Confinement and viscoelastic effects on chain closure dynamics

Chemical reactions inside cells are typically subject to the effects both of the cell's confining surfaces and of the viscoelastic behavior of its contents. In this paper, we show how the outcome of one particular reaction of relevance to cellular biochemistry - the diffusion-limited cyclization of long chain polymers - is influenced by such confinement and crowding effects. More specifically, starting from the Rouse model of polymer dynamics, and invoking the Wilemski-Fixman approximation, we determine the scaling relationship between the mean closure time t(c) of a flexible chain (no excluded volume or hydrodynamic interactions) and the length N of its contour under the following separate conditions: (a) confinement of the chain to a sphere of radius d and (b) modulation of its dynamics by colored Gaussian noise. Among other results, we find that in case (a) when d is much smaller than the size of the chain, t(c) similar to Nd-2, and that in case (b), t(c) similar to N-2/(2 (2H)), H being a number between 1/2 and 1 that characterizes the decay of the noise correlations. H is not known a priori, but values of about 0.7 have been used in the successful characterization of protein conformational dynamics. At this value of H (selected for purposes of illustration), t(c) similar to N-3.4, the high scaling exponent reflecting the slow relaxation of the chain in a viscoelastic medium. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4729041]

Revision of the scolopendrid centipede digitipes Attems, 1930, from India (Chilopoda: Scolopendromorpha): reconciling molecular and morphological estimates of species diversity

Recent work on molecular phylogenetics of Scolopendridae from the Western Ghats, Peninsular India, has suggested the presence of six cryptic species of the otostigmine Digitipes Attems, 1930, together with three species described in previous taxonomic work by Jangi and Dass (1984). Digitipes is the correct generic attribution for a monophyletic group of Indian species, these being united with three species from tropical Africa (including the type) that share a distomedial process on the ultimate leg femur of males that is otherwise unknown in Otostigminae. Second maxillary characters previously used in the diagnosis of Digitipes are dismissed because Indian species do not possess the putatively diagnostic character states. Two new species from the Western Ghats that correspond to groupings identified based on monophyly, sequence divergence and coalescent analysis using molecular data are diagnosed based on distinct morphological characters. They are D. jangii and D. periyarensis n. spp. Three species named by Jangi and Dass (Digitipes barnabasi, D. coonoorensis and D. indicus) are revised based on new collections; D. indicus is a junior subjective synonym of Arthrorhabdus jonesii Verhoeff, 1938, the combination becoming Digitipes jonesii (Verhoeff, 1938) n. comb. The presence of Arthrorhabdus in India is accordingly refuted. Three putative species delimited by molecular and ecological data remain cryptic from the perspective of diagnostic morphological characters and are presently retained in D. barnabasi, D. jangii and D. jonesii. A molecularly-delimited species that resolved as sister group to a well-supported clade of Indian Digitipes is identified as Otostigmus ruficeps Pocock, 1890, originally described from a single specimen and revised herein. One Indian species originally assigned to Digitipes, D. gravelyi, deviates from confidently-assigned Digitipes with respect to several characters and is reassigned to Otostigmus, as O. gravelyi (Jangi and Dass, 1984) n. comb.

The diffusion and relaxation of Gaussian chains in narrow rectangular slits

The confinement of a polymer to volumes whose characteristic linear dimensions are comparable to or smaller than its bulk radius of gyration R-G,R-bulk can produce significant changes in its static and dynamic properties, with important implications for the understanding of single-molecule processes in biology and chemistry. In this paper, we present calculations of the effects of a narrow rectangular slit of thickness d on the scaling behavior of the diffusivity D and relaxation time tau(r) of a Gaussian chain of polymerization index N and persistence length l(0). The calculations are based on the Rouse-Zimm model of chain dynamics, with the pre-averaged hydrodynamic interaction being obtained from the solutions to Stokes equations for an incompressible fluid in a parallel plate geometry in the limit of small d. They go beyond de Gennes' purely phenomenological analysis of the problem based on blobs, which has so far been the only analytical route to the determination of chain scaling behavior for this particular geometry. The present model predicts that D similar to dN(-1) ln(N/d(2)) and tau(r) similar to N(2)d(-1) ln(N/d(2))(-1) in the regime of moderate confinement, where l(0) << d < R-G,R-bulk. The corresponding results for the blob model have exactly the same power law behavior, but contain no logarithmic corrections; the difference suggests that segments within a blob may actually be partially draining and not non-draining as generally assumed.

