface of rod-like and spherical obstacles. For the three adsorption geometries investigated, the theory yields simple scaling relations for the minimal surface charge density that triggers the chain adsorption, as a function of the Debye screening length and surface curvature. The encapsulation of polyelectrolytes is governed by interplay of the electrostatic attraction energy toward the adsorbing surface and entropic repulsion of the chain squeezed into a thin slit or small cavities. Under the conditions of surface-mediated confinement, substantially larger polymer linear charge densities are required to adsorb a polyelectrolyte inside a charged spherical cavity, relative to a cylindrical pore and to a planar slit (at the same interfacial surface charge density). Possible biological implications are discussed briefly in the end.
One of the main milestones in the study of opto- and electromechanical systems is to certify entanglement between a mechanical resonator and an optical or microwave mode of a cavity field. In this work, we show how a suitable time-periodic modulation can help to achieve large degrees of entanglement, building upon the framework introduced in Mari and Eisert (2009 Phys. Rev. Lett. 103 213603). It is demonstrated that with suitable driving, the maximum degree of entanglement can be significantly enhanced, in a way exhibiting a nontrivial dependence on the specifics of the modulation. Such time-dependent driving might help to experimentally achieve entangled mechanical systems also in situations when quantum correlations are otherwise suppressed by thermal noise.
We analyze theoretically the influence of low-dielectric boundaries on the adsorption of flexible polyelectrolytes onto planar and spherical oppositely charged surfaces in electrolyte solutions. We rationalize to what extent polymer chains are depleted from adsorbing interfaces by repulsive image forces. We employ the WKB (Wentzel-Kramers-Brillouin) quantum mechanical method for the Green function of the Edwards equation to determine the adsorption equilibrium. Scaling relations are determined for the critical adsorption strength required to initiate polymer adsorption onto these low-dielectric supports. Image-force repulsion shifts the equilibrium toward the desorbed state, demanding larger surface charge densities and polyelectrolyte linear charge densities for the adsorption to take place. The effect is particularly pronounced for a planar interface in a low-salt regime, where a dramatic change in the scaling behavior for the adsorption-desorption transition is predicted. For the adsorbed state, polymers with higher charge densities are displaced further from the interface by image-charge repulsions. We discuss relevant experimental evidence and argue about possible biological applications of the results.
In this paper, we analytically study a star motif of Stuart-Landau oscillators, derive the bifurcation diagram and discuss the different forms of synchronization arising in such a system. Despite the parameter mismatch between the central node and the peripheral ones, an analytical approach independent of the number of units in the system has been proposed. The approach allows to calculate the separatrices between the regions with distinct dynamical behavior and to determine the nature of the different transitions to synchronization appearing in the system. The theoretical analysis is supported by numerical results.
Particles in Saturn's main rings range in size from dust to kilometer-sized objects. Their size distribution is thought to be a result of competing accretion and fragmentation processes. While growth is naturally limited in tidal environments, frequent collisions among these objects may contribute to both accretion and fragmentation. As ring particles are primarily made of water ice attractive surface forces like adhesion could significantly influence these processes, finally determining the resulting size distribution. Here, we derive analytic expressions for the specific self-energy Q and related specific break-up energy Q(star) of aggregates. These expressions can be used for any aggregate type composed of monomeric constituents. We compare these expressions to numerical experiments where we create aggregates of various types including: regular packings like the face-centered cubic (fcc), Ballistic Particle Cluster Aggregates (BPCA), and modified BPCAs including e.g. different constituent size distributions. We show that accounting for attractive surface forces such as adhesion a simple approach is able to: (a) generally account for the size dependence of the specific break-up energy for fragmentation to occur reported in the literature, namely the division into "strength" and "gravity" regimes and (b) estimate the maximum aggregate size in a collisional ensemble to be on the order of a few tens of meters, consistent with the maximum particle size observed in Saturn's rings of about 10 m.
A membrane of a dielectric elastomer coated with compliant electrodes may form wrinkles as the applied voltage is ramped up. We present a combination of experiment and theory to investigate the transition to wrinkles using a clamped membrane subject to a constant force and a voltage ramp. Two types of transitions are identified. In type-I transition, the voltage-stretch curve is N-shaped, and flat and wrinkled regions coexist in separate areas of the membrane. The type-I transition progresses by nucleation of small wrinkled regions, followed by the growth of the wrinkled regions at the expense of the flat regions, until the entire membrane is wrinkled. By contrast, in type-II transition, the voltage-stretch curve is monotonic, and the entire flat membrane becomes wrinkled with no nucleation barrier. The two types of transitions are analogous to the first and the second order phase transitions. While the type-I transition is accompanied by a jump in the vertical displacement, type-II transition is accompanied by a continuous change in the vertical displacement. Such transitions may enable applications in muscle-like actuation and energy harvesting, where large deformation and large energy of conversion are desired.
