Deterministic Symmetry Breaking in Ring Networks

We study a distributed coordination mechanism for uniform agents located on a circle. The agents perform their actions in synchronised rounds. At the beginning of each round an agent chooses the direction of its movement from clockwise, anticlockwise, or idle, and moves at unit speed during this round. Agents are not allowed to overpass, i.e., when an agent collides with another it instantly starts moving with the same speed in the opposite direction (without exchanging any information with the other agent). However, at the end of each round each agent has access to limited information regarding its trajectory of movement during this round. We assume that $n$ mobile agents are initially located on a circle unit circumference at arbitrary but distinct positions unknown to other agents. The agents are equipped with unique identifiers from a fixed range. The {\em location discovery} task to be performed by each agent is to determine the initial position of every other agent. Our main result states that, if the only available information about movement in a round is limited to %information about distance between the initial and the final position, then there is a superlinear lower bound on time needed to solve the location discovery problem. Interestingly, this result corresponds to a combinatorial symmetry breaking problem, which might be of independent interest. If, on the other hand, an agent has access to the distance to its first collision with another agent in a round, we design an asymptotically efficient and close to optimal solution for the location discovery problem.Comment: Conference version accepted to ICDCS 201

Path Integral Molecular Dynamics of Liquid Water in a Mean-Field Particle Reservoir

We present a simulation scheme for path integral simulation of molecular liquids where a small open region is embedded in a large reservoir of non interacting point-particles. The scheme is based on the latest development of the adaptive resolution technique AdResS and allows for the space-dependent change of molecular resolution from a path integral representation with 120 degrees of freedom to a point particle that does not interact with other molecules and vice versa. The method is applied to liquid water and implies a sizable gain regarding the request of computational resources compared to full path integral simulations. Given the role of water as universal solvent with a specific hydrogen bonding network, the path integral treatment of water molecules is important to describe the quantum effects of hydrogen atoms’ delocalization in space on the hydrogen bonding network. The method presented here implies feasible computational efforts compared to full path integral simulations of liquid water which, on large scales, are often prohibitive

Coarse-grained models for self-assembling systems

In the last years, a considerable deal of work has so far been spent to understand and hence harness the physical principles that underpin the general properties of self-assembling systems. In particular, theoretical and computational modelling have been extensively used to obtain a detailed description of the actual process. This thesis reports on computational work, focusing on two different self-assembling systems and from two distinct perspectives. In the first part, a computational study of the self-assembly of string-like rigid templates in solution aims to explore to what extent it is possible to direct the assembly of the templates into knotted or linked structures by suitably tuning geometrical parameters of the system. The second part is devoted to some of the smallest instances of molecular self-assembly in nature, that is viral capsids. We report on the development of a physics-based algorithm to subdivide the structure of a capsid in quasi-rigid units, helping to elucidate the pathway of assembly from the identification of its building blocks with a top-down approach

Simulating rare events using a Weighted Ensemble-based string method

We introduce an extension to the Weighted Ensemble (WE) path sampling method to restrict sampling to a one dimensional path through a high dimensional phase space. Our method, which is based on the finite-temperature string method, permits efficient sampling of both equilibrium and non-equilibrium systems. Sampling obtained from the WE method guides the adaptive refinement of a Voronoi tessellation of order parameter space, whose generating points, upon convergence, coincide with the principle reaction pathway. We demonstrate the application of this method to several simple, two-dimensional models of driven Brownian motion and to the conformational change of the nitrogen regulatory protein C receiver domain using an elastic network model. The simplicity of the two-dimensional models allows us to directly compare the efficiency of the WE method to conventional brute force simulations and other path sampling algorithms, while the example of protein conformational change demonstrates how the method can be used to efficiently study transitions in the space of many collective variables

PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution

Live-cell imaging by light microscopy has demonstrated that all cells are spatially and temporally organized. Quantitative, computational image analysis is an important part of cellular imaging, providing both enriched information about individual cell properties and the ability to analyze large datasets. However, such studies are often limited by the small size and variable shape of objects of interest. Here, we address two outstanding problems in bacterial cell division by developing a generally applicable, standardized, and modular software suite termed Projected System of Internal Coordinates from Interpolated Contours (PSICIC) that solves common problems in image quantitation. PSICIC implements interpolated-contour analysis for accurate and precise determination of cell borders and automatically generates internal coordinate systems that are superimposable regardless of cell geometry. We have used PSICIC to establish that the cell-fate determinant, SpoIIE, is asymmetrically localized during Bacillus subtilis sporulation, thereby demonstrating the ability of PSICIC to discern protein localization features at sub-pixel scales. We also used PSICIC to examine the accuracy of cell division in Esherichia coli and found a new role for the Min system in regulating division-site placement throughout the cell length, but only prior to the initiation of cell constriction. These results extend our understanding of the regulation of both asymmetry and accuracy in bacterial division while demonstrating the general applicability of PSICIC as a computational approach for quantitative, high-throughput analysis of cellular images

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology

Development of small-scale fluidised bed bioreactor for 3D cell culture

Three-dimensional cell culture has gained significant importance by producing physiologically relevant in vitro models with complex cell-cell and cell-matrix interactions. However, current constructs lack vasculature, efficient mass transport and tend to reproduce static or short-term conditions. The work presented aimed to design a benchtop fluidised bed bioreactor (sFBB) for hydrogel encapsulated cells to generate perfusion for homogenous diffusion of nutrients and, host substantial biomass for long-term evolution of tissue-like structures and “per cell” performance analysis. The sFBB induced consistent fluidisation of hydrogel spheres while maintaining their shape and integrity. Moreover, this system expanded into a multiple parallel units’ setup with equivalent performances enabling simultaneous comparisons. Long term culture of alginate encapsulated hepatoblastoma cells under dynamic environment led to proliferation of highly viable cell spheroids with a 2-fold increase in cellular density over static (27.3 vs 13.4 million cells/mL beads). Upregulation of hepatic phenotype markers (transcription factor C/EBP-α and drug-metabolism CYP3A4) was observed from an early stage in dynamic culture. This environment also affected ERK1/2 signalling pathway, progressively reducing its activation while increasing it in static conditions. Furthermore, culture of primary human mesenchymal stem cells was evaluated. Cell proliferation was not observed but continuous perfusion sustained their viability and undifferentiated phenotype, enabling differentiation into chondrogenic and adipogenic lineages after de-encapsulation. These biological readouts validated the sFBB as a robust dynamic platform and the prototype design was optimised using computer-aided design and computational fluid dynamics, followed by experimental tests. This thesis proved that dynamic environment promoted by fluidisation sustains biomass viability in long-term cell culture and leads 3D cell constructs with physiologically relevant phenotype. Therefore, this bioreactor would constitute a simple and versatile tool to generate in vitro tissue models and test their response to different agents, potentially increasing the complexity of the system by modifying the scaffold or co-culturing relevant cell types