On the Nature and Shape of Tubulin Trails: Implications on Microtubule Self-Organization

Microtubules, major elements of the cell skeleton are, most of the time, well organized in vivo, but they can also show self-organizing behaviors in time and/or space in purified solutions in vitro. Theoretical studies and models based on the concepts of collective dynamics in complex systems, reaction-diffusion processes and emergent phenomena were proposed to explain some of these behaviors. In the particular case of microtubule spatial self-organization, it has been advanced that microtubules could behave like ants, self-organizing by 'talking to each other' by way of hypothetic (because never observed) concentrated chemical trails of tubulin that are expected to be released by their disassembling ends. Deterministic models based on this idea yielded indeed like-looking spatio-temporal self-organizing behaviors. Nevertheless the question remains of whether microscopic tubulin trails produced by individual or bundles of several microtubules are intense enough to allow microtubule self-organization at a macroscopic level. In the present work, by simulating the diffusion of tubulin in microtubule solutions at the microscopic scale, we measure the shape and intensity of tubulin trails and discuss about the assumption of microtubule self-organization due to the production of chemical trails by disassembling microtubules. We show that the tubulin trails produced by individual microtubules or small microtubule arrays are very weak and not elongated even at very high reactive rates. Although the variations of concentration due to such trails are not significant compared to natural fluctuations of the concentration of tubuline in the chemical environment, the study shows that heterogeneities of biochemical composition can form due to microtubule disassembly. They could become significant when produced by numerous microtubule ends located in the same place. Their possible formation could play a role in certain conditions of reaction. In particular, it gives a mesoscopic basis to explain the collective dynamics observed in excitable microtubule solutions showing the propagation of concentration waves of microtubules at the millimeter scale, although we doubt that individual microtubules or bundles can behave like molecular ants

Deterministic mechanical model of T-killer cell polarization reproduces the wandering of aim between simultaneously engaged targets

T-killer cells of the immune system eliminate virus-infected and tumorous cells through direct cell-cell interactions. Reorientation of the killing apparatus inside the T cell to the T-cell interface with the target cell ensures specificity of the immune response. The killing apparatus can also oscillate next to the cell-cell interface. When two target cells are engaged by the T cell simultaneously, the killing apparatus can oscillate between the two interface areas. This oscillation is one of the most striking examples of cell movements that give the microscopist an unmechanistic impression of the cell's fidgety indecision. We have constructed a three-dimensional, numerical biomechanical model of the molecular-motor-driven microtubule cytoskeleton that positions the killing apparatus. The model demonstrates that the cortical pulling mechanism is indeed capable of orienting the killing apparatus into the functional position under a range of conditions. The model also predicts experimentally testable limitations of this commonly hypothesized mechanism of T-cell polarization. After the reorientation, the numerical solution exhibits complex, multidirectional, multiperiodic, and sustained oscillations in the absence of any external guidance or stochasticity. These computational results demonstrate that the strikingly animate wandering of aim in T-killer cells has a purely mechanical and deterministic explanation. © 2009 Kim, Maly

Dynamics And Surface Forces Experienced By An Anisotropic Colloidal Particle Near A Boundary

Colloidal interactions play an important role in determining the macroscopic properties of different materials. Recent work in this area has focused on the role anisotropic particles play in these materials. This thesis summarizes work conducted on the dynamics and interactions of an anisotropic colloid particle near a solid wall. Specifically, the methodology for conducting Total Internal Reflection Microscopy (TIRM) on anisotropic colloidal systems near a boundary was developed. This new method is called “Scattering Morphology Resolved - TIRM” (SMR-TIRM). Simulations of the Brownian motion of a sphere comprising hemispheres of different composition (i.e. a Janus particle) very near a wall were conducted. Trajectories obtained from these simulations were used to construct 3D potential energy landscapes. Results showed that the potential energy landscape of a Janus sphere has a transition region at the location of the boundary between the two Janus halves, which depended on the relative zeta potential magnitude. In this thesis, an experimental technique for the direct and local measure of cap thickness of a coated Janus particle was summarized. It is found that the cap varied in thickness continuously along the perimeter ofthe particle. To better understand the impact ofthe coating on the dynamics of Janus particle, Brownian dynamics simulations to predict the translational and rotational fluctuations of a Janus sphere with a cap of non-matching density near a boundary was utilized. The simulation results show that the presence of the cap significantly impacts the rotational dynamics of the particle as a consequence of gravitational torque. vi In the last part of this thesis, the SMR-TIRM was used to map scattering from ellipsoid particles. The hypothesis driving this work was that evanescent wave scattering from an ellipsoidal particle depended on both the aspect ratio and orientation. Analysis of the light scattered from the particle showed that both ellipticity and directionality correlated with particle orientation and aspect ratio. In principle, these relationships will allow tracking of the particle’s position and orientation via the scattered light morphology