Dielectric elastomer actuators (DEAs) draw their function from their dielectric and mechanical properties. The paper describes the fabrication and various properties of molecularly grafted silicone elastomer films. This was achieved by addition of high-dipole molecular co-substituents to off-the-shelf silicone elastomer kits, Elastosil RT 625 and Sylgard 184 by Wacker and Dow Corning, respectively. Strong push-pull dipoles were chemically grafted to both polymer networks during a one step film formation process. All manufactured films were characterized using (13) C-NMR and FT-IR spectroscopy, confirming a successful attachment of the dipoles to the silicone network. Differential scanning calorimetry (DSC) results showed that grafted dipoles were distributed homogeneously throughout the material avoiding the formation of nano-scale aggregates. The permittivity increased with the amount of dipole at all frequencies, while the Young's modulus and electrical breakdown strength were reduced. Actuation strain measurements in the pure shear configuration independently confirmed the increase in electromechanical sensitivity. The ability to enhance electromechanical properties of off-the-shelf materials could strongly expand the range of actuator properties available to researchers and end-users.
It is well known that the spacetime diagrams of some cellular automata have a self-similar fractal structure: for instance Wolfram's rule 90 generates a Sierpinski triangle. Explaining the self-similarity of the spacetime diagrams of cellular automata is a well-explored topic, but virtually all of the results revolve around a special class of automata, whose typical features include irreversibility, an alphabet with a ring structure, a global evolution that is a ring homomorphism, and a property known as (weakly) p-Fermat. The class of automata that we study in this article has none of these properties. Their cell structure is weaker, as it does not come with a multiplication, and they are far from being p-Fermat, even weakly. However, they do produce self-similar spacetime diagrams, and we explain why and how.
In both eukaryotic and prokaryotic DNA sequences of 30-100 base-pairs rich in AT base-pairs have been identified at which the double helix preferentially unwinds. Such DNA unwinding elements are commonly associated with origins for DNA replication and transcription, and with chromosomal matrix attachment regions. Here we present a quantitative study of local DNA unwinding based on extensive single DNA plasmid imaging. We demonstrate that long-lived single-stranded denaturation bubbles exist in negatively supercoiled DNA, at the expense of partial twist release. Remarkably, we observe a linear relation between the degree of supercoiling and the bubble size, in excellent agreement with statistical modelling. Furthermore, we obtain the full distribution of bubble sizes and the opening probabilities at varying salt and temperature conditions. The results presented herein underline the important role of denaturation bubbles in negatively supercoiled DNA for biological processes such as transcription and replication initiation in vivo.
We present a model for cosmological inflation which has a natural "turn on'' and a natural "turn off'' mechanism. In our model inflation is driven by the Hawking-like radiation that occurs in Friedmann-Robertson-Walker (FRW) space-time. This Hawking-like radiation results in an effective negative pressure "fluid'' which leads to a rapid period of expansion in the very early Universe. As the Universe expands the FRW Hawking temperature decreases and the inflationary expansion turns off and makes a natural transition to the power-law expansion of a radiation dominated universe. The turn on mechanism is more speculative, but is based on the common hypothesis that in a quantum theory of gravity at very high temperatures/high densities Hawking radiation will stop. Applying this speculation to the very early Universe implies that the Hawking-like radiation of the FRW space-time will be turned off and therefore the inflation driven by this radiation will turn off.
Combining extensive molecular dynamics simulations of lipid bilayer systems of varying chemical compositions with single-trajectory analyses, we systematically elucidate the stochastic nature of the lipid motion. We observe subdiffusion over more than 4 orders of magnitude in time, clearly stretching into the submicrosecond domain. The lipid motion depends on the lipid chemistry, the lipid phase, and especially the presence of cholesterol. We demonstrate that fractional Langevin equation motion universally describes the lipid motion in all phases, including the gel phase, and in the presence of cholesterol. The results underline the relevance of anomalous diffusion in lipid bilayers and the strong effects of the membrane composition.
Long-range corrected hybrid functionals that employ a nonempirically tuned range-separation parameter have been demonstrated to yield accurate ionization potentials and fundamental gaps for a wide range of finite systems. Here, we address the question of whether this high level of accuracy is limited to the highest occupied/lowest unoccupied energy levels to which the range-separation parameter is tuned or whether it is retained for the entire valence spectrum. We examine several pi-conjugated molecules and find that orbitals of a different character and symmetry require significantly different range-separation parameters and fractions of exact exchange. This imbalanced treatment of orbitals of a different nature biases the resulting eigenvalue spectra. Thus, the existing schemes for the tuning of range-separated hybrid functionals, while providing for good agreement between the highest occupied energy level and the first ionization potential, do not achieve accuracy comparable to reliable G(0)W(0) computations for the entire quasiparticle spectrum.
