Physik - Open Access LMU - Teil 01/02

Localized wave fronts are a fundamental feature of biological systems from cell biology to ecology. Here, we study a broad class of bistable models subject to self-activation, degradation, and spatially inhomogeneous activating agents. We determine the conditions under which wave-front localization is possible and analyze the stability thereof with respect to extrinsic perturbations and internal noise. It is found that stability is enhanced upon regulating a positional signal and, surprisingly, also for a low degree of binding cooperativity. We further show a contrasting impact of self-activation to the stability of these two sources of destabilization. DOI: 10.1103/PhysRevLett.110.038102

Actively propelled particles undergoing dissipative collisions are known to develop a state of spatially distributed coherently moving clusters. For densities larger than a characteristic value, clusters grow in time and form a stationary well-ordered state of coherent macroscopic motion. In this work we address two questions. (i) What is the role of the particles’ aspect ratio in the context of cluster formation, and does the particle shape affect the system’s behavior on hydrodynamic scales? (ii) To what extent does particle conservation influence pattern formation? To answer these questions we suggest a simple kinetic model permitting us to depict some of the interaction properties between freely moving particles and particles integrated in clusters. To this end, we introduce two particle species: single and cluster particles. Specifically, we account for coalescence of clusters from single particles, assembly of single particles on existing clusters, collisions between clusters and cluster disassembly. Coarse graining our kinetic model, (i) we demonstrate that particle shape (i.e. aspect ratio) shifts the scale of the transition density, but does not impact the instabilities at the ordering threshold and (ii) we show that the validity of particle conservation determines the existence of a longitudinal instability, which tends to amplify density heterogeneities locally, and in turn triggers a wave pattern with wave vectors parallel to the axis of macroscopic order. If the system is in contact with a particle reservoir, this instability vanishes due to a compensation of density heterogeneities.

Eine naturphilosophische Leitwährung für die Beschreibung der Wirlichkeit ist bereits bei Aristoteles die Form. Sie informiert die Materie und vermittelt dadurch das Sein. Der Informationsbegriff jedoch ist multivalent: man kann zwischen potentieller Information (QuBits), basaler einfacher Information (Bits) und komplexer Information (Systemordner-Information) unterscheiden. Die komplexe Information wird im Bit kodiert, indem es das QuBit disponiert. Die Kodierung erfolgt holografisch und somit analog. Letztlich inkarnieren sich Systeme in der physikalischen Wirklichkeit, indem sie sie komplex informieren (ordnen, ermöglichen, steuern, formieren). Das Universum würde dann der Materialisierung und Dekodierung von autopoetischen Systemen dienen.

Tue, 1 Jan 2013 12:00:00 +0100 http://scitation.aip.org/content/aip/journal/apl/102/15/10.1063/1.4802746 https://epub.ub.uni-muenchen.de/17464/1/weig_17464.pdf Weig, Eva M.; Favero, Ivan; Reichel, Jakob; Hunger, D.; Ost, Lukas; Stapfner, Sebastian ddc:530, Physik

Sat, 29 Dec 2012 12:00:00 +0100 http://scitation.aip.org/content/aip/journal/apl/100/14/10.1063/1.3701588 https://epub.ub.uni-muenchen.de/17393/1/Few_electron_17393.pdf Ludwig, Stefan; Bougeard, D.; Abstreiter, G.; Haller, E. E.; Ager, Joel W.; Sailer, J.; Kierig, J.; Wild, A. ddc:530,

We demonstrate how organic solar cell efficiency can be increased by introducing a pure polymer interlayer between the PEDOT:PSS layer and the polymer: fullerene blend. We observe an increase in device efficiency with three different material systems over a number of devices. Using both electrical characterization and numerical modeling we show that the increase in efficiency is caused by optical absorption in the pure polymer layer and hence efficient charge separation at the polymer bulkheterojunction interface.

While the existence of polar ordered states in active systems is well established, the dynamics of the self-assembly processes are still elusive. We study a lattice gas model of self-propelled elongated particles interacting through excluded volume and alignment interactions, which shows a phase transition from an isotropic to a polar ordered state. By analyzing the ordering process we find that the transition is driven by the formation of a critical nucleation cluster and a subsequent coarsening process. Moreover, the time to establish a polar ordered state shows a power-law divergence.

Length regulation of microtubules (MTs) is essential for many cellular processes. Molecular motors like kinesin-8, which move along MTs and also act as depolymerases, are known as key players in MT dynamics. However, the regulatory mechanisms of length control remain elusive. Here, we investigate a stochastic model accounting for the interplay between polymerization kinetics and motor-induced depolymerization. We determine the dependence of MT length and variance on rate constants and motor concentration. Moreover, our analyses reveal how collective phenomena lead to a well-defined MT length.