The diffusion and relaxation of Gaussian chains in narrow rectangular slits

The confinement of a polymer to volumes whose characteristic linear dimensions are comparable to or smaller than its bulk radius of gyration R-G,R-bulk can produce significant changes in its static and dynamic properties, with important implications for the understanding of single-molecule processes in biology and chemistry. In this paper, we present calculations of the effects of a narrow rectangular slit of thickness d on the scaling behavior of the diffusivity D and relaxation time tau(r) of a Gaussian chain of polymerization index N and persistence length l(0). The calculations are based on the Rouse-Zimm model of chain dynamics, with the pre-averaged hydrodynamic interaction being obtained from the solutions to Stokes equations for an incompressible fluid in a parallel plate geometry in the limit of small d. They go beyond de Gennes' purely phenomenological analysis of the problem based on blobs, which has so far been the only analytical route to the determination of chain scaling behavior for this particular geometry. The present model predicts that D similar to dN(-1) ln(N/d(2)) and tau(r) similar to N(2)d(-1) ln(N/d(2))(-1) in the regime of moderate confinement, where l(0) << d < R-G,R-bulk. The corresponding results for the blob model have exactly the same power law behavior, but contain no logarithmic corrections; the difference suggests that segments within a blob may actually be partially draining and not non-draining as generally assumed. (C) 2013 AIP Publishing LLC.

Moving to stay in place: behavioral mechanisms for coexistence of African large carnivores

Most ecosystems have multiple predator species that not only compete for shared prey, but also pose direct threats to each other. These intraguild interactions are key drivers of carnivore community structure, with ecosystem-wide cascading effects. Yet, behavioral mechanisms for coexistence of multiple carnivore species remain poorly understood. The challenges of studying large, free-ranging carnivores have resulted in mainly coarse-scale examination of behavioral strategies without information about all interacting competitors. We overcame some of these challenges by examining the concurrent fine-scale movement decisions of almost all individuals of four large mammalian carnivore species in a closed terrestrial system. We found that the intensity of intraguild interactions did not follow a simple hierarchical allometric pattern, because spatial and behavioral tactics of subordinate species changed with threat and resource levels across seasons. Lions (Panthera leo) were generally unrestricted and anchored themselves in areas rich in not only their principal prey, but also, during periods of resource limitation (dry season), rich in the main prey for other carnivores. Because of this, the greatest cost (potential intraguild predation) for subordinate carnivores was spatially coupled with the highest potential benefit of resource acquisition (prey-rich areas), especially in the dry season. Leopard (P. pardus) and cheetah (Acinonyx jubatus) overlapped with the home range of lions but minimized their risk using fine-scaled avoidance behaviors and restricted resource acquisition tactics. The cost of intraguild competition was most apparent for cheetahs, especially during the wet season, as areas with energetically rewarding large prey (wildebeest) were avoided when they overlapped highly with the activity areas of lions. Contrary to expectation, the smallest species (African wild dog, Lycaon pictus) did not avoid only lions, but also used multiple tactics to minimize encountering all other competitors. Intraguild competition thus forced wild dogs into areas with the lowest resource availability year round. Coexistence of multiple carnivore species has typically been explained by dietary niche separation, but our multi-scaled movement results suggest that differences in resource acquisition may instead be a consequence of avoiding intraguild competition. We generate a more realistic representation of hierarchical behavioral interactions that may ultimately drive spatially explicit trophic structures of multi-predator communities.

Diurnal and seasonal variation of mixing ratio and delta C-13 of air CO2 observed at an urban station Bangalore, India

We present here observations on diurnal and seasonal variation of mixing ratio and delta C-13 of air CO2, from an urban station-Bangalore (BLR), India, monitored between October 2008 and December 2011. On a diurnal scale, higher mixing ratio with depleted delta C-13 of air CO2 was found for the samples collected during early morning compared to the samples collected during late afternoon. On a seasonal scale, mixing ratio was found to be higher for dry summer months (April-May) and lower for southwest monsoon months (June-July). The maximum enrichment in delta C-13 of air CO2 (-8.04 +/- 0.02aEuro degrees) was seen in October, then delta C-13 started depleting and maximum depletion (-9.31 +/- 0.07aEuro degrees) was observed during dry summer months. Immediately after that an increasing trend in delta C-13 was monitored coincidental with the advancement of southwest monsoon months and maximum enrichment was seen again in October. Although a similar pattern in seasonal variation was observed for the three consecutive years, the dry summer months of 2011 captured distinctly lower amplitude in both the mixing ratio and delta C-13 of air CO2 compared to the dry summer months of 2009 and 2010. This was explained with reduced biomass burning and increased productivity associated with prominent La Nina condition. While compared with the observations from the nearest coastal and open ocean stations-Cabo de Rama (CRI) and Seychelles (SEY), BLR being located within an urban region captured higher amplitude of seasonal variation. The average delta C-13 value of the end member source CO2 was identified based on both diurnal and seasonal scale variation. The delta C-13 value of source CO2 (-24.9 +/- 3aEuro degrees) determined based on diurnal variation was found to differ drastically from the source value (-14.6 +/- 0.7aEuro degrees) identified based on seasonal scale variation. The source CO2 identified based on diurnal variation incorporated both early morning and late afternoon sample; whereas, the source CO2 identified based on seasonal variation included only afternoon samples. Thus, it is evident from the study that sampling timing is one of the important factors while characterizing the composition of end member source CO2 for a particular station. The difference in delta C-13 value of source CO2 obtained based on both diurnal and seasonal variation might be due to possible contribution from cement industry along with fossil fuel / biomass burning as predominant sources for the station along with differential meteorological conditions prevailed.