We studied transitions between spatiotemporal patterns that can be induced in a spatially extended nonlinear chemical system by a unidirectional flow in combination with constant inflow concentrations. Three different scenarios were investigated. (i) Under conditions where the system exhibited two stable fixed points, the propagation direction of trigger fronts could be reversed, so that domains of the less stable fixed point invaded the system. (ii) For bistability between a stable fixed point and a limit cycle we observed that above a critical flow velocity, the unstable focus at the center of the limit cycle could be stabilized. Increasing the flow speed further, a regime of damped flow-distributed oscillations was found and, depending on the boundary values at the inflow, finally the stable fixed point dominated. Similarly, also in the case of spatiotemporal chaos (iii), the unstable steady state could be stabilized and was replaced by the stable fixed point with increasing flow velocity. We finally outline a linear stability analysis that can explain part of our findings.
We study transient work fluctuation relations (FRs) for Gaussian stochastic systems generating anomalous diffusion. For this purpose we use a Langevin approach by employing two different types of additive noise: (i) internal noise where the fluctuation dissipation relation of the second kind (FDR II) holds, and (ii) external noise without FDR II. For internal noise we demonstrate that the existence of FDR II implies the existence of the fluctuation dissipation relation of the first kind (FDR I), which in turn leads to conventional (normal) forms of transient work FRs. For systems driven by external noise we obtain violations of normal FRs, which we call anomalous FRs. We derive them in the long-time limit and demonstrate the existence of logarithmic factors in FRs for intermediate times. We also outline possible experimental verifications.
In this work we construct a unified model of dark energy and dark matter. This is done with the following three elements: a gravitating scalar field, phi with a non-conventional kinetic term, as in the string theory tachyon; an arbitrary potential, V (phi); two measures - a metric measure (root-g) and a non-metric measure (Phi). The model has two interesting features: (i) For potentials which are unstable and would give rise to tachyonic scalar field, this model can stabilize the scalar field. (ii) The form of the dark energy and dark matter that results from this model is fairly insensitive to the exact form of the scalar field potential.
The present work was carried out to compare the formation of single icosahedral phase during conventional heating and microwave processing. Al67Cu23Fe10 alloy powder was synthesized from high purity (99.9%) powder elements by mechanical alloying. Differential scanning calorimetry combined with in-situ synchrotron energy dispersive X-ray diffraction was used to identify the main solid state reactions and the phase evolution of the powders. Inductive microwave processing in the magnetic field anti-node was performed to obtain the quasicrystalline phase in only a few seconds. Due to the rapid cooling of the sample it was possible to stabilize the icosahedral phase against its competing quasicrystalline approximants. Laboratory X-ray diffraction analysis was used to characterise the atomic structure of the specimen and scanning electron microscopy was used to characterise the microstructure after the microwave processing.
The role of ergodicity in anomalous stochastic processes - analysis of single-particle trajectories
(2012)
Single-particle experiments produce time series x(t) of individual particle trajectories, frequently revealing anomalous diffusion behaviour. Typically, individual x(t) are evaluated in terms of time-averaged quantities instead of ensemble averages. Here we discuss the behaviour of the time-averaged mean squared displacement of different stochastic processes giving rise to anomalous diffusion. In particular, we pay attention to the ergodic properties of these processes, i.e. the (non)equivalence of time and ensemble averages.
We study the dynamics of Dirac-Born-Infeld (DBI) dark energy interacting with dark matter. The DBI dark energy model considered here has a scalar field with a nonstandard kinetic energy term, and has potential and brane tension that are power-law functions. The new feature considered here is an interaction between the DBI dark energy and dark matter through a phenomenological interaction between the DBI scalar field and the dark matter fluid. We analyze two different types of interactions between the DBI scalar field and the dark matter fluid. In particular we study the phase-space diagrams of and look for critical points of the phase space that are both stable and lead to accelerated, late-time expansion. In general we find that the interaction between the two dark components does not appear to give rise to late-time accelerated expansion. However, the interaction can make the critical points in the phase space of the system stable. Whether such stabilization occurs or not depends on the form of the interaction between the two dark components.
The class of 2,5 disubstituted-1,3,4-oxadiazoles containing a biphenyl unit on one side is intensively used as electron transport materials to enhance the performance of organic light emitting diodes (OLEDs). In contrast to the ongoing research on these materials insights in their structure-property relationships are still incomplete. To overcome the structural tentativeness and ambiguities the crystal structures of 2-(4-biphenylyl)-5-(4-tert-butylphenyl)-1,3,4-oxadiazole, that of the related compound 2-(4-biphenylyl)-5-phenyl-1,3,4-oxadiazole and of 2-(4-biphenylyl)-5-(2,6-dimethylphenyl)-1,3,4-oxadiazole are determined. A comparison with the results of GAUSSIAN03 calculations and similar compounds in the Cambridge Structural Database leads to a profound characterization.