Thu, 24 May 2012 12:00:00 +0100 http://scitation.aip.org/content/aip/journal/jcp/136/20/10.1063/1.4720492 https://epub.ub.uni-muenchen.de/17384/1/Riedle_17384.pdf Christensson, Niklas; Kauffmann, Harald F.; Riedle, Eberhard; Schmid, Walther; Bradler, Maximilian; Pugliesi, Igor; Fischer, Michael; Milota, Franz; Hauer, Jürgen; Mančal, Tomáš; Lukeš, Vladimír; Bixner, Oliver

Populations of competing biological species exhibit a fascinating interplay between the nonlinear dynamics of evolutionary selection forces and random fluctuations arising from the stochastic nature of the interactions. The processes leading to extinction of species, whose understanding is a key component in the study of evolution and biodiversity, are influenced by both of these factors. Here, we investigate a class of stochastic population dynamics models based on generalized Lotka-Volterra systems. In the case of neutral stability of the underlying deterministic model, the impact of intrinsic noise on the survival of species is dramatic: It destroys coexistence of interacting species on a time scale proportional to the population size. We introduce a new method based on stochastic averaging which allows one to understand this extinction process quantitatively by reduction to a lower-dimensional effective dynamics. This is performed analytically for two highly symmetrical models and can be generalized numerically to more complex situations. The extinction probability distributions and other quantities of interest we obtain show excellent agreement with simulations.

Tue, 27 Mar 2012 12:00:00 +0100 http://scitation.aip.org/content/aip/journal/jcp/136/12/10.1063/1.3696880 https://epub.ub.uni-muenchen.de/17385/1/Tavan_17385.pdf Tavan, Paul; Schmidt, Maximilian ddc:530, Physik

Fri, 9 Mar 2012 12:00:00 +0100 http://scitation.aip.org/content/aip/journal/jap/111/7/10.1063/1.3678434 https://epub.ub.uni-muenchen.de/16211/1/Winklhofer_16211.pdf Zimanyi, Gergely; Yano, Masao; Oezelt, Harald; Winklhofer, Michael; Shoji, Tetsuya; Schrefl, Thomas ddc:550, ddc:530, Physik

Diffusion-limited reactions are studied in detail on the classical coalescing process. We demonstrate how, with the aid of a recent renormalization group approach, fluctuations can be integrated systematically. We thereby obtain an exact relation between the microscopic physics (lattice structure and particle shape and size) and the macroscopic decay rate in the law of mass action. Moreover, we find a strong violation of the law of mass action. The corresponding term in the kinetic equations originates in longwavelength fluctuations and is a universal function of the macroscopic decay rate.

Microbes providing public goods are widespread in nature despite running the risk of being exploited by free-riders. However, the precise ecological factors supporting cooperation are still puzzling. Following recent experiments, we consider the role of population growth and the repetitive fragmentation of populations into new colonies mimicking simple microbial life-cycles. Individual-based modeling reveals that demographic fluctuations, which lead to a large variance in the composition of colonies, promote cooperation. Biased by population dynamics these fluctuations result in two qualitatively distinct regimes of robust cooperation under repetitive fragmentation into groups. First, if the level of cooperation exceeds a threshold, cooperators will take over the whole population. Second, cooperators can also emerge from a single mutant leading to a robust coexistence between cooperators and free-riders. We find frequency and size of population bottlenecks, and growth dynamics to be the major ecological factors determining the regimes and thereby the evolutionary pathway towards cooperation.

Die Aufgaben und Übungen beziehen sich auf das Buch: , das im Hochschulnetz der LMU abrufbar ist unter der URL: http://dx.doi.org/10.1007/978-3-642-05098-5

Min-protein oscillations in Escherichia coli are characterized by the remarkable robustness with which spatial patterns dynamically adapt to variations of cell geometry. Moreover, adaption, and therefore proper cell division, is independent of temperature. These observations raise fundamental questions about the mechanisms establishing robust Min oscillations, and about the role of spatial cues, as they are at odds with present models. Here, we introduce a robust model based on experimental data, consistently explaining the mechanisms underlying pole-to-pole, striped, and circular patterns, as well as the observed temperature dependence of the oscillation period. Contrary to prior conjectures, the model predicts that MinD and cardiolipin domains are not colocalized. The transient sequestration of MinE and highly canalized transfer of MinD between polar zones are the key mechanisms underlying oscillations. MinD channeling enhances midcell localization and facilitates stripe formation, revealing the potential optimization process from which robust Min-oscillations originally arose.

