Thermodynamics of hot dense H-plasmas: Path integral Monte Carlo simulations and analytical approximations

This work is devoted to the thermodynamics of high-temperature dense hydrogen plasmas in the pressure region between $10^{-1}$ and $10^2$ Mbar. In particular we present for this region results of extensive calculations based on a recently developed path integral Monte Carlo scheme (direct PIMC). This method allows for a correct treatment of the thermodynamic properties of hot dense Coulomb systems. Calculations were performed in a broad region of the nonideality parameter $\Gamma \lesssim 3$ and degeneracy parameter $n_e \Lambda^3 \lesssim 10$. We give a comparison with a few available results from other path integral calculations (restricted PIMC) and with analytical calculations based on Pade approximations for strongly ionized plasmas. Good agreement between the results obtained from the three independent methods is found.Comment: RevTex file, 21 pages, 5 ps-figures include

Reconstruction of a first-order phase transition from computer simulations of individual phases and subphases

We present a new method for investigating first-order phase transitions using Monte Carlo simulations. It relies on the multiple-histogram method and uses solely histograms of individual phases. In addition, we extend the method to include histograms of subphases. The free energy difference between phases, necessary for attributing the correct statistical weights to the histograms, is determined by a detour in control parameter space via auxiliary systems with short relaxation times. We apply this method to a recently introduced model for structure formation in polypeptides for which other methods fail.Comment: 13 pages in preprint mode, REVTeX, 2 Figures available from the authors ([email protected], [email protected]

Statistical Mechanics of Canonical-Dissipative Systems and Applications to Swarm Dynamics

We develop the theory of canonical-dissipative systems, based on the assumption that both the conservative and the dissipative elements of the dynamics are determined by invariants of motion. In this case, known solutions for conservative systems can be used for an extension of the dynamics, which also includes elements such as the take-up/dissipation of energy. This way, a rather complex dynamics can be mapped to an analytically tractable model, while still covering important features of non-equilibrium systems. In our paper, this approach is used to derive a rather general swarm model that considers (a) the energetic conditions of swarming, i.e. for active motion, (b) interactions between the particles based on global couplings. We derive analytical expressions for the non-equilibrium velocity distribution and the mean squared displacement of the swarm. Further, we investigate the influence of different global couplings on the overall behavior of the swarm by means of particle-based computer simulations and compare them with the analytical estimations.Comment: 14 pages incl. 13 figures. v2: misprints in Eq. (40) corrected, ref. updated. For related work see also: http://summa.physik.hu-berlin.de/~frank/active.htm

A Lensed Arc in the Low Redshift Cluster Abell 2124

We report the discovery of an arc-like object 27" from the center of the cD galaxy in the redshift $z=0.066$ cluster A2124. Observations with the Keck II telescope reveal that the object is a background galaxy at $z=0.573$, apparently lensed into an arc of length \sim 8 \farcs5 and total R magnitude $m_R = 20.86\pm0.07$. The width of the arc is resolved; we estimate it to be $\sim$0\farcs6 after correcting for seeing. A lens model of the A2124 core mass distribution consistent with the cluster galaxy velocity dispersion reproduces the observed arc geometry and indicates a magnification factor \gta 9. With this magnification, the strength of the [OII] \lambda 3727 line implies a star-formation rate of SFR \sim 0.4 h^{-2}\msun yr^{-1}$. A2124 thus appears to be the lowest redshift cluster known to exhibit strong lensing of a distant background galaxy.Comment: 6 pages using emulateapj.sty; 4 Postscript figures; Figure 4 uses color. Accepted for publication, but ApJ Letters' new policy of counting data images makes the manuscript too long; will appear in main journal. This final version has minor correction

The WARPS survey: III. The discovery of an X-ray luminous galaxy cluster at z=0.833 and the impact of X-ray substructure on cluster abundance measurements

