Radial Distribution Function for Semiflexible Polymers Confined in Microchannels

An analytic expression is derived for the distribution $G(\vec{R})$ of the end-to-end distance $\vec{R}$ of semiflexible polymers in external potentials to elucidate the effect of confinement on the mechanical and statistical properties of biomolecules. For parabolic confinement the result is exact whereas for realistic potentials a self-consistent ansatz is developed, so that $G(\vec{R})$ is given explicitly even for hard wall confinement. The theoretical result is in excellent quantitative agreement with fluorescence microscopy data for actin filaments confined in rectangularly shaped microchannels. This allows an unambiguous determination of persistence length $L_P$ and the dependence of statistical properties such as Odijk's deflection length $\lambda$ on the channel width $D$. It is shown that neglecting the effect of confinement leads to a significant overestimation of bending rigidities for filaments

Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks

This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA length. The DNA is modeled by the Worm-Like Chain model, and the probability of loop formation is calculated in two ways: exact numerical evaluation of the constrained path integral and the extension of the Shimada and Yamakawa saddle point approximation. For example, we find that the looping free energy of a 100 base pairs DNA decreases from 24 kT to 13 kT when the loop is closed by a protein of r = 10 nm length. It further decreases to 5 kT when the loop has a kink of 120 degrees at half-length.Comment: corrected typos and figures, references updated; 13 pages, 7 figures, accepted for publication in Phys. Rev.

Influence of the vegetation structure on the nest-site selection of birds of prey in the March floodplain forests, Lower Austria

