Numerical simulation of solid deformation driven by creeping flow using an immersed finite element method

An immersed finite element method for solid–fluid interaction is presented with application focus on highly deformable elastic bodies in a Stokes flow environment. The method is based on a global balance equation which combines the solid and fluid momentum balances, the fluid mass balance and, in weak form, the interface conditions. By means of an Updated Lagrangian description for finite elasticity, only one analysis mesh is used, where the solid particles are backtracked in order to preserve the deformation history. The method results in a full coupling of the solid-fluid system which is solved by an exact Newton method. The location of the material interface is captured by a signed distance function and updated according to the computed displacement increments and the help of an explicit surface parameterisation; no body-fitted volume meshes are needed. Special emphasis is placed on the accurate integration of finite elements traversed by the interface and the related numerical stability of the shape function basis. A number of applications for compressible Neo-Hookean solids subject to creeping flow are presented, motivated by microfluidic experimentation in mechanobiology

An unstructured immersed finite element method for nonlinear solid mechanics.

We present an immersed finite element technique for boundary-value and interface problems from nonlinear solid mechanics. Its key features are the implicit representation of domain boundaries and interfaces, the use of Nitsche's method for the incorporation of boundary conditions, accurate numerical integration based on marching tetrahedrons and cut-element stabilisation by means of extrapolation. For discretisation structured and unstructured background meshes with Lagrange basis functions are considered. We show numerically and analytically that the introduced cut-element stabilisation technique provides an effective bound on the size of the Nitsche parameters and, in turn, leads to well-conditioned system matrices. In addition, we introduce a novel approach for representing and analysing geometries with sharp features (edges and corners) using an implicit geometry representation. This allows the computation of typical engineering parts composed of solid primitives without the need of boundary-fitted meshes.This work was partially supported by the EPSRC (second author, Grant #EP/G008531/1), by the European Research Council (third author, Grant #ERC-2012-StG 306751), and by the Spanish Ministry of Economy and Competitiveness (third author, Grant #DPI2015-64221-C2-1-R).This is the final version of the article. It first appeared from Springer at http://dx.doi.org/10.1186/s40323-016-0077-5

Electromagnetic Devices with Moving Parts—Simulation with FEM/BEM Coupling

The numerical analysis of electromagnetic devices by means of finite element methods (FEM) is often hindered by the need to incorporate the surrounding domain. The discretisation of the air may become complex and has to be truncated by artificial boundaries incurring a modelling error. Even more problematic are moving parts that require tedious re-meshing and mapping techniques. In this work, we tackle these problems by using the boundary element method (BEM) in conjunction with FEM. Whereas the solid parts of the electrical device are discretised by FEM, which can easily account for material non-linearities, the surrounding domain is represented by BEM, which requires only a surface discretisation. This approach completely avoids an air mesh and its re-meshing during the simulation with moving or deforming parts. Our approach is robust, shows optimal complexity, and provides an accurate calculation of electromagnetic forces that are required to study the mechanical behaviour of the device

MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors

Many critical advances in research utilize techniques that combine high-resolution with high-content characterization at the single cell level. We introduce the MICS (MACSima Imaging Cyclic Staining) technology, which enables the immunofluorescent imaging of hundreds of protein targets across a single specimen at subcellular resolution. MICS is based on cycles of staining, imaging, and erasure, using photobleaching of fluorescent labels of recombinant antibodies (REAfinity Antibodies), or release of antibodies (REAlease Antibodies) or their labels (REAdye_lease Antibodies). Multimarker analysis can identify potential targets for immune therapy against solid tumors. With MICS we analysed human glioblastoma, ovarian and pancreatic carcinoma, and 16 healthy tissues, identifying the pair EPCAM/THY1 as a potential target for chimeric antigen receptor (CAR) T cell therapy for ovarian carcinoma. Using an Adapter CAR T cell approach, we show selective killing of cells only if both markers are expressed. MICS represents a new high-content microscopy methodology widely applicable for personalized medicine

Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study

MicroRNAs are important negative regulators of protein-coding gene expression and have been studied intensively over the past years. Several measurement platforms have been developed to determine relative miRNA abundance in biological samples using different technologies such as small RNA sequencing, reverse transcription quantitative PCR (RT-qPCR) and (microarray) hybridization. In this study, we systematically compared 12 commercially available platforms for analysis of microRNA expression. We measured an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples and synthetic spikes from micro RNA family members with varying homology. We developed robust quality metrics to objectively assess platform performance in terms of reproducibility, sensitivity, accuracy, specificity and concordance of differential expression. The results indicate that each method has its strengths and weaknesses, which help to guide informed selection of a quantitative microRNA gene expression platform for particular study goals