Soil carbon in the Jena Experiment from intensive sampling campaigns (only block 2 Main Experiment up to 1 m depth, year 2002)

This data set contains soil carbon measurements (Organic carbon, inorganic carbon, and total carbon; all measured in dried soil samples) from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Stratified soil sampling to a depth of 1 m was performed before sowing in April 2002. Three independent samples per plot were taken of all plots in block 2 using a motor-driven soil column cylinder (Cobra, Eijkelkamp, 8.3 cm in diameter). Soil samples were dried at 40°C and segmented to a depth resolution of 5 cm giving 20 depth subsamples per core. All samples were analyzed independently. All soil samples were passed through a sieve with a mesh size of 2 mm. Rarely present visible plant remains were removed using tweezers. Total carbon concentration was analyzed on ball-milled subsamples (time 4 min, frequency 30 s**-1) by an elemental analyzer at 1150°C (Elementaranalysator vario Max CN; Elementar Analysensysteme GmbH, Hanau, Germany). We measured inorganic carbon concentration by elemental analysis at 1150°C after removal of organic carbon for 16 h at 450°C in a muffle furnace. Organic carbon concentration was calculated as the difference between both measurements of total and inorganic carbon.

Abundance and biomass of macrobenthos in the Black Sea during Mare Nigrum cruise S-RO1

Dataset containing macrobenthos data for samples collected during April 2008 in the North-West Black Sea (between 44°46' - 43°45' N latitude and 30° 11' - 29°35' E longitude). Macrobenthos sampling was done in 4 stations using a 0.14 m**2 Van Veen grab. Washing of the sample through two sieves - 1 mm and 0.25 mm mesh size; the material retained by the two sieves was examined at the binocular microscope; all animals were extracted, using fine tweezers and the species or group of species were identified and counted (in order to determine the density of populations); the larger organisms were measured and weighed (structure and biomass); for smaller organisms, the average wet weights inscribed in standard tables were used to calculate the biomass. Taxonomic identification was done at the GeoEcoMar by A. Teaca and T. Begun using the relevant taxonomic literature (Key-book for the identification of the Black Sea and Sea of Azov Fauna, 1968 -1972, Kiev - in Russian, V 1-4; BACESCU, M.C., MÜLLER, G. I., GOMOIU, M.-T., 1971 and BACESCU, M.C., MÜLLER, G. I., GOMOIU, M.-T., 1971-Benthic ecological research to Black Sea. Comparative quantitative and qualitative analyse of pontic benthic fauna. Marine Ecology, 4, 1-357 (in Romanian).

Total nitrogen from solid phase in the Jena Experiment (Main Experiment up to 30cm depth, year 2002)

This data set contains measurements of total nitrogen from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Stratified soil sampling was performed before sowing in April 2002. Five independent samples per plot were taken using a split tube sampler with an inner diameter of 4.8 cm (Eijkelkamp Agrisearch Equipment, Giesbeek, the Netherlands). Soil samples were dried at 40°C and then segmented to a depth resolution of 5 cm giving six depth subsamples per core. All samples were analyzed independently and averaged values per depth layer are reported. Sampling locations were less than 30 cm apart from sampling locations in other years. Subsequently, samples were dried at 40°C. All soil samples were passed through a sieve with a mesh size of 2 mm. Rarely present visible plant remains were removed using tweezers. Total nitrogen concentration was analyzed on ball-milled subsamples (time 4 min, frequency 30 s-1) by an elemental analyzer at 1150°C (Elementaranalysator vario Max CN; Elementar Analysensysteme GmbH, Hanau, Germany).

Abundance and biomass of macrobenthos in the western part of the Black Sea during Mare Nigrum cruise S-RO2

Dataset containing macrobenthos data for samples collected during September 2008 in the North-West Black Sea (between 44°46' - 43°45' N latitude and 30° 11' - 29°35' E longitude). Macrobenthos sampling was done in 4 stations using a 0.14 m**2 Van Veen grab. Washing of the sample through two sieves - 1 mm and 0.25 mm mesh size; the material retained by the two sieves was examined at the binocular microscope; all animals were extracted, using fine tweezers and the species or group of species were identified and counted (in order to determine the density of populations); the larger organisms were measured and weighed (structure and biomass); for smaller organisms, the average wet weights inscribed in standard tables were used to calculate the biomass. Taxonomic identification was done at the GeoEcoMar by A. Teaca and T. Begun using the relevant taxonomic literature ( "Key-book for the identification of the Black Sea and Sea of Azov Fauna, 1968 -1972, Kiev - in Russian, V 1-4; BACESCU, M.C., MÜLLER, G. I., GOMOIU, M.-T., 1971). BACESCU, M.C., MÜLLER, G. I., GOMOIU, M.-T., 1971-Benthic ecological research to Black Sea. Comparative quantitative and qualitative analyse of pontic benthic fauna. Marine Ecology, 4, 1-357 (in Romanian). Key-book for the identification of the Black Sea and Sea of Azov Fauna, 1968 -1972, Kiev, V. 1-4 (in Russian).