Sun, 1 Jan 2012 12:00:00 +0100 http://scitation.aip.org/content/aip/journal/pop/19/2/10.1063/1.3684658 https://epub.ub.uni-muenchen.de/17453/1/toshiki_17453.pdf Yu, M. Y.; Tajima, Toshiki; Yan, X. Q.; Wang, H. Y.; Zheng, F. L.

Sun, 1 Jan 2012 12:00:00 +0100 http://scitation.aip.org/content/aip/journal/apl/101/10/10.1063/1.4751351 https://epub.ub.uni-muenchen.de/17465/1/weig_17465.pdf Weig, Eva M.; Kotthaus, Jörg P.; Seitner, Maximilian J.; Faust, Thomas; Rieger, Johannes ddc:530, Physik

Sun, 1 Jan 2012 12:00:00 +0100 http://scitation.aip.org/content/aip/journal/apl/101/21/10.1063/1.4767359 https://epub.ub.uni-muenchen.de/17470/1/weig_17470.pdf Weig, Eva M.; Koenig, D. R. ddc:530, Physi

Solution-based self-assembly of quasi-one-dimensional semiconductor nanostructures (nanowires) from quasi-zero-dimensional (quantum dots) colloidal nanocrystal building blocks has proven itself as a powerful and flexible preparation technique. Polycrystalline CdTe nanowires self-assembled from light-emitting thiol-capped CdTe nanocrystals are the focus of this Feature Article. These nanowires represent an interesting model system for quantum dot solids, where electronic coupling between the individual nanocrystals can be optically accessed and controlled. We provide a literature-based summary of the formation mechanism and the morphology-related aspects of self-assembled CdTe nanowires, and highlight several fundamental and application-related optical properties of these nanostructures. These include fundamental aspects of polarization anisotropies in photoluminescence excitation and emission, the electronic coupling between individual semiconductor nanocrystals constituting the nanowires, and more applied, waveguiding properties of CdTe nanowire bundles and anti-Stokes photoluminescence in a prototypical structure of co-axial nanowires. The optical properties of self-assembled CdTe nanowires considered here render them potential candidates for photonic nanoscale devices.

We study the mechanical relaxation behavior of human red blood cells by observing the time evolution of shape change of cells flowing through microchannels with abrupt constrictions. We observe two types of relaxation processes. In the first fast process (tau(1) similar to 200 ms) the initially parachute shaped cells relax into cup-shaped cells (stomatocytes). These cells relax and reorient in a second relaxation process with a response time of tau(1/2) similar to 10 s into the equilibrium discoid shapes. The values for the relaxation times of single red blood cells in the population scatter significantly within the cell population between 0.11 s < tau(1) < 0.52 s and 9 s < tau(1/2) < 49 s, respectively. However, when plotting tau(1/2) against tau(1), we find a linear relationship between the two timescales and are able to relate both to the elastic properties of the spectrin cytoskeleton underlying the red cell's plasma membrane. Adenosine Triphosphate (ATP) enhances dissociation of spectrin filaments resulting in a reduced shear modulus. We modify the cytoskeleton connectivity by depletion and repletion of ATP and study the effect on relaxation. Both the linear relationship of timescales as well as the ATP dependence can be understood by theoretical models.

The light-driven disassembly process of amyloid-like structures formed by azobenzene model peptides is studied by time-resolved mid-IR spectroscopy from nanoseconds to minutes. The investigated peptide consists of two amino acid strands connected by the azobenzene switch. The peptides aggregate to amyloid-like structures when the azobenzene chromophore is in the trans-conformation. Illumination, resulting in a trans-to cis-isomerization of the azobenzene, leads to disaggregation of the aggregated structures. After optical excitation and isomerization of the azobenzene, one finds absorption changes which recover to a large extent on the time scale of few nanoseconds. These early absorption transients are assigned to the relaxation of vibrational excess energy (heat) or to structural rearrangements of isomerized azobenzene and the aggregated surroundings. It is only on the time scale of minutes that spectral signatures appear which are characteristic for the disassembly of the aggregated structure.

Studies have suggested that there is a strong correlation between the masses of nuclear star clusters (NSCs) and their host galaxies, a correlation which is said to be an extension of the well-known correlations between supermassive black holes (SMBHs) and their host galaxies. But careful analysis of disk galaxies-including 2D bulge/disk/bar decompositions-shows that while SMBHs correlate with the stellar mass of the bulge component of galaxies, the masses of NSCs correlate much better with the total galaxy stellar mass. In addition, the mass ratio M-NSC/M-star,M- tot for NSCs in spirals (at least those with Hubble types Sc and later) is typically an order of magnitude smaller than the mass ratio M-BH/M-star,M- bul of SMBHs. The absence of a universal ``central massive object'' correlation argues against common formation and growth mechanisms for both SMBHs and NSCs. We also discuss evidence for a break in the NSC-host galaxy correlation, galaxies with Hubble types earlier than Sbc appear to host systematically more massive NSCs than do types Sc and later.