Zwischen Januar und Juli 2008 wurden im March-Auwald zwischen Hohenau und Drösing im niederösterreichischen Bezirk Gänserndorf (19,7 km2) systematisch Greifvogelhorste kartiert, und auf Besetzung und Bruterfolg kontrolliert. Im weitgehend geschlossenen Waldgebiet sind zwei unterschiedliche Forstwirtschaftsformen vorrangig. Der nördliche Teil wird als Hochwald (960 ha) geführt, der südliche Teil als Mittel- und Niederwald (1010 ha). Analysen zur Waldstruktur rund um jeden Horstplatz (Mikrohabitat, r=15 m, 706,5 m2), sowie zum Anteil verschiedener Biotoptypen im Kernbereich der Greifvogelreviere (Makrohabitat, r=250 m, 19,6 ha) geben Aufschluss, welche Faktoren die Verbreitung der Greifvögel in den March-Auen beeinflussen. Um einen repräsentativen Querschnitt des vorhandenen Strukturangebots zu erhalten, wurden die Erhebungen in gleicher Art auf 50 zufällig bestimmten Flächen wiederholt. Die erhobenen Daten zur Habitatwahl wurden in einem geographischen Informationssystem ausgewertet. Insgesamt wurden 167 Horste kartiert, davon waren 57 von Greifvögeln besetzt. Die häufigste Art ist der Mäusebussard (Buteo buteo) mit 34 besetzten Horsten, gefolgt von der Rohrweihe (Circus aeroginosus) mit 5-6 Brutpaaren. Der Rotmilanbestand (Milvus milvus) von 3 Brutpaaren ist von nationaler Bedeutung. Schwarzmilan (Milvus migrans), Wespenbussard (Pernis apivorus) und Habicht (Accipiter gentilis) sind mit je 3 Brutpaaren, Turmfalke (Falco tinnunculus) und Baumfalke (Falco subbuteo) mit je 2 Brutpaaren vertreten. Seit 2002 brütet auch ein Seeadlerpaar (Haliaeetus albicilla) erfolgreich im Untersuchungsgebiet. Zusätzlich brüten Sperber (Accipiter nisus), Sakerfalke (Falco cherrug) und Kaiseradler (Aquila heliaca) in den umliegenden Flächen. Die Greifvogelbestände sind seit den 1990er Jahren weitgehend stabil. Allein beim Mäusebussard ist eine Bestandszunahme zu verzeichnen, die auf natürliche Schwankungen entsprechend der Mäusegradation und auf eine Entdynamisierung der Au zurückzuführen ist. Die vorgefundenen Siedlungsdichten der Greifvögel an der March sind auch in einem mitteleuropäischen Vergleich als hoch einzustufen. Die Habitatanalyse hat gezeigt, dass Greifvögel Stieleichenüberhälter und zusammenhängende, alte Pappelkulturen als Horstbäume bevorzugen. Diese Baumarten finden sich im Mittelwald häufiger als im Hochwald. Auch sind im Mittelwald mehr Großhorste zu finden, die wertvoll für Seeadler und Kaiseradler, sowie den Schwarzstorch sind. Darüber hinaus bevorzugen Greifvögel strukturierte Altholzbestände mit einer ausgeprägten vertikalen Schichtung und einem hohen Totholzanteil. Diese Strukturen deuten auf einen geringen forstlichen Nutzen und dadurch eine geringe menschliche Störung der Nistplätze hin. Die genannten Kriterien erfüllen insbesondere eingerichtete Horstschutzgebiete, die frei von forstlicher Nutzung sind. Die Ausdehnung der Altholzbestände, die Reduzierung von Störungen durch den Menschen sowie die Dynamisierung der Au durch Revitalisierungsprojekte sind wichtige Schritte für einen langfristigen Erhalt der vielfältigen Greifvogelfauna der March-Auen.Between Austria, Slovakia and the Czech Republic, were studied in 2008. The study area (19.7 km2) had not been explored by ornithologists until the 1990s due to the considerable flood dynamics and the subsequent limited accessibility. The present field study was performed between January and July 2008 between Hohenau and Drösing (Lower Austria), consisting of two reference areas of comparable size but with different cultivation techniques, i.e. the high forest cultivation in the North (960 ha) and the middle forest cultivation in the South (1010 ha). Additionally, the field study was conducted to explore the influence of the vegetation structure around the nesting site (microhabitat, r=15 m, 706.5 m2) and the landscape characteristics (macrohabitat, r=250 m, 19.6 ha) on the habitat choices of birds of prey. To get a representative sample for comparison, the same data were collected at 50 randomly selected sites. Aeries were mapped along transects between 50 m intervals, and 167 were found in total. 57 out of 167 aeries were occupied by birds of prey. In total, nine breeding raptor species were recorded. The most abundant species was the Common Buzzard (Buteo buteo), occupying 34 aeries, followed by the Marsh Harrier (Circus aeroginosus) with five or six pairs. The Red Kite (Milvus milvus) population, with a quantity of three pairs was remarkable on a national scale. The Black Kite (Milvus migrans) (three pairs), the Honey Buzzard (Pernis apivorus) (three pairs), the Goshawk (Accipiter gentilis) (three pairs), the Kestrel (Falco tinnunculus) (two pairs) and the Hobby (Falco subbuteo) (two pairs) also bred in the study area. Since 2002 the White-tailed Eagle (Haliaeetus albicilla) has bred successfully in the floodplains. The Sparrowhawk (Accipiter nisus), the Saker Falcon (Falco cherrug) and the Imperial Eagle (Aquila heliaca) were not found as breeders in the study area, but were known to breed nearby. The results indicated a population growth of the Common Buzzard, whereas the density of other predatory birds has been steady for the last 15 years. The density is high compared to other places in central Europe, including the Danube floodplains in Austria. Besides, the density seems to be independent from the type of cultivation. The data concerning the habitat structure were analyzed in a Geographic Information System (GIS) and indicate the March flood-plain forests as very attractive for raptors. The investigation area offers a varied and structured landscape with abundant waterbodies and meadows. Predatory birds prefer old growth trees, particularly oaks (Quercus sp.) and poplars (Populus sp.) for nesting. These types of trees are numerous in middle forest cultivation. Additionally, a higher number of older aeries can be found there compared to high forest cultivations. Birds of prey prefer a distinctive forest structure with plenty of deadwood, far away from paths or protected by dense shrub and undergrowth. Therefore, the conservation of mature forests, the reduction of human disturbance and the reactivation of the flood dynamics could have a positive effect on the raptor population in the long term

Entropic forces generated by grafted semiflexible polymers

The entropic force exerted by the Brownian fluctuations of a grafted semiflexible polymer upon a rigid smooth wall are calculated both analytically and by Monte Carlo simulations. Such forces are thought to play an important role for several cellular phenomena, in particular, the physics of actin-polymerization-driven cell motility and movement of bacteria like Listeria. In the stiff limit, where the persistence length of the polymer is larger than its contour length, we find that the entropic force shows scaling behavior. We identify the characteristic length scales and the explicit form of the scaling functions. In certain asymptotic regimes we give simple analytical expressions which describe the full results to a very high numerical accuracy. Depending on the constraints imposed on the transverse fluctuations of the filament there are characteristic differences in the functional form of the entropic forces; in a two-dimensional geometry the entropic force exhibits a marked peak.Comment: 21 pages, 18 figures, minor misprints correcte