Refined second law of thermodynamics for fast random processes

We establish a refined version of the Second Law of Thermodynamics for Langevin stochastic processes describing mesoscopic systems driven by conservative or non-conservative forces and interacting with thermal noise. The refinement is based on the Monge-Kantorovich optimal mass transport and becomes relevant for processes far from quasi-stationary regime. General discussion is illustrated by numerical analysis of the optimal memory erasure protocol for a model for micron-size particle manipulated by optical tweezers.

Electro y dielectroforesis de nanopartículas por efecto fotovoltaico

El objetivo de esta tesis doctoral es la investigación del nuevo concepto de pinzas fotovoltaicas, es decir, del atrapamiento, ordenación y manipulación de partículas en las estructuras generadas en la superficie de materiales ferroeléctricos mediante campos fotovoltaicos o sus gradientes. Las pinzas fotovoltaicas son una herramienta prometedora para atrapar y mover las partículas en la superficie de un material fotovoltaico de una manera controlada. Para aprovechar esta nueva técnica es necesario conocer con precisión el campo eléctrico creado por una iluminación específica en la superficie del cristal y por encima de ella. Este objetivo se ha dividido en una serie de etapas que se describen a continuación. La primera etapa consistió en la modelización del campo fotovoltaico generado por iluminación no homogénea en substratos y guías de onda de acuerdo al modelo de un centro. En la segunda etapa se estudiaron los campos y fuerzas electroforéticas y dielectroforéticas que aparecen sobre la superficie de substratos iluminados inhomogéneamente. En la tercera etapa se estudiaron sus efectos sobre micropartículas y nanopartículas, en particular se estudió el atrapamiento superficial determinando las condiciones que permiten el aprovechamiento como pinzas fotovoltaicas. En la cuarta y última etapa se estudiaron las configuraciones más eficientes en cuanto a resolución espacial. Se trabajó con distintos patrones de iluminación inhomogénea, proponiéndose patrones de iluminación al equipo experimental. Para alcanzar estos objetivos se han desarrollado herramientas de cálculo con las cuales obtenemos temporalmente todas las magnitudes que intervienen en el problema. Con estas herramientas podemos abstraernos de los complicados mecanismos de atrapamiento y a partir de un patrón de luz obtener el atrapamiento. Todo el trabajo realizado se ha llevado a cabo en dos configuraciones del cristal, en corte X ( superficie de atrapamiento paralela al eje óptico) y corte Z ( superficie de atrapamiento perpendicular al eje óptico). Se ha profundizado en la interpretación de las diferencias en los resultados según la configuración del cristal. Todas las simulaciones y experimentos se han realizado utilizando como soporte un mismo material, el niobato de litio, LiNbO3, con el f n de facilitar la comparación de los resultados. Este hecho no ha supuesto una limitación en los resultados pues los modelos no se limitan a este material. Con respecto a la estructura del trabajo, este se divide en tres partes diferenciadas que son: la introducción (I), la modelización del atrapamiento electroforético y dielectroforético (II) y las simulaciones numéricas y comparación con experimentos (III). En la primera parte se fijan las bases sobre las que se sustentarán el resto de las partes. Se describen los efectos electromagnéticos y ópticos a los que se hará referencia en el resto de los capítulos, ya sea por ser necesarios para describir los experimentos o, en otros casos, para dejar constancia de la no aparición de estos efectos para el caso en que nos ocupa y justificar la simplificación que en muchos casos se hace del problema. En esta parte, se describe principalmente el atrapamiento electroforético y dielectroforético, el efecto fotovoltaico y las propiedades del niobato de litio por ser el material que utilizaremos en experimentos y simulaciones. Así mismo, como no debe faltar en ninguna investigación, se ha analizado el state of the art, revisando lo que otros científicos del campo en el que estamos trabajando han realizado y escrito con el fin de que nos sirva de cimiento a la investigación. Con el capítulo 3 finalizamos esta primera parte describiendo las técnicas experimentales que hoy en día se están utilizando en los laboratorios para realizar el atrapamiento de partículas mediante el efecto fotovoltaico, ya que obtendremos ligeras diferencias en los resultados según la técnica de atrapamiento que se utilice. En la parte I I , dedicada a la modelización del atrapamiento, empezaremos con el capítulo 4 donde modelizaremos el campo eléctrico interno de la muestra, para a continuación modelizar el campo eléctrico, los potenciales y las fuerzas externas a la muestra. En capítulo 5 presentaremos un modelo sencillo para comprender el problema que nos aborda, al que llamamos Modelo Estacionario de Separación de Carga. Este modelo da muy buenos resultados a pesar de su sencillez. Pasamos al capítulo 6 donde discretizaremos las ecuaciones que intervienen en la física interna de la muestra mediante el método de las diferencias finitas, desarrollando el Modelo de Distribución de Carga Espacial. Para terminar esta parte, en el capítulo 8 abordamos la