Observational constraints on the average radial distribution profile of AGN in distant galaxy clusters can provide important clues on the triggering mechanisms of AGN activity in dense environments and are essential for a completeness evaluation of cluster selection techniques in the X-ray and mm wavebands. The aim of this work is a statistical study with XMM-Newton of the presence and distribution of X-ray AGN in the large-scale structure environments of 22 X-ray luminous galaxy clusters in the redshift range 0.9 < z less than or similar to 1.6 compiled by the XMM-Newton Distant Cluster Project (XDCP). To this end, the X-ray point source lists from detections in the soft band (0.35-2.4 keV) and full band (0.3-7.5 keV) were stacked in cluster-centric coordinates and compared to average background number counts extracted from three independent control fields in the same observations. A significant full-band (soft-band) excess of similar to 78 (67) X-ray point sources is found in the cluster fields within an angular distance of 8' (4 Mpc) at a statistical confidence level of 4.0 sigma (4.2 sigma), corresponding to an average number of detected excess AGN per cluster environment of 3.5 +/- 0.9 (3.0 +/- 0.7). The data point towards a rising radial profile in the cluster region (r < 1Mpc) of predominantly low-luminosity AGN with an average detected excess of about one point source per system, with a tentative preferred occurrence along the main cluster elongation axis. A second statistically significant overdensity of brighter soft-band-detected AGN is found at cluster-centric distances of 4'-6' (2-3 Mpc), corresponding to about three times the average cluster radius R-200 of the systems. If confirmed, these results would support the idea of two different physical triggering mechanisms of X-ray AGN activity in dependence of the radially changing large-scale structure environment of the distant clusters. For high-z cluster studies at lower spatial resolution with the upcoming eROSITA all-sky X-ray survey, the results suggest that cluster-associated X-ray AGN may impose a bias in the spectral analysis of high-z systems, while their detection and flux measurements in the soft band may not be significantly affected.

Thu, 29 Dec 2011 12:00:00 +0100 http://scitation.aip.org/content/aip/journal/rsi/82/12/10.1063/1.3673003 https://epub.ub.uni-muenchen.de/17388/1/Ludwig_17388.pdf Ludwig, Stefan; Wegscheider, W.; Schuh, D.; Taubert, Daniela ddc:530, Physik

We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by population dynamics in general. Especially for fast reproducing microbes which are subject to selection, both types of dynamics are often closely intertwined. We illustrate this by considering different growth scenarios. Depending on whether microbes die or stop to reproduce (dormancy), qualitatively different behaviors emerge. For cooperating bacteria, a permanent increase of costly cooperation can occur. Even if not permanent, cooperation can still increase transiently due to demographic fluctuations. We validate our analysis via stochastic simulations and analytic calculations. In particular, we derive a condition for an increase in the level of cooperation.

The colonization of unoccupied territory by invading species, known as range expansion, is a spatially heterogeneous non-equilibrium growth process. We introduce a two-species Eden growth model to analyze the interplay between uni-directional (irreversible) mutations and selection at the expanding front. While the evolutionary dynamics leads to coalescence of both wild-type and mutant clusters, the non-homogeneous advance of the colony results in a rough front. We show that roughening and domain dynamics are strongly coupled, resulting in qualitatively altered bulk and front properties. For beneficial mutations the front is quickly taken over by mutants and growth proceeds Eden-like. In contrast, if mutants grow slower than wild-types, there is an antagonism between selection pressure against mutants and growth by the merging of mutant domains with an ensuing absorbing state phase transition to an all-mutant front. We find that surface roughening has a marked effect on the critical properties of the absorbing state phase transition. While reference models, which keep the expanding front flat, exhibit directed percolation critical behavior, the exponents of the two-species Eden model strongly deviate from it. In turn, the mutation-selection process induces an increased surface roughness with exponents distinct from that of the classical Eden model.

A punctured Riemann surface is a compact Riemann surface with finitely many points removed. We will discuss an equivalence by [Sim90] between tame harmonic bundles, regular filtered stable Higgs bundles resp. D-modules and regular filtered local systems over these surfaces.