Revalidation of Natrix clerki Wall, 1925, an overlooked species in the genus Amphiesma Dumeril, Bibron & Dumeril, 1854 (Squamata: Natricidae)

Natrix clerki Wall, 1925, previously known from its sole holotype and considered a synonym of Amphiesma parallelum (Boulenger, 1890), is resurrected in the genus Amphiesma on the basis of the analysis of morphological variation in 28 specimens of ``Amphiesma parallelum'' auctorum, plus six living, unvouchered specimens discovered in Arunachal Pradesh and Nagaland, India, and one vouchered specimen from Talle Valley in Arunachal Pradesh. Specimens from northeast India (Nagaland), northern Myanmar, and China (Yunnan), previously identified as Amphiesma parallelum either in the literature or in museum's catalogues, are also here referred to A. clerki. The holotype of Amphiesma clerki is redescribed. As a consequence, the definition of Amphiesma parallelum is modified. A. parallelum inhabits the Khasi Hills and Naga Hills in Northeast India, whereas A. clerki has a wider range in the Eastern Himalayas, northern Myanmar and Yunnan (China). Amphiesma clerki differs from A. parallelum by its longer tail, dorsal scales more strongly keeled, scales of the first dorsal scale row strongly keeled vs. smooth, a postocular streak not interrupted at the level of the neck, and a much more vivid pattern on a darker background colour. Characters of species of the Amphiesma parallelum group, i.e. A. clerki, A. parallelum, A. bitaeniatum, A. platyceps and A. sieboldii are compared. A key to this group is provided.

In the elephant's seed shadow: the prospects of domestic bovids as replacement dispersers of three tropical Asian trees

As populations of the world's largest animal species decline, it is unclear how ecosystems will react to their local extirpation. Due to the unique ecological characteristics of megaherbivores such as elephants, seed dispersal is one ecosystem process that may be affected as populations of large animals are decimated. In typically disturbed South Asian ecosystems, domestic bovids (cattle, Bos primigenius, and buffalo, Bubalus bubalis) may often be the species most available to replace Asian elephants (Elephas maximus) as endozoochorous dispersers of large-fruited mammal-dispersed species. We use feeding trials, germination trials, and movement data from the tropical moist forests of Buxa Tiger Reserve (India) to examine whether domestic bovids are viable replacements for elephants in the dispersal of three largefruited species: Dillenia indica, Artocarpus chaplasha, and Careya arborea. We find that (1) once consumed, seeds are between 2.5 (C. arborea) and 26.5 (D. indica) times more likely to pass undigested into elephant dung than domestic bovid dung; and (2) seeds from elephant dung germinated as well as or better than seeds taken from bovid dung for all plant species, with D. indica seeds from elephant dung 1.5 times more likely to germinate. Furthermore, since wild elephants have less constrained movements than even free-roaming domestic bovids, we calculate that maximum dispersal by elephants is between 9.5 and 11.2 times farther than that of domestic bovids, with about 20% of elephant-dispersed seeds being moved farther than the maximum distance seeds are moved by bovids. Our findings suggest that, while bovids are able to disperse substantial numbers of seeds over moderate distances for two of the three study species, domestic bovids will be unable to routinely emulate the reliable, long-distance dispersal of seeds executed by elephants in this tropical moist forest. Thus while domestic bovids can attenuate the effects of losing elephants as dispersers, they may not be able to prevent the decline of various mammal-dispersed fruiting species in the face of overhunting, habitat fragmentation, and climate change.

