On the effect of fluid-structure interactions and choice of algorithm in multi-physics topology optimisation

This article presents an optimisation framework for the compliance minimisation of structures subjected to design-dependent pressure loads. A finite element solver coupled to a Lattice Boltzmann method is employed, such that the effect of the fluid-structure interactions on the optimised design can be considered. It is noted that the main computational expense of the algorithm is the Lattice Boltzmann method. Therefore, to improve the computational efficiency and to assess the effect of the fluid-structure interactions on the fi nal optimised design, the degree of coupling is changed. Several successful topology optimisation algorithms exist with thousands of associated publications in the literature. However, only a small portion of these are applied to real-world problems, with even fewer offering a comparison of methodologies. This is especially important for problems involving fluid-structure interactions, where discrete and continuous methods can provide different advantages. The goal of this research is to couple two key disciplines, fluids and structures, into a topology optimisation framework, which shows fast convergence for multi-physics optimisation problems. This is achieved by offering a comparison of three popular, but competing, optimisation methodologies. The needs for the exploration of larger design spaces and to produce innovative designs make meta-heuristic algorithms less efficient for this task. A coupled analysis, where the fluid and structural mechanics are updated, provides superior results compared with an uncoupled analysis approach, however at some computational expense. The results in this article show that the method is sensitive to whether fluid-structure coupling is included, i.e. if the fluid mechanics are updated with design changes, but not to the degree of the coupling, i.e. how regularly the fluid mechanics are updated, up to a certain limit. Therefore, the computational efficiency of the algorithm can be considerably increased with small penalties in the quality of the objective by relaxing the coupling

Topology optimisation of micro fluidic mixers considering fluid-structure interactions with a coupled Lattice Boltzmann algorithm

Recently, the study of micro fluidic devices has gained much interest in various fi elds from biology to engineering. In the constant development cycle, the need to optimise the topology of the interior of these devices, where there are two or more optimality criteria, is always present. In this work, twin physical situations, whereby optimal fluid mixing in the form of vorticity maximisation is accompanied by the requirement that the casing in which the mixing takes place has the best structural performance in terms of the greatest speci c stiffness, are considered. In the steady state of mixing this also means that the stresses in the casing are as uniform as possible, thus giving a desired operating life with minimum weight. The ultimate aim of this research is to couple two key disciplines, fluids and structures, into a topology optimisation framework, which shows fast convergence for multidisciplinary optimisation problems. This is achieved by developing a bi-directional evolutionary structural optimisation algorithm that is directly coupled to the Lattice Boltzmann method, used for simulating the flow in the micro fluidic device, for the objectives of minimum compliance and maximum vorticity. The needs for the exploration of larger design spaces and to produce innovative designs make meta-heuristic algorithms, such as genetic algorithms, particle swarms and Tabu Searches, less efficient for this task. The multidisciplinary topology optimisation framework presented in this article is shown to increase the stiffness of the structure from the datum case and produce physically acceptable designs. Furthermore, the topology optimisation method outperforms a Tabu Search algorithm in designing the baffle to maximise the mixing of the two fluids

Multiobjective and multi-physics topology optimization using an updated smart normal constraint bi-directional evolutionary structural optimization method

To date the design of structures using topology optimization methods has mainly focused on single-objective problems. Since real-world design problems typically involve several different objectives, most of which counteract each other, it is desirable to present the designer with a set of Pareto optimal solutions that capture the trade-off between these objectives, known as a smart Pareto set. Thus far only the weighted sums and global criterion methods have been incorporated into topology optimization problems. Such methods are unable to produce evenly distributed smart Pareto sets. However, recently the smart normal constraint method has been shown to be capable of directly generating smart Pareto sets. Therefore, in the present work, an updated smart Normal Constraint Method is combined with a Bi-directional Evolutionary Structural Optimization (SNC-BESO) algorithm to produce smart Pareto sets for multiobjective topology optimization problems. Two examples are presented, showing that the Pareto solutions found by the SNC-BESO method make up a smart Pareto set. The first example, taken from the literature, shows the benefits of the SNC-BESO method. The second example is an industrial design problem for a micro fluidic mixer. Thus, the problem is multi-physics as well as multiobjective, highlighting the applicability of such methods to real-world problems. The results indicate that the method is capable of producing smart Pareto sets to industrial problems in an effective and efficient manner.D.J. Munk thanks the Australian government for their financial support through the Endeavour Fellowship scheme

Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments

Peer reviewedPublisher PD

A computational framework to emulate the human perspective in flow cytometric data analysis

Background: In recent years, intense research efforts have focused on developing methods for automated flow cytometric data analysis. However, while designing such applications, little or no attention has been paid to the human perspective that is absolutely central to the manual gating process of identifying and characterizing cell populations. In particular, the assumption of many common techniques that cell populations could be modeled reliably with pre-specified distributions may not hold true in real-life samples, which can have populations of arbitrary shapes and considerable inter-sample variation. <p/>Results: To address this, we developed a new framework flowScape for emulating certain key aspects of the human perspective in analyzing flow data, which we implemented in multiple steps. First, flowScape begins with creating a mathematically rigorous map of the high-dimensional flow data landscape based on dense and sparse regions defined by relative concentrations of events around modes. In the second step, these modal clusters are connected with a global hierarchical structure. This representation allows flowScape to perform ridgeline analysis for both traversing the landscape and isolating cell populations at different levels of resolution. Finally, we extended manual gating with a new capacity for constructing templates that can identify target populations in terms of their relative parameters, as opposed to the more commonly used absolute or physical parameters. This allows flowScape to apply such templates in batch mode for detecting the corresponding populations in a flexible, sample-specific manner. We also demonstrated different applications of our framework to flow data analysis and show its superiority over other analytical methods. <p/>Conclusions: The human perspective, built on top of intuition and experience, is a very important component of flow cytometric data analysis. By emulating some of its approaches and extending these with automation and rigor, flowScape provides a flexible and robust framework for computational cytomics

Read-through Activation of Transcription in a Cellular Genomic Context

Read-through transcription from the adjacent E1a gene region is required for wild-type (wt) activity of the downstream adenovirus E1b promoter early after infection (read-through activation). However, whether a cellular chromosomal template can support read-through activation is not known. To address this issue, read-through activation was evaluated in the context of stably expressed templates in transfected cells. Inhibition of read-through transcription by insertion of a transcription termination sequence between the E1a and E1b promoters reduced downstream gene expression from stably integrated templates. The results indicate that the mechanism of read-through activation does not depend on the structure of early adenovirus nucleoprotein complexes, a structure that is likely to be different from that of cellular chromatin. Accordingly, this regulatory interaction could participate in the coordinated control of the expression of closely linked cellular genes

S021-04 OA. A large-scale analysis of immunoglobulin sequences derived from plasmablasts/plasma cells in acute HIV-1 infection subjects

Background In acute HIV-1 infection (AHI) there are infectioninduced polyclonal shifts in blood and bone marrow Bcell subsets from naïve to memory cells and plasmablasts/ plasma cells (PCs) coupled with decreased numbers of naive B cells. To study the initial antibody response to HIV, we have used recombinant technology to create a database of PC antibody sequences derived from 3 early stage AHI subjects

Testing for differential abundance in mass cytometry data.

When comparing biological conditions using mass cytometry data, a key challenge is to identify cellular populations that change in abundance. Here, we present a computational strategy for detecting 'differentially abundant' populations by assigning cells to hyperspheres, testing for significant differences between conditions and controlling the spatial false discovery rate. Our method (http://bioconductor.org/packages/cydar) outperforms other approaches in simulations and finds novel patterns of differential abundance in real data.This work was supported by Cancer Research UK (core funding to J.C.M., award no. A17197), the University of Cambridge and Hutchison Whampoa Limited. J.C.M. was also supported by core funding from EMBL