1,721,000 research outputs found
Collective Phototaxis of Chlamydomonas reinhardtii Cells
No full textMicroorganisms are omnipresent in our life and the environment, such as microbes in the gut, spermatozoa in reproductive organs, algae and protozoa in the aquatic ecosystem, and bacterial colonization and infection. Motility in microorganisms is an essential feature of life that facilitates the search for food, avoidance of possible life-threatening cues, and spatially distributing cells for thriving. Often taxis phenomena wherein microorganisms exhibit directed motion in response to external physio-chemical stimuli or nutrient gradients constitute a coordinated complex movement of a large collection of microorganisms such as phototaxis of phytoplankton in response to light and chemotaxis of bacteria or sperm cells in response to a chemical gradient. Therefore, it is essential to understand the effect and origin of emerging collective behavior in dense suspension and the nature of crossover from an individual cell to the population level.
This thesis presents a comprehensive experimental study of collective behavior in phototaxis of Chlamydomonas reinhardtii (CR) cells, a single-cell biflagellate microswimmer widely considered as model organism. We divide the study of phototaxis into three major parts - (i) steady-state phototactic response of cells (when cells are already oriented towards the light exhibiting directed motion), (ii) Response: transition from random motion of cells to steady-state directed phototactic motion when light is switched on (iii) Recovery: transition from steady-state directed phototactic motion of cells to random motion when light is switched off.
In the first part of the thesis, we describe the steady-state phototactic response of CR cells. We show that at a given light intensity, the phototactic efficiency of CR cells is minimal (even lower than a single isolated cell) at a well-defined threshold cell concentration, above which the efficiency of a large collection of cells can even exceed the efficiency obtainable from a single isolated cell. We demonstrate that the origin of enhancement in phototactic efficiency in collective regime lies in the slowing down cell speed, leading them to better light sensing capabilities. We further show that the steady-state phenomenology observed in this study is well captured by modeling the phototactic response as an active Brownian particle subject to density-dependent external aligning torque.
In the second part, we discuss the kinetics of phototactic reorientation during - (i) Response and (ii) Recovery. Due to the single eyespot in unicellular microorganisms, navigation to the light source in a three-dimensional world entails a specific control mechanism. The mechanism consists of detecting light direction by comparing light intensity while moving on a helical path and then translating that information to motility apparatus such as flagella which consequently turns the microorganism towards the light source. We show that the response kinetics, i.e., dynamics of photo turn of a population of CR cells, depends on the cell concentration and light intensity. The response time is faster and independent of stimulus light intensity at low cell concentrations. In contrast, at high cell concentrations, the response is slower and depends non-monotonically on the light intensity. We show that such effects on the response kinetics originate from the coupling between swim speed and received photon flux.
Further, in the second part, we present the results on the recovery (orientational diffusion) of cells that have already achieved a steady state phototactic motion. The kinetics of orientational recovery of oriented cell population reveals a characteristic time independent of their cell concentration and light intensity. Finally, we extend our model of active Brownian particle subject to aligning torque to capture the time-dependent reorientation process.
These results demonstrate that cell populations modulate fundamental quantities such as phototactic efficiency and response time. Coupling between collective effects and external physio-chemical stimuli results in complex modulation of single-cell behavior in the dense suspension. We have elucidated a simple physical and phenomenological mechanism governing such complex collective behavior.Wellcome Trust/DBT India Alliance Fellowshi
Sculpting colloidal membranes through phase transformations
No full textShaping macroscopic 2-D thin elastic sheets through differential strains in the system is a widely studied phenomenon applicable in diverse areas such as flexible electronics, origami and tissue growth. In contrast, at the molecular scales of lipid bilayers and cell membranes which are classic examples of thin fluid sheets, external agents such as proteins typically modulate their curvature and shape. This thesis work designs new strategies, at the intermediate colloidal length scales, to shape model fluid membranes using internal phase transitions based on intrinsic interactions and physical properties of the constituent rod-like colloidal particles.