The WARPS team reviews the properties and history of discovery of ClJ0152.7-1357, an X-ray luminous, rich cluster of galaxies at z=0.833. At L_X = 8 x 10^44 h^(-2) erg/s (0.5-2.0 keV) ClJ0152.7-1357 is the most X-ray luminous cluster known at redshifts z>0.55. The high X-ray luminosity of the system suggests that massive clusters may begin to form at redshifts considerably greater than unity. This scenario is supported by the high degree of optical and X-ray substructure in ClJ0152.7-1357, which is similarly complex as that of other X-ray selected distant clusters and consistent with the picture of cluster formation by mass infall along large-scale filaments. X-ray emission from ClJ0152.7-1357 was detected already in 1980 with the EINSTEIN IPC. However, because the complex morphology of the emission caused its significance to be underestimated, the corresponding source was not included in the EMSS cluster sample and hence not previously identified. Simulations of the EMSS source detection and selection procedure suggest a general bias of the EMSS against X-ray luminous clusters with pronounced substructure. If highly unrelaxed, merging clusters are common at high redshift, they could create a bias in some samples as the morphological complexity of mergers may cause them to fall below the flux limit of surveys that assume a unimodal spatial source geometry. Conversely, the enhanced X-ray luminosity of mergers might cause them to, temporarily, rise above the flux limit. Either effect could lead to erroneous conclusions about the evolution of the comoving cluster space density. A high fraction of morphologically complex clusters at high redshift would also call into question the validity of cosmological studies that assume that the systems under investigation are virialized.Comment: 17 pages, 7 figures; revised to focus on possible detection biases caused by substructure in clusters; accepted for publication in ApJ; uses emulateapj.sty; eps files of figures 1 and 2 can be obtained from ftp://hubble.ifa.hawaii.edu/pub/ebeling/warp

The 89,000-Mr murine cytomegalovirus immediate-early protein activates gene transcription

To study trans-activation of gene expression by murine cytomegalovirus (MCMV) immediate-early (IE) proteins, the IE coding region 1 (ie1), which encodes the 89,000-Mr IE phosphoprotein (pp89), was stably introduced into L cells. A cell line was selected and characterized that efficiently expressed the authentic viral protein. The pp89 that was constitutively expressed in L cells stimulated the expression of transfected recombinant constructs containing the bacterial chloramphenicol acetyltransferase (CAT) gene under the control of viral promoters. The regulatory function of the ie1 product was confirmed by transient expression assays in which MCMV IE genes were cotransfected into L cells together with recombinant constructs of the CAT gene. For CAT activation by the ie1 product, a promoter region was required, but there was no preferential activation of a herpes simplex virus type 1 delayed-early promoter. All plasmid constructs that contained the intact coding sequences for pp89 induced gene expression in trans. The MCMV enhancer region was not essential for the expression of a functional IE gene product, and testing of the cis-regulatory activity of the MCMV enhancer revealed a low activity in L cells. Another region transcribed at IE times of infection, IE coding region 2, was unable to induce CAT expression and also did not augment the functional activity of ie1 after cotransfection

Path integral Monte Carlo calculations of helium and hydrogen-helium plasma thermodynamics and of the deuterium shock Hugoniot

In this work we calculate the thermodynamic properties of hydrogen-helium plasmas with different mass fractions of helium by the direct path integral Monte Carlo method. To avoid unphysical approximations we use the path integral representation of the density matrix. We pay special attention to the region of weak coupling and degeneracy and compare the results of simulation with a model based on the chemical picture. Further with the help of calculated deuterium isochors we compute the shock Hugoniot of deuterium. We analyze our results in comparison with recent experimental and calculated data on the deuterium Hugoniot.Comment: 7 pages, 5 Postscript figures, accepted for publication in J. Phys. A: Math. Ge

Agent-Based Modeling of Intracellular Transport

We develop an agent-based model of the motion and pattern formation of vesicles. These intracellular particles can be found in four different modes of (undirected and directed) motion and can fuse with other vesicles. While the size of vesicles follows a log-normal distribution that changes over time due to fusion processes, their spatial distribution gives rise to distinct patterns. Their occurrence depends on the concentration of proteins which are synthesized based on the transcriptional activities of some genes. Hence, differences in these spatio-temporal vesicle patterns allow indirect conclusions about the (unknown) impact of these genes. By means of agent-based computer simulations we are able to reproduce such patterns on real temporal and spatial scales. Our modeling approach is based on Brownian agents with an internal degree of freedom, $\theta$, that represents the different modes of motion. Conditions inside the cell are modeled by an effective potential that differs for agents dependent on their value $\theta$. Agent's motion in this effective potential is modeled by an overdampted Langevin equation, changes of $\theta$ are modeled as stochastic transitions with values obtained from experiments, and fusion events are modeled as space-dependent stochastic transitions. Our results for the spatio-temporal vesicle patterns can be used for a statistical comparison with experiments. We also derive hypotheses of how the silencing of some genes may affect the intracellular transport, and point to generalizations of the model