programación de las modelizaciones presentadas en los anteriores capítulos con el fn de dotarnos de herramientas para realizar las simulaciones de una manera rápida. En la última parte, III, presentaremos los resultados de las simulaciones numéricas realizadas con las herramientas desarrolladas y comparemos sus resultados con los experimentales. Fácilmente podremos comparar los resultados en las dos configuraciones del cristal, en corte X y corte Z. Finalizaremos con un último capítulo dedicado a las conclusiones, donde resumiremos los resultados que se han ido obteniendo en cada apartado desarrollado y daremos una visión conjunta de la investigación realizada. ABSTRACT The aim of this thesis is the research of the new concept of photovoltaic or optoelectronic tweezers, i.e., trapping, management and manipulation of particles in structures generated by photovoltaic felds or gradients on the surface of ferroelectric materials. Photovoltaic tweezers are a promising tool to trap and move the particles on the surface of a photovoltaic material in a monitored way. To take advantage of this new technique is necessary to know accurately the electric field created by a specifc illumination in the crystal surface and above it. For this purpose, the work was divided into the stages described below. The first stage consisted of modeling the photovoltaic field generated by inhomogeneous illumination in substrates and waveguides according to the one-center model. In the second stage, electrophoretic and dielectrophoretic fields and forces appearing on the surface of substrates and waveguides illuminated inhomogeneously were studied. In the third stage, the study of its effects on microparticles and nanoparticles took place. In particular, the trapping surface was studied identifying the conditions that allow its use as photovoltaic tweezers. In the fourth and fnal stage the most efficient configurations in terms of spatial resolution were studied. Different patterns of inhomogeneous illumination were tested, proposing lightning patterns to the laboratory team. To achieve these objectives calculation tools were developed to get all magnitudes temporarily involved in the problem . With these tools, the complex mechanisms of trapping can be simplified, obtaining the trapping pattern from a light pattern. All research was carried out in two configurations of crystal; in X section (trapping surface parallel to the optical axis) and Z section (trapping surface perpendicular to the optical axis). The differences in the results depending on the configuration of the crystal were deeply studied. All simulations and experiments were made using the same material as support, lithium niobate, LiNbO3, to facilitate the comparison of results. This fact does not mean a limitation in the results since the models are not limited to this material. Regarding the structure of this work, it is divided into three clearly differentiated sections, namely: Introduction (I), Electrophoretic and Dielectrophoretic Capture Modeling (II) and Numerical Simulations and Comparison Experiments (III). The frst section sets the foundations on which the rest of the sections will be based on. Electromagnetic and optical effects that will be referred in the remaining chapters are described, either as being necessary to explain experiments or, in other cases, to note the non-appearance of these effects for the present case and justify the simplification of the problem that is made in many cases. This section mainly describes the electrophoretic and dielectrophoretic trapping, the photovoltaic effect and the properties of lithium niobate as the material to use in experiments and simulations. Likewise, as required in this kind of researches, the state of the art have been analyzed, reviewing what other scientists working in this field have made and written so that serve as a foundation for research. With chapter 3 the first section finalizes describing the experimental techniques that are currently being used in laboratories for trapping particles by the photovoltaic effect, because according to the trapping technique in use we will get slightly different results. The section I I , which is dedicated to the trapping modeling, begins with Chapter 4 where the internal electric field of the sample is modeled, to continue modeling the electric field, potential and forces that are external to the sample. Chapter 5 presents a simple model to understand the problem addressed by us, which is called Steady-State Charge Separation Model. This model gives very good results despite its simplicity. In chapter 6 the equations involved in the internal physics of the sample are discretized by the finite difference method, which is developed in the Spatial Charge Distribution Model. To end this section, chapter 8 is dedicated to program the models presented in the previous chapters in order to provide us with tools to perform simulations in a fast way. In the last section, III, the results of numerical simulations with the developed tools are presented and compared with the experimental results. We can easily compare outcomes in the two configurations of the crystal, in section X and section Z. The final chapter collects the conclusions, summarizing the results that were obtained in previous sections and giving an overview of the research.