We investigate a driven two-channel system where particles on different lanes mutually obstruct each other's motion, extending an earlier model by Popkov and Peschel Phys. Rev. E 64, 026126 (2001)]. This obstruction may occur in biological contexts due to steric hinderance where motor proteins carry cargos by "walking" on microtubules. Similarly, the model serves as a description for classical spin transport where charged particles with internal states move unidirectionally on a lattice. Three regimes of qualitatively different behavior are identified, depending on the strength of coupling between the lanes. For small and large coupling strengths the model can be mapped to a one-channel problem, whereas a rich phase behavior emerges for intermediate ones. We derive an approximate but quantitatively accurate theoretical description in terms of a one-site cluster approximation, and obtain insight into the phase behavior through the current-density relations combined with an extremal-current principle. Our results are confirmed by stochastic simulations.

Tue, 1 Feb 2011 12:00:00 +0100 https://epub.ub.uni-muenchen.de/16011/1/oa_comment.pdf Frey, Erwin; Reese, Louis; Hinsch, Hauke dd

The longitudinal response of single semiflexible polymers to sudden changes in externally applied forces is known to be controlled by the propagation and relaxation of backbone tension. Under many experimental circumstances, realized, for example, in nanofluidic devices or in polymeric networks or solutions, these polymers are effectively confined in a channel-or tubelike geometry. By means of heuristic scaling laws and rigorous analytical theory, we analyze the tension dynamics of confined semiflexible polymers for various generic experimental setups. It turns out that in contrast to the well-known linear response, the influence of confinement on the nonlinear dynamics can largely be described as that of an effective prestress. We also study the free relaxation of an initially confined chain, finding a surprising superlinear similar to t(9/8) growth law for the change in end-to-end distance at short times.

Species extinction occurs regularly and unavoidably in ecological systems. The time scales for extinction can broadly vary and inform on the ecosystem's stability. We study the spatio-temporal extinction dynamics of a paradigmatic population model where three species exhibit cyclic competition. The cyclic dynamics reflects the non-equilibrium nature of the species interactions. While previous work focusses on the coarsening process as a mechanism that drives the system to extinction, we found that unexpectedly the dynamics to extinction is much richer. We observed three different types of dynamics. In addition to coarsening, in the evolutionary relevant limit of large times, oscillating traveling waves and heteroclinic orbits play a dominant role. The weight of the different processes depends on the degree of mixing and the system size. By analytical arguments and extensive numerical simulations we provide the full characteristics of scenarios leading to extinction in one of the most surprising models of ecology

Sat, 1 Jan 2011 12:00:00 +0100 http://scitation.aip.org/content/aip/journal/jap/109/10/10.1063/1.3577959 https://epub.ub.uni-muenchen.de/16214/1/an_electron_jet.pdf Ludwig, Stefan; Wegscheider, W.; Tranitz, H. P.; Tomaras, Constantin; Schinner, Georg J.; Taubert, Daniela ddc:530, Physik

The electronic structure of ErGa3 and its isostructural compounds with Tm, Yb, and Lu are investigated with a highly accurate band structure scheme in LDA and GGA and warped muffin-tin approximation. In contrast to other investigations, the 4f electrons of the constituent Re are also treated as part of the valence bands. The position of the corresponding 4f bands relative to the Fermi energy E-F strongly depends on the nuclear charge of Re. In Lu, they lie almost by 0.5 Ryd below E-F and are extremely narrow. In Er, both in LDA and GGA, the 4f bands are found to be very close to the Fermi level E-F. Assuming most of the 4f electrons to be part of the core removes the disagreement almost completely but produces a Fermi surface with a topology markedly different from that proposed in previous investigations. The intersections of the Fermi surface with planes are strongly varying within the Brillouin zone, they do not well match with the sparse experimental results. Investigations using the LDA + U scheme as well as investigations of the dielectric response function are sketched.

Sat, 1 Jan 2011 12:00:00 +0100 https://epub.ub.uni-muenchen.de/25746/1/Musselman_SchmidtMende_Nanostructured_Inorganic_Solar_cells.pdf Schmidt-Mende, Lukas; Musselman, Kevin P. ddc:530, Physik

We developed a bioadhesive coating based on a synthetic peptide-conjugate (AK-cycloRGDfC]) which contains multiples of the arginyl-glycyl-aspartic acid (RGD) amino acid sequence. Biotinylated AK-cycloRGDfC] is bound to a supported lipid bilayer via a streptavidin interlayer. Layering, hydration and packing of the coating is quantified by X-ray and neutron reflectometry experiments. AK-cycloRGDfC] binds to the streptavidin interlayer in a stretched-out on edge configuration. The highly packed configuration with only 12% water content maximizes the number of accessible adhesion sites. Enhanced cell spreading of neural stem cells was observed for AK-cycloRGDfC] functionalized bilayers. Due to the large variety of surfaces which can be coated by physisorption of lipid bilayers, this approach is of general interest for the fabrication of biocompatible surfaces.

