GPU Parallel Computation of Morse-Smale Complexes

The Morse-Smale complex is a well studied topological structure that represents the gradient flow behavior of a scalar function. It supports multi-scale topological analysis and visualization of large scientific data. Its computation poses significant algorithmic challenges when considering large scale data and increased feature complexity. Several parallel algorithms have been proposed towards the fast computation of the 3D Morse-Smale complex. The non-trivial structure of the saddle-saddle connections are not amenable to parallel computation. This paper describes a fine grained parallel method for computing the Morse-Smale complex that is implemented on a GPU. The saddle-saddle reachability is first determined via a transformation into a sequence of vector operations followed by the path traversal, which is achieved via a sequence of matrix operations. Computational experiments show that the method achieves up to 7x speedup over current shared memory implementations

Soft matter roadmap

Soft materials are usually defined as materials made of mesoscopic entities, often self-organised, sensitive to thermal fluctuations and to weak perturbations. Archetypal examples are colloids, polymers, amphiphiles, liquid crystals, foams. The importance of soft materials in everyday commodity products, as well as in technological applications, is enormous, and controlling or improving their properties is the focus of many efforts. From a fundamental perspective, the possibility of manipulating soft material properties, by tuning interactions between constituents and by applying external perturbations, gives rise to an almost unlimited variety in physical properties. Together with the relative ease to observe and characterise them, this renders soft matter systems powerful model systems to investigate statistical physics phenomena, many of them relevant as well to hard condensed matter systems. Understanding the emerging properties from mesoscale constituents still poses enormous challenges, which have stimulated a wealth of new experimental approaches, including the synthesis of new systems with, e.g. tailored self-assembling properties, or novel experimental techniques in imaging, scattering or rheology. Theoretical and numerical methods, and coarse-grained models, have become central to predict physical properties of soft materials, while computational approaches that also use machine learning tools are playing a progressively major role in many investigations. This Roadmap intends to give a broad overview of recent and possible future activities in the field of soft materials, with experts covering various developments and challenges in material synthesis and characterisation, instrumental, simulation and theoretical methods as well as general concepts

Microfluidic methods for single cell analysis in clinically relevant samples

Single cell protein analysis has the potential to comprehensively profile cellular heterogeneity advancing the understanding of cell function, disease progression and drug development. Although it is a possible contributor to the discovery of novel therapy, the protein mapping on the individual cell basis is complex and poses challenges. For example, cancer is a heterogeneous disease which analysis using conventional bulk methods can potentially conceal a dangerous population like Circulating Tumour Cells (CTCs). Analysis of CTCs can only be reliably attained using single cell technologies. The Microfluidic Affinity Capture (MAC) chip is a tool that was developed in our group to study cellular heterogeneity by measuring protein abundance in single cells. Another problem in analysing cancer cells is the difficulty in obtaining samples in a non-invasive manner. This thesis reports on attempts to obtain, concentrate and analyse CTCs from blood using a composite MAC-based device. The ability to analyse single cells has advantages beyond the potential for analysing heterogeneity. Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous illness that is characterised by a chronic inflammation. Although the immune response in COPD requires investigation, it is complicated by a lack of biomarkers and methods to non-invasively collect samples. The ability to obtain and effectively analyse precious and scarce biomaterial from lungs, is greatly advantageous for both diagnosis and tracking of COPD. Here, we report on a workflow to achieve this using sputum from negative control volunteers and COPD+ patients. Also, we describe the establishment of a novel MAC chip assay targeting FOXO3 protein which is involved in regulation of processes like tumour suppression, inflammation and senescence. Therefore, it has a biomarker potential to monitor and study diseases like cancer and COPD. We developed the protocol to analyse Forkhead box 3 (FOXO3) protein expression in nasal cells from healthy donor samples that were retrieved with a non-invasive tool (NASAM, nasal synthetic absorptive matrix). Nasal cavity is a front line of exposure to inhaled pernicious substances and, it is speculated to reflect anomalous bioprocesses in lungs preceding respiratory disease development and progression. This study provides the first-time quantification of FOXO3 protein in single cells from nasal samples. This work shows the analytical capacity of the MAC chip to study cellular heterogeneity and quantify important biomarkers in single cells of clinically relevant material.Open Acces