The active digestion of uniparental chloroplast DNA in a single zygote of Chlamydomonas reinhardtii is revealed by using the optical tweezer

The non-Mendelian inheritance of organelle genes is a phenomenon common to almost all eukaryotes, and in the isogamous alga Chlamydomonas reinhardtii, chloroplast (cp) genes are transmitted from the mating type positive (mt+) parent. In this study, the preferential disappearance of the fluorescent cp nucleoids of the mating type negative (mt−) parent was observed in living young zygotes. To study the change in cpDNA molecules during the preferential disappearance, the cpDNA of mt+ or mt− origin was labeled separately with bacterial aadA gene sequences. Then, a single zygote with or without cp nucleoids was isolated under direct observation by using optical tweezers and investigated by nested PCR analysis of the aadA sequences. This demonstrated that cpDNA molecules are digested completely during the preferential disappearance of mt− cp nucleoids within 10 min, whereas mt+ cpDNA and mitochondrial DNA are protected from the digestion. These results indicate that the non-Mendelian transmission pattern of organelle genes is determined immediately after zygote formation.

Torsional rigidity of single actin filaments and actin–actin bond breaking force under torsion measured directly by in vitro micromanipulation

Knowledge of the elastic properties of actin filaments is crucial for considering its role in muscle contraction, cellular motile events, and formation of cell shape. The stiffness of actin filaments in the directions of stretching and bending has been determined. In this study, we have directly determined the torsional rigidity and breaking force of single actin filaments by measuring the rotational Brownian motion and tensile strength using optical tweezers and microneedles, respectively. Rotational angular fluctuations of filaments supplied the torsional rigidity as (8.0 ± 1.2) × 10−26 Nm2. This value is similar to that deduced from the longitudinal rigidity, assuming the actin filament to be a homogeneous rod. The breaking force of the actin–actin bond was measured while twisting a filament through various angles using microneedles. The breaking force decreased greatly under twist, e.g., from 600–320 pN when filaments were turned through 90°, independent of the rotational direction. Our results indicate that an actin filament exhibits comparable flexibility in the rotational and longitudinal directions, but breaks more easily under torsional load.

Optical trapping and manipulation of neutral particles using lasers

The techniques of optical trapping and manipulation of neutral particles by lasers provide unique means to control the dynamics of small particles. These new experimental methods have played a revolutionary role in areas of the physical and biological sciences. This paper reviews the early developments in the field leading to the demonstration of cooling and trapping of neutral atoms in atomic physics and to the first use of optical tweezers traps in biology. Some further major achievements of these rapidly developing methods also are considered.

Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure

Single chicken erythrocyte chromatin fibers were stretched and released at room temperature with force-measuring laser tweezers. In low ionic strength, the stretch-release curves reveal a process of continuous deformation with little or no internucleosomal attraction. A persistence length of 30 nm and a stretch modulus of ≈5 pN is determined for the fibers. At forces of 20 pN and higher, the fibers are modified irreversibly, probably through the mechanical removal of the histone cores from native chromatin. In 40–150 mM NaCl, a distinctive condensation-decondensation transition appears between 5 and 6 pN, corresponding to an internucleosomal attraction energy of ≈2.0 kcal/mol per nucleosome. Thus, in physiological ionic strength the fibers possess a dynamic structure in which the fiber locally interconverting between “open” and “closed” states because of thermal fluctuations.