Self-organized monolayers of highly flexible Frechet dendrons were deposited on graphite surfaces by solution casting. Scanning tunneling microscopy (STM) reveals an unprecedented variety of patterns with up to seven stable hierarchical ordering motifs allowing us to use these molecules as a versatile model system. The essential molecular properties determined by molecular mechanics simulations are condensed to a coarse grained interaction-site model of various chain configurations. In a Monte Carlo approach with random starting configurations, the experimental pattern diversity can be reproduced in all facets of the local and global ordering. Based on an energy analysis of the Monte Carlo and molecular mechanics modeling, the thermodynamically most stable pattern is predicted and shown to coincide with the pattern which dominates the STM images after several hours or upon moderate heating.

Existing theoretical models of evolution focus on the relative fitness advantages of different mutants in a population while the dynamic behavior of the population size is mostly left unconsidered. We present here a generic stochastic model which combines the growth dynamics of the population and its internal evolution. Our model thereby accounts for the fact that both evolutionary and growth dynamics are based on individual reproduction events and hence are highly coupled and stochastic in nature. We exemplify our approach by studying the dilemma of cooperation in growing populations and show that genuinely stochastic events can ease the dilemma by leading to a transient but robust increase in cooperation.

The constraints imposed by nano- and microscale confinement on the conformational degrees of freedom of thermally fluctuating biopolymers are utilized in contemporary nano-devices to specifically elongate and manipulate single chains. A thorough theoretical understanding and quantification of the statistical conformations of confined polymer chains is thus a central concern in polymer physics. We present an analytical calculation of the radial distribution function of harmonically confined semiflexible polymers in the weakly bending limit. Special emphasis has been put on a proper treatment of global modes, i.e. the possibility of the chain to perform global movements within the channel. We show that the effect of these global modes significantly impacts the chain statistics in cases of weak and intermediate confinement. Comparing our analytical model to numerical data from Monte Carlo simulations we find excellent agreement over a broad range of parameters

The positions of nucleosomes in eukaryotic genomes determine which parts of the DNA sequence are readily accessible for regulatory proteins and which are not. Genome-wide maps of nucleosome positions have revealed a salient pattern around transcription start sites, involving a nucleosome-free region (NFR) flanked by a pronounced periodic pattern in the average nucleosome density. While the periodic pattern clearly reflects well-positioned nucleosomes, the positioning mechanism is less clear. A recent experimental study by Mavrich et al. argued that the pattern observed in Saccharomyces cerevisiae is qualitatively consistent with a "barrier nucleosome model," in which the oscillatory pattern is created by the statistical positioning mechanism of Kornberg and Stryer. On the other hand, there is clear evidence for intrinsic sequence preferences of nucleosomes, and it is unclear to what extent these sequence preferences affect the observed pattern. To test the barrier nucleosome model, we quantitatively analyze yeast nucleosome positioning data both up- and downstream from NFRs. Our analysis is based on the Tonks model of statistical physics which quantifies the interplay between the excluded-volume interaction of nucleosomes and their positional entropy. We find that although the typical patterns on the two sides of the NFR are different, they are both quantitatively described by the same physical model with the same parameters, but different boundary conditions. The inferred boundary conditions suggest that the first nucleosome downstream from the NFR (the +1 nucleosome) is typically directly positioned while the first nucleosome upstream is statistically positioned via a nucleosome-repelling DNA region. These boundary conditions, which can be locally encoded into the genome sequence, significantly shape the statistical distribution of nucleosomes over a range of up to approximately 1,000 bp to each side.

Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for the study of extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction for the microorganism. The reconstruction itself represents a knowledge base of the haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, we experimentally determined several parameters relevant to growth, including a characterization of the biomass composition and a quantification of carbon and oxygen consumption. Using the metabolic reconstruction and the experimental data, we formulated a constraints-based model which we used to analyze the behavior of the archaeon when grown on a single carbon source. Results of the analysis include the finding that Natronomonas pharaonis, when grown aerobically on acetate, uses a carbon to oxygen consumption ratio that is theoretically near-optimal with respect to growth and energy production. This supports the hypothesis that, under simple conditions, the microorganism optimizes its metabolism with respect to the two objectives. We also found that the archaeon has a very low carbon efficiency of only about 35%. This inefficiency is probably due to a very low P/O ratio as well as to the other difficulties posed by its extreme environment.