Hierarchical Coarse-Grained Strategy for Macromolecular Self-Assembly: Application to Hepatitis B Virus-Like Particles

Macromolecular self-assembly is at the basis of many phenomena in material and life sciences that find diverse applications in technology. One example is the formation of virus-like particles (VLPs) that act as stable empty capsids used for drug delivery or vaccine fabrication. Similarly to the capsid of a virus, VLPs are protein assemblies, but their structural formation, stability, and properties are not fully understood, especially as a function of the protein modifications. In this work, we present a data-driven modeling approach for capturing macromolecular self-assembly on scales beyond traditional molecular dynamics (MD), while preserving the chemical specificity. Each macromolecule is abstracted as an anisotropic object and high-dimensional models are formulated to describe interactions between molecules and with the solvent. For this, data-driven protein–protein interaction potentials are derived using a Kriging-based strategy, built on high-throughput MD simulations. Semi-automatic supervised learning is employed in a high performance computing environment and the resulting specialized force-fields enable a significant speed-up to the micrometer and millisecond scale, while maintaining high intermolecular detail. The reported generic framework is applied for the first time to capture the formation of hepatitis B VLPs from the smallest building unit, i.e., the dimer of the core protein HBcAg. Assembly pathways and kinetics are analyzed and compared to the available experimental observations. We demonstrate that VLP self-assembly phenomena and dependencies are now possible to be simulated. The method developed can be used for the parameterization of other macromolecules, enabling a molecular understanding of processes impossible to be attained with other theoretical models

Nanoscale Manipulation, Probing, and Assembly Using Microfluidic Flow Control

Nanoparticles have unique properties that can be beneficial in fields ranging from quantum information to biological sensing. To take advantage of some of some of these benefits, techniques are required that can select single particles and place them at desired locations with nanoscale precision. This capability allows for bottom-up assembly of nanoparticle systems and facilitates development of improved tools for probing nanoscale physics. Current manipulation approaches are inadequate for positioning nanoparticles such as single quantum dots. Quantum dots can act as single photon sources, and are useful for applications in nanophotonics and quantum optics. In this thesis, I present a technique for manipulation of single quantum dots and other nano-objects. Using this technique, I demonstrate nanoparticle manipulation, assembly, and probing with nanoscale precision. The nanomanipulation approach I introduce employs electroosmotic flow to position colloidal nanoparticles suspended in an aqueous system. Single quantum dot manipulation is demonstrated with a precision better than 50 nm for holding times of up to one hour. This technique is useful for studying the behavior of single quantum dots and their interactions with the environment in real time. A fluid chemistry was developed for the deterministic immobilization of nanoparticles along a two-dimensional surface with 130 nm precision. In addition, a technique for assembling systems of silver nanowires is demonstrated. A method for imaging the local density of optical states of silver nanowires is presented using single quantum dots as probes, achieving an imaging accuracy of 12 nm. Spontaneous emission control is accomplished simultaneously by placing the quantum dot at various locations along the wire. Together, these experiments illustrate the versatility of microfluidics for the advancement of nanoscience research and engineering

Large-Scale Galaxy Bias

This review presents a comprehensive overview of galaxy bias, that is, the statistical relation between the distribution of galaxies and matter. We focus on large scales where cosmic density fields are quasi-linear. On these scales, the clustering of galaxies can be described by a perturbative bias expansion, and the complicated physics of galaxy formation is absorbed by a finite set of coefficients of the expansion, called bias parameters. The review begins with a detailed derivation of this very important result, which forms the basis of the rigorous perturbative description of galaxy clustering, under the assumptions of General Relativity and Gaussian, adiabatic initial conditions. Key components of the bias expansion are all leading local gravitational observables, which include the matter density but also tidal fields and their time derivatives. We hence expand the definition of local bias to encompass all these contributions. This derivation is followed by a presentation of the peak-background split in its general form, which elucidates the physical meaning of the bias parameters, and a detailed description of the connection between bias parameters and galaxy statistics. We then review the excursion-set formalism and peak theory which provide predictions for the values of the bias parameters. In the remainder of the review, we consider the generalizations of galaxy bias required in the presence of various types of cosmological physics that go beyond pressureless matter with adiabatic, Gaussian initial conditions: primordial non-Gaussianity, massive neutrinos, baryon-CDM isocurvature perturbations, dark energy, and modified gravity. Finally, we discuss how the description of galaxy bias in the galaxies' rest frame is related to clustering statistics measured from the observed angular positions and redshifts in actual galaxy catalogs.Comment: 259 pages, 39 figures, 15 tables; published in Physics Reports; v2: minor corrections and clarifications, references added; v3: substantially revised and improved version; v4: minor edits and clarifications reflecting published version, corrected mistakes in Eqs. (7.57)-(7.58); v5: minor corrections [Eq. (5.5)] and updated reference