A Status of NASA Rotorcraft Research

In 2006, NASA rotorcraft research was refocused to emphasize high-fidelity first-principles predictive tool development and validation. As part of this new emphasis, documenting the status of NASA rotorcraft research and defining the state-of-the-art in rotorcraft predictive capability were undertaken. This report is the result of this two-year effort. Contributors to this work encompass a wide range of expertise covering the technical disciplines of aeromechanics, acoustics, computational fluid dynamics (CFD), flight dynamics and control, experimental capabilities, propulsion, structures and materials, and multi-disciplinary analysis

Discontinuous Fiber Composites, Volume II

Discontinuous fiber-reinforced polymers have gained importance in transportation industries due to their outstanding material properties, lower manufacturing costs and superior lightweight characteristics. One of the most attractive attributes of discontinuous fiber-reinforced composites is the ease with which they can be manufactured in large numbers, using injection and compression molding processes. The main aim of this Special Issue is to collect various investigations focused on the processing of discontinuous fiber-reinforced composites and the effect that processing has on fiber orientation, fiber length and fiber density distributions throughout the final product. Papers presenting investigations on the effect that fiber configurations have on the mechanical properties of the final composite products and materials were welcome in the Special Issue. Researchers who model and simulate processes involving discontinuous fiber composites as well as those performing experimental studies involving these composites were welcomed to submit papers. The authors were encouraged to present new models, constitutive laws, and measuring and monitoring techniques to provide a complete framework on these groundbreaking materials and to facilitate their use in different engineering applications

Chemomechanics of attached and suspended cells

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2012.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student submitted PDF version of thesis.Includes bibliographical references (p. 173-184).Chemomechanical coupling in single eukaryotic animal cells is investigated in the con- text of the attached (substratum-adhered) and the suspended (free-floating) states. These dichotomous configurations determine behavioral differences and commonalities relevant to therapeutic reimplantation of stem cells and to our general under- standing of the cell as an animate material. Analytical, simulation, and experimental techniques are applied to key questions including: (1) How deep can mechanosensitive attached cells "feel" into the adjacent environment? (2) In what manner do suspended cells deform, absent the prominent actomyosin stress fibers that arise upon attachment to a rigid substratum? (3) What explains the remarkable mechanical heterogeney among single cells within a population? (4) Can we leverage putative mechanical markers of useful stem cells to sort them before reimplantation in tissue generation therapies? Attached cells are found to barely detect an underlying rigid base more than 10 micrometers below the surface of a compliant coating. This conclusion, based on ex- tensions to the Boussinesq problem of elasticity theory, is validated by observations of cell morphology on compliant polyacrylamide coatings in a range of thicknesses. Analytical equations are developed for estimating the effective stiffness sensed by a cell atop a compliant layer. We also identify and consider conceptualizations of a "critical thickness," representing the minimum suitable thickness for a specific application. This parameter depends on the cell behavior of interest; the particular case of stem cell culture for paracrine extraction is presented as a case study. Suspended cells are found to exhibit no single characteristic time scale during de- formation; rather, they behave as power-law (or "soft glassy") materials. Here, optical stretching is used as a non-contact technique to show that stress fibers and probe-cell contact are not critical in enabling power-law rheological behavior of cells. Further- more, suspended cell fluidity, as characterized by both the hysteresivity of complex modulus and the power-law exponent of creep compliance, is found to be unaffected by adenosine triphosphate (ATP) depletion, showing that ATP hydrolysis is not the origin of fluidity in cells during deformation. However, ATP depletion does reduce the natural variation in hysteresivity values among cells. This finding, and the finding that changes in the power-law exponent and stiffness of single cells are correlated upon repeated loading, motivates study of how and why these parameters are coupled. To further explore this coupling, chemomechanical cues are applied to cell populations to elucidate the origin of the wide, right-skewed distribution of stiffness values that is consistently observed. The distribution and width are found to be not detectably dependent on cell-probe contact, cell lineage, cell cycle, mechanical perturbation, or fixation by chemical crosslinking. However, ATP depletion