Cyclic (rock-paper-scissors-type) population models serve to mimic complex species interactions. Focusing on a paradigmatic three-species model with mutations in one dimension, we observe an interplay between equilibrium and nonequilibrium processes in the stationary state. We exploit these insights to obtain asymptotically exact descriptions of the emerging reactive steady state in the regimes of high and low mutation rates. The results are compared to stochastic lattice simulations. Our methods and findings are potentially relevant for the spatiotemporal evolution of other nonequilibrium stochastic processes.

Confinement is a versatile and well-established tool to study the properties of polymers either to understand biological processes or to develop new nanobiomaterials. We investigate the conformations of a semiflexible polymer ring in weak spherical confinement imposed by an impenetrable shell. We develop an analytic argument for the dominating polymer trajectory depending on polymer flexibility considering elastic and entropic contributions. Monte Carlo simulations are performed to assess polymer ring conformations in probability densities and by the shape measures asphericity and nature of asphericity. Comparison of the analytic argument with the mean asphericity and the mean nature of asphericity confirm our reasoning to explain polymer ring conformations in the stiff regime, where elastic response prevails.

Bundles of filamentous polymers are primary structural components of a broad range of cytoskeletal structures, and their mechanical properties play key roles in cellular functions ranging from locomotion to mechanotransduction and fertilization. We give a detailed derivation of a wormlike bundle model as a generic description for the statics and dynamics of polymer bundles consisting of semiflexible polymers interconnected by crosslinking agents. The elastic degrees of freedom include bending as well as twist deformations of the filaments and shear deformation of the crosslinks. We show that a competition between the elastic properties of the filaments and those of the crosslinks leads to renormalized effective bend and twist rigidities that become mode-number dependent. The strength and character of this dependence is found to vary with bundle architecture, such as the arrangement of filaments in the cross section and pretwist. We discuss two paradigmatic cases of bundle architecture, a uniform arrangement of filaments as found in F-actin bundles and a shell-like architecture as characteristic for microtubules. Each architecture is found to have its own universal ratio of maximal to minimal bending rigidity, independent of the specific type of crosslink-induced filament coupling; our predictions are in reasonable agreement with available experimental data for microtubules. Moreover, we analyze the predictions of the wormlike bundle model for experimental observables such as the tangent-tangent correlation function and dynamic response and correlation functions. Finally, we analyze the effect of pretwist (helicity) on the mechanical properties of bundles. We predict that microtubules with different number of protofilaments should have distinct variations in their effective bending rigidity.

The dynamic patterning of the plant hormone auxin and its efflux facilitator the PIN protein are the key regulator for the spatial and temporal organization of plant development. In particular auxin induces the polar localization of its own efflux facilitator. Due to this positive feedback auxin flow is directed and patterns of auxin and PIN arise. During the earliest stage of vein initiation in leaves auxin accumulates in a single cell in a rim of epidermal cells from which it ows into the ground meristem tissue of the leaf blade. There the localized auxin supply yields the successive polarization of PIN distribution along a strand of cells. We model the auxin and PIN dynamics within cells with a minimal canalization model. Solving the model analytically we uncover an excitable polarization front that triggers a polar distribution of PIN proteins in cells. As polarization fronts may extend to opposing directions from their initiation site we suggest a possible resolution to the puzzling occurrence of bipolar cells, such we offer an explanation for the development of closed, looped veins. Employing non-linear analysis we identify the role of the contributing microscopic processes during polarization. Furthermore, we deduce quantitative predictions on polarization fronts establishing a route to determine the up to now largely unknown kinetic rates of auxin and PIN dynamics.

The information content of a non-enzymatic self-replicator is limited by Eigen’s error threshold. Presumably, enzymatic replication can maintain higher complexity, but in a competitive environment such a replicator is faced with two problems related to its twofold role as enzyme and substrate: as enzyme, it should replicate itself rather than wastefully copy non-functional substrates, and as substrate it should preferably be replicated by superior enzymes instead of less-efficient mutants. Because specific recognition can enforce these propensities, we thoroughly analyze an idealized quasispecies model for enzymatic replication, with replication rates that are either a decreasing (self-specific) or increasing (cross-specific) function of the Hamming distance between the recognition or “tag” sequences of enzyme and substrate. We find that very weak self-specificity suffices to localize a population about a master sequence and thus to preserve its information, while simultaneous localization about complementary sequences in the cross-specific case is more challenging. A surprising result is that stronger specificity constraints allow longer recognition sequences, because the populations are better localized. Extrapolating from experimental data, we obtain rough quantitative estimates for the maximal length of the recognition or tag sequence that can be used to reliably discriminate appropriate and infeasible enzymes and substrates, respectively