Behaviour of a puff of resuspended sediment: a conceptual model

The particulate matter concentration above the seabed is usually assumed to decrease with height, following an exponential or Rouse profile. Many particulate matter concentration profiles with a peak were found on the North Mediterranean bottom water at a few tens of metres above the bottom. A particle size signal at the same altitude was found in this area and on the New York Eight shelf. It is assumed that this unexpected shape is due to a cloud of resuspended cohesive sediments originating from an impulse resuspension process. A simplified three-dimensional numerical model is proposed to describe the behaviour of resuspended particulate matter that originates from a sediment impulse vertically injected in the bottom water. This model reproduces the concentration profile shape observed, and it gives indications concerning the length and time characteristics of such a cloud, depending on the water velocity and bottom boundary layer properties.

Scaling, Dimensional Analysis, and Indentation Measurements

We provide an overview of the basic concepts of scaling and dimensional analysis, followed by a review of some of the recent work on applying these concepts to modeling instrumented indentation measurements. Specifically, we examine conical and pyramidal indentation in elastic-plastic solids with power-law work-hardening, in power-law creep solids, and in linear viscoelastic materials. We show that the scaling approach to indentation modeling provides new insights into several basic questions in instrumented indentation, including, what information is contained in the indentation load-displacement curves? How does hardness depend on the mechanical properties and indenter geometry? What are the factors determining piling-up and sinking-in of surface profiles around indents? Can stress-strain relationships be obtained from indentation load-displacement curves? How to measure time dependent mechanical properties from indentation? How to detect or confirm indentation size effects? The scaling approach also helps organize knowledge and provides a framework for bridging micro- and macroscales. We hope that this review will accomplish two purposes: (1) introducing the basic concepts of scaling and dimensional analysis to materials scientists and engineers, and (2) providing a better understanding of instrumented indentation measurements.

Efecto del revestimiento de la semilla con fosforo sobre el crecimiento y rendimiento de tres variedades de frijol común (Phaseolus vulgaris L.)

Este experimento fue realizado en la finca experimental “La Compañía”, localizada en San Marcos, Carazo, en el periodo comprendido del 15 de Junio al 2 de Septiembre del 2002, con el propósito de evaluar el efecto de la semilla revestida con fósforo sobre las primeras etapas de crecimiento y rendimiento del frijol común (Phaseolus vulgaris L.). Los tratamientos en estudio se evaluaron en un diseño con arreglo bifactorial propiamente dicho con distribuciónen bloques completos al azar (BCA) y cuatro repeticiones. Los factores en estudio fueron A: Tres variedades de frijol común y el factor B: Dosis y revestimiento con fertilizante fosfórico a la semilla de frijol. En las variables analizadas se observaron diferencias estadísticas significativas solamente en las variables altura y biomasa. En la altura de las plantas se observaron diferencias estadísticas altamente significativas en las tres fechas exceptuando la altura a los 48 días después de la siembra (dds) en la variedad INTA-Canela (0.0468). Las mayores alturas se obtuvieron con la dosis 60 kg/ha de fertilizante fosfórico y con semilla sin revestir con excepción de las variedades INTA-Canela que a los 21, 33 y 48 dds e INTA-Masatepe a los 33 dds las mayores alturas se obtuvieron cuando la semilla fue revestida con el fertilizante fosfórico. Con respecto a la variable biomasa seca a los 21 dds solo se encontró diferencia estadística significativa en la va riedad INTA-Masatepe (0.0217). El mayor peso (19.31 g) se obtuvo cuando se aplicó la dosis de 60 kg/ha de fertilizante fosfórico y se utilizó semilla revestida, mientras que a la floración se observaron diferencias estadísticas significativas (0.0152) en la variedad INTA-Canela y diferencias altamente significativas (0.0004) en la variedad INTA-Masatepe, obteniéndose en ambas los mayores pesos cuando se aplicó la dosis de 60 kg/ha de fertilizante fosfórico y se utilizó semilla revestida. En la variable extracción de fósforo por las plantas se obtuvieron resultados similares a los de la variable biomasa seca tanto a los 21 dds como a la floración. Para las variables de rendimiento y peso de mil granos no se encontró diferencias estadísticas significativas. Los resultados indican que el mayor efecto en términos de rendimiento se obtienen cuando se aplicó la dosis 60 kg/ha de fertilizante fosfórico ya sea cuando se utilizó la semilla revestida con fósforo o sin revestir.