An isotropic mixture of highly monodispersed rod-like viruses spontaneously assemble into the membranes of aligned rods on the addition of non-adsorbing polymer through depletion attraction. The membranes are of one-rod-length thick and exhibit long wavelength thermal elastic fluctuations. The constituent virus rods are intrinsically chiral and thus trap a uniform chiral rod twist at the membrane edge. We utilize this intrinsic chiral interaction of the virus rods to shape the membranes into a three-dimensional globally buckled and locally wrinkled structures through crystallization. Moreover, we demonstrate that the surface roughness of a crystalline membrane can be tuned with the number of nucleation centers.
The finite line tension of the membrane edge causes the membrane to have circular geometry. However, on the introduction of another rod having similar handedness in chirality but different aspect ratio shapes the membranes into an implausible geometry of cyclic polygon. We show that the origin of this anisotropic shape lies in the spreading phenomenon of a colloidal membrane of short-thick rods over another membrane composed of purely long rods in the presence of disorder. The pinning junctions that form the cornerstones of this membrane geometry are the location of compressed defective rods which are weakly cross-linked in nature instead of being topological defects. In another scenario, a binary mixture of two virus rods of similar length with opposite chirality and significantly different rigidity self-assembles into colloidal membranes containing finite sized solid anisotropic colloidal rafts in their bulk on the addition of non-adsorbing polymer. The nature and morphology of these anisotropic rafts are entirely dependent on the kinetics of phase separation and concentration of the depletant polymer. Remarkably, we demonstrate unique assembly conditions that enable access to different regimes of the phase separation in a single sample chamber.
Lastly, we use the knowledge gathered from the core part of the thesis work to assemble colloidal membranes with rafts mimicking Pickering emulsions in appearance using a ternary mixture of virus rods. We discovered the presence of weak repulsive forces between these rafts, which switch to attractive in the absence of the rods that form its inner core. The results in this thesis work demonstrate various self-assembly conditions to sculpt the colloidal membranes into different morphologies through its associated phase transformations
Role of Friction in Microswimmer and Active Filament Motion
No full textFriction is pervasive in all fields of science. It is the key factor that emerging technologies involving autonomous motion at micron scales such as micro-bots need to overcome in order to be efficient. They fall in the new paradigm of active matter which in its scope also covers the biological world. In this talk, I will present my thesis work on the role of frictional stresses in the motion of two model biological systems: (a) a microswimmer, Chlamydomonas which swims through the fluid by using the motion of its two anterior flagella/cilia, and (b) an active filament, the cell-free isolated cilium from the same microswimmer and reactivated in the presence of an external energy source. These prototypical active systems, driven by oscillatory motion of the cilia, generate fluid motion at the micron-scale. Naturally, these systems operating in low Reynolds number regime are expected to be governed by the ambient fluid friction. We, therefore, explore the role of hydrodynamics and other sources of friction, if any, in these model systems through simultaneous measurements of their motion and flow fields. In the first part of my thesis, I discuss the role of confinement in coupling cell motility and fluid flow of the microswimmer. Extreme confinement of this swimmer between rigid boundaries often arises in natural and technological contexts, yet measurements of its mechanics in this regime are absent. We show that strongly confining Chlamydomonas between two parallel plates not only inhibits its motility but also leads, for purely mechanical reasons, to inversion of the surrounding vortex flows due to contact friction with the walls. This contrasts with expectations based on the source-dipole description of confined swimmers. Insights from the experiment lead to a simplified theoretical description of flow fields based on a quasi-2D Brinkman approximation to the Stokes equation than the usual method of recursive images. We argue that this vortex flow inversion provides the advantage of enhanced fluid mixing despite higher friction. In the second part of the thesis, I study the mechanics of the active cilium which undergoes spontaneous oscillations by continuously consuming chemical energy and dissipating them through mechanical motion. Therefore, stable oscillations require that the elastic stresses due to the active energy input must be balanced by a significant source of dissipation. Conventionally, it stems from the external fluid. We show, in contrast, that external fluid friction is negligibly small to counteract the passive elastic stresses within the isolated and active Chlamydomonas cilium beating near the instability threshold. Consequently, internal friction emerges as the sole source of dissipation for ciliary oscillations. We combine these experimental insights with theoretical modeling of active filaments to show that an instability to oscillations takes place when active stresses are strain softening and shear thinning. Together, these results demonstrate that it is not always the external fluid friction, but friction from the external boundaries as well as internal degrees of freedom, which govern confined microswimmer motion and active ciliary oscillations, respectively
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
- …