Measuring the forces involved in polyvalent adhesion of uropathogenic Escherichia coli to mannose-presenting surfaces

Mechanisms of bacterial pathogenesis have become an increasingly important subject as pathogens have become increasingly resistant to current antibiotics. The adhesion of microorganisms to the surface of host tissue is often a first step in pathogenesis and is a plausible target for new antiinfective agents. Examination of bacterial adhesion has been difficult both because it is polyvalent and because bacterial adhesins often recognize more than one type of cell-surface molecule. This paper describes an experimental procedure that measures the forces of adhesion resulting from the interaction of uropathogenic Escherichia coli to molecularly well defined models of cellular surfaces. This procedure uses self-assembled monolayers (SAMs) to model the surface of epithelial cells and optical tweezers to manipulate the bacteria. Optical tweezers orient the bacteria relative to the surface and, thus, limit the number of points of attachment (that is, the valency of attachment). Using this combination, it was possible to quantify the force required to break a single interaction between pilus and mannose groups linked to the SAM. These results demonstrate the deconvolution and characterization of complicated events in microbial adhesion in terms of specific molecular interactions. They also suggest that the combination of optical tweezers and appropriately functionalized SAMs is a uniquely synergistic system with which to study polyvalent adhesion of bacteria to biologically relevant surfaces and with which to screen for inhibitors of this adhesion.

Free energy reconstruction from nonequilibrium single-molecule pulling experiments

Laser tweezers and atomic force microscopes are increasingly used to probe the interactions and mechanical properties of individual molecules. Unfortunately, using such time-dependent perturbations to force rare molecular events also drives the system away from equilibrium. Nevertheless, we show how equilibrium free energy profiles can be extracted rigorously from repeated nonequilibrium force measurements on the basis of an extension of Jarzynski's remarkable identity between free energies and the irreversible work.

Mechanism for nucleic acid chaperone activity of HIV-1 nucleocapsid protein revealed by single molecule stretching

The nucleocapsid protein (NC) of HIV type 1 is a nucleic acid chaperone that facilitates the rearrangement of nucleic acids into conformations containing the maximum number of complementary base pairs. We use an optical tweezers instrument to stretch single DNA molecules from the helix to coil state at room temperature in the presence of NC and a mutant form (SSHS NC) that lacks the two zinc finger structures present in NC. Although both NC and SSHS NC facilitate annealing of complementary strands through electrostatic attraction, only NC destabilizes the helical form of DNA and reduces the cooperativity of the helix-coil transition. In particular, we find that the helix-coil transition free energy at room temperature is significantly reduced in the presence of NC. Thus, upon NC binding, it is likely that thermodynamic fluctuations cause continuous melting and reannealing of base pairs so that DNA strands are able to rapidly sample configurations to find the lowest energy state. The reduced cooperativity allows these fluctuations to occur in the middle of complex double-stranded structures. The reduced stability and cooperativity, coupled with the electrostatic attraction generated by the high charge density of NC, is responsible for the nucleic acid chaperone activity of this protein.

Dynamics of active lamellae in cultured epithelial cells: effects of expression of exogenous N-ras oncogene.

We examined the functional consequences of cellular transformation of rat IAR-2 epithelial cells, by a mutant N-ras oncogene, on the dynamics of active lamellae, structures that play an important role in cell motility, adhesion, and surface-receptor capping. Lamellar activity was assessed by measuring the rate of outer-edge pseudopodial activity and by analyzing the motility of Con A-coated beads placed on lamellar surfaces with optical tweezers. Although transformation dramatically affected the shape and size of active cellular lamellae, there was little detectable effect on either pseudopodial activity or bead movement. To investigate the potential relationship between functional lamellar activity and the microtubule cytoskeleton, lamellar activity was examined in nontransformed and transformed cells treated with the microtubule-disrupting drug nocodazole. In the absence of microtubules, transformed cells were less polarized and possessed decreased rates of pseudopodial and bead motility. On the basis of these observations, it is suggested that ras-induced transformation of epithelial cells consists of two cytoskeletal modifications: overall diminished actin cytoskeletal dynamics in lamellae and reorganization of the microtubule cytoskeleton that directs pseudopodial activity to smaller polarized lamellae.

Multipole expansion of strongly focussed laser beams

Multipole expansion of an incident radiation field-that is, representation of the fields as sums of vector spherical wavefunctions-is essential for theoretical light scattering methods such as the T-matrix method and generalised Lorenz-Mie theory (GLMT). In general, it is theoretically straightforward to find a vector spherical wavefunction representation of an arbitrary radiation field. For example, a simple formula results in the useful case of an incident plane wave. Laser beams present some difficulties. These problems are not a result of any deficiency in the basic process of spherical wavefunction expansion, but are due to the fact that laser beams, in their standard representations, are not radiation fields, but only approximations of radiation fields. This results from the standard laser beam representations being solutions to the paraxial scalar wave equation. We present an efficient method for determining the multipole representation of an arbitrary focussed beam. (C) 2003 Elsevier Science Ltd. All rights reserved.