Evaluación agronómica y uso eficiente de nitrógeno en veinticuatro lineas de sorgo (Sorghum bicolor L. Moench) en el municipio de Posoltega, departamento de Chinandega, 2003

La producción de alimentos básicos es una prioridad que está siendo fuertemente investigada en la actualidad, entre éstos se encuentra el sorgo con endosperma blanco que constituye una alternativa viable para el consumo en zonas de escasas precipitaciones. Con el fin de evaluar el comportamiento agronómico y productivo de líneas, se condujo este estudio en el Centro Experimental de Occidente (CEO), ubicado en el municipio de Posoltega, departamento de Chinandega con coordenadas de 12º33’ de latitud norte y 85º59’ de longitud oeste a una elevación de 80 msnm, en suelos de textura franco-arenosa en la época de postrera comprendida de septiembre a diciembre de 2003. Se utilizó un diseño bifactorial en Bloques Completos al Azar (BCA) con cuatro repeticiones. Los factores evaluados fueron 24 líneas de sorgo y un testigo local (Pinolero 1) con aplicación de fondo de 193.64 kg de completo 12-30-10 ha-1, y dos niveles de fertilización nitrogenada 0 y 112 kg de N ha-1 con UREA 46%, fraccionada en dos aplicaciones. Los resultados reflejan que la mayoría de las variables evaluadas presentan diferencias significativas para ambos factores (A y B) a excepción de la variable altura de planta que no presenta significancia para el factor B, la interacción no tuvo significancia para ninguna variable. El rendimiento de grano mostró diferencias altamente significativas para ambos factores y para la interacción, sobresaliendo la línea SOBERANO con 3271.44 kg ha-1 para el factor A. En la interacción, los mayores rendimientos de grano se presentaron cuando se aplicó 112 kg de N ha-1 al suelo, sobresaliendo las líneas ICSVLM_ 89513, 89524, 93081, 90510, 93074 y SOBERANO con rendimientos de grano entre 4844.08 y 4016.22 kg ha-1 en orden descendiente. Sin embargo la línea ICSVLM_90538 con rendimiento de 2847 kg ha-1 con el nivel cero aplicación de nitrógeno (UREA 46%) logró superar el rendimiento promedio nacional. Las líneas que expresaron un mejor Uso Eficiente de Nitrógeno (UEN) fueron ICSVLM_89544 con 93.5% de relación de eficiencia, ICSVLM_93065 con 90% de eficiencia fisiológica e ICSVLM_89524 con 80.3% de eficiencia de recuperación.

Creemos porque amamos : la estructura interna del acto de fe en John Henry Newman

El autor nos introduce en la cuestión de los motivos racionales de la fe. Las operaciones llevadas a cabo por la inteligencia y la voluntad en el acto de creer, constituyen el fundamento por el cual la Verdad revelada entabla históricamente el diálogo con el hombre. El tema se halla en el centro de la experiencia religiosa y de la reflexión teológica de Newman, y ha significado un aporte indiscutible a la teología contemporánea.

La “experiencia religiosa” forjadora de un lenguaje teológico significativo en John Henry Newman

El autor plantea la cuestión de lo significativo del lenguaje teológico a partir del concepto de experiencia en el pensamiento del cardenal Newman. Su itinerario de fe y conversión, enraizado en un diálogo personal con Dios, le ha dado tanto a su teología como a su predicación, un atractivo que trasciende su época y que puede servir de estímulo actualmente en la comunicación teológica.

Newman y “La idea de una universidad”

El papa Benedicto XVI beatificó el 19 de septiembre del año pasado a John Henry Newman, en la Misa final de su visita oficial al Reino Unido. En un pasaje de la homilía dijo así: “Me gustaría rendir especial homenaje a su visión de la educación, que ha hecho tanto por formar el ethos que es la fuerza motriz de las escuelas y facultades católicas actuales. Firmemente contrario a cualquier enfoque reductivo o utilitarista, buscó lograr unas condiciones educativas en las que se unificara el esfuerzo intelectual, la disciplina moral y el compromiso religioso. El proyecto de fundar una Universidad Católica en Irlanda le brindó la oportunidad de desarrollar sus ideas al respecto, y la colección de discursos que publicó con el título La Idea de una Universidad sostiene un ideal mediante el cual todos los que están inmersos en la formación académica pueden seguir aprendiendo”. Estas palabras por sí solas justifican que nos ocupemos aquí de Newman y la Universidad, recordando que el suyo no fue solo un pensamiento teórico sino fruto de su experiencia personal: anglicano en Oxford, como fellow y tutor en el Oriel College, y católico en Dublín, como fundador y rector de la Universidad Católica de Irlanda. Vivió entre 1801 y 1890, y se convirtió en 1845, y en su paso del anglicanismo al catolicismo mantuvo los mismos principios esenciales, a los cuales pretendo acercarme en esta exposición.