We show that for particles performing Brownian motion in a frozen array of scatterers long-time correlations emerge in the mean-square displacement. Defining the velocity autocorrelation function (VACF) via the second time-derivative of the mean-square displacement, power-law tails govern the long-time dynamics similar to the case of ballistic motion. The physical origin of the persistent memory is due to repeated encounters with the same obstacle which occurs naturally in Brownian dynamics without involving other scattering centers. This observation suggests that in this case the VACF exhibits these anomalies already at first order in the scattering density. Here we provide an analytic solution for the dynamics of a tracer for a dilute planar Lorentz gas and compare our results to computer simulations. Our result support the idea that quenched disorder provides a generic mechanism for persistent correlations irrespective of the microdynamics of the tracer particle

Ecological systems are complex assemblies of large numbers of individuals, interacting competitively under multifaceted environmental conditions. Recent studies using microbial laboratory communities have revealed some of the self-organization principles underneath the complexity of these systems. A major role of the inherent stochasticity of its dynamics and the spatial segregation of different interacting species into distinct patterns has thereby been established. It ensures the viability of microbial colonies by allowing for species diversity, cooperative behavior and other kinds of “social” behavior. A synthesis of evolutionary game theory, nonlinear dynamics, and the theory of stochastic processes provides the mathematical tools and a conceptual framework for a deeper understanding of these ecological systems. We give an introduction into the modern formulation of these theories and illustrate their effectiveness focussing on selected examples of microbial systems. Intrinsic fluctuations, stemming from the discreteness of individuals, are ubiquitous, and can have an important impact on the stability of ecosystems. In the absence of speciation, extinction of species is unavoidable. It may, however, take very long times. We provide a general concept for defining survival and extinction on ecological time-scales. Spatial degrees of freedom come with a certain mobility of individuals. When the latter is sufficiently high, bacterial community structures can be understood through mapping individual-based models, in a continuum approach, onto stochastic partial differential equations. These allow progress using methods of nonlinear dynamics such as bifurcation analysis and invariant manifolds. We conclude with a perspective on the current challenges in quantifying bacterial pattern formation, and how this might have an impact on fundamental research in non-equilibrium physics.

We review recent progress on holographic renormalization in the context of the gauge-gravity correspondence when the bulk geometry is not asymptotically AdS. The prime example is the Klebanov-Strassler background, whose dual gauge theory has logarithmically running couplings at all energy scales. The presented formalism provides the counterterms necessary for obtaining finite two-point functions of the scalar operators in the corresponding dual gauge theories. The presentation is self-contained and reviews all the relevant background material concerning a gauge-invariant description of the fluctuations around holographic renormalization group backgrounds.

The dynamic response of prestressed semiflexible biopolymers is characterized by the propagation and relaxation of tension, which arises due to the near inextensibility of a stiff backbone. It is coupled to the dynamics of contour length stored in thermal undulations but also to the local relaxation of elongational strain. We present a systematic theory of tension dynamics for stiff yet extensible wormlike chains. Our results show that even moderate prestress gives rise to distinct Rouse-like extensibility signatures in the high-frequency viscoelastic response.

Halobacterium salinarum is a bioenergetically flexible, halophilic microorganism that can generate energy by respiration, photosynthesis, and the fermentation of arginine. In a previous study, using a genome-scale metabolic model, we have shown that the archaeon unexpectedly degrades essential amino acids under aerobic conditions, a behavior that can lead to the termination of growth earlier than necessary. Here, we further integratively investigate energy generation, nutrient utilization, and biomass production using an extended methodology that accounts for dynamically changing transport patterns, including those that arise from interactions among the supplied metabolites. Moreover, we widen the scope of our analysis to include phototrophic conditions to explore the interplay between different bioenergetic modes. Surprisingly, we found that cells also degrade essential amino acids even during phototropy, when energy should already be abundant. We also found that under both conditions considerable amounts of nutrients that were taken up were neither incorporated into the biomass nor used as respiratory substrates, implying the considerable production and accumulation of several metabolites in the medium. Some of these are likely the products of forms of overflow metabolism. In addition, our results also show that arginine fermentation, contrary to what is typically assumed, occurs simultaneously with respiration and photosynthesis and can contribute energy in levels that are comparable to the primary bioenergetic modes, if not more. These findings portray a picture that the organism takes an approach toward growth that favors the here and now, even at the cost of longer-term concerns. We believe that the seemingly "greedy" behavior exhibited actually consists of adaptations by the organism to its natural environments, where nutrients are not only irregularly available but may altogether be absent for extended periods that may span several years. Such a setting probably predisposed the cells to grow as much as possible when the conditions become favorable.