Elasticity of semi-flexible polymers

We present a numerical solution of the Worm-Like Chain (WLC) model for semi-flexible polymers. We display graphs for the end-to-end distance distribution and the force-extension relation expected from the model. We predict the expected level of fluctuations around the mean value in force-extension curves. Our treatment analyses the entire range of polymer lengths and reproduces interesting qualitative features seen in recent computer simulations for polymers of intermediate length. These results can be tested against experiments on single molecules. This study is relevant to mechanical properties of biological molecules.Comment: five pages revtex five figures, slightly improved version with recent references adde

Elasticity of semiflexible polymers in two dimensions

We study theoretically the entropic elasticity of a semi-flexible polymer, such as DNA, confined to two dimensions. Using the worm-like-chain model we obtain an exact analytical expression for the partition function of the polymer pulled at one end with a constant force. The force-extension relation for the polymer is computed in the long chain limit in terms of Mathieu characteristic functions. We also present applications to the interaction between a semi-flexible polymer and a nematic field, and derive the nematic order parameter and average extension of the polymer in a strong field.Comment: 16 pages, 3 figure

Balancing torques in membrane-mediated interactions: Exact results and numerical illustrations

Torques on interfaces can be described by a divergence-free tensor which is fully encoded in the geometry. This tensor consists of two terms, one originating in the couple of the stress, the other capturing an intrinsic contribution due to curvature. In analogy to the description of forces in terms of a stress tensor, the torque on a particle can be expressed as a line integral along any contour surrounding the particle. Interactions between particles mediated by a fluid membrane are studied within this framework. In particular, torque balance places a strong constraint on the shape of the membrane. Symmetric two-particle configurations admit simple analytical expressions which are valid in the fully nonlinear regime; in particular, the problem may be solved exactly in the case of two membrane-bound parallel cylinders. This apparently simple system provides some flavor of the remarkably subtle nonlinear behavior associated with membrane-mediated interactions.Comment: 16 pages, 10 figures, REVTeX4 style. The Gaussian curvature term was included in the membrane Hamiltonian; section II.B was rephrased to smoothen the flow of presentatio

Semiflexible chains in confined spaces

We develop an analytical method for studying the properties of a noninteracting wormlike chain (WLC) in confined geometries. The mean-field-like theory replaces the rigid constraints of confinement with average constraints, thus allowing us to develop a tractable method for treating a WLC wrapped on the surface of a sphere, and fully encapsulated within it. The efficacy of the theory is established by reproducing the exact correlation functions for a WLC confined to the surface of a sphere. In addition, the coefficients in the free energy are exactly calculated. We also describe the behavior of a surface-confined chain under external tension that is relevant for single molecule experiments on histone-DNA complexes. The force-extension curves display spatial oscillations, and the extension of the chain, whose maximum value is bounded by the sphere diameter, scales as f−1 at large forces, in contrast to the unconfined chain that approaches the contour length as f−1∕2. A WLC encapsulated in a sphere, that is relevant for the study of the viral encapsulation of DNA, can also be treated using the mean-field approach. The predictions of the theory for various correlation functions are in excellent agreement with Langevin simulations. We find that strongly confined chains are highly structured by examining the correlations using a local winding axis. The predicted pressure of the system is in excellent agreement with simulations but, as is known, is significantly lower than the pressures seen for DNA packaged in viral capsids

Investigating the effects of laser beams (532 and 660 nm) in annihilation of pistachio mould fungus using spectrophotometry analysis

When moulds are illuminated by visible electromagnetic-EM radiations, several effects on nucleus materials and nucleotides can be detected. These effects have a significant influence on mould generation or destruction. This paper presents the effects and implications of a red diode laser beam (660 nm), a second-harmonics of a Nd:YAG laser emitting green beam (532 nm), or the combination of both, on the eradication of Pistachio mould fungus. Incident doses (ID) of both beams are kept identical throughout the experiment. The absorption spectrums of irradiated mouldy samples and the bright-greenish-yellow-fluorescence (BGYF) of fungus occurring in mould texture due to electronic excitation are investigated. We found that a combination of a green and a red laser beam with an ID of 0.5 J/cm^2 provides the optimal effects on Pistachio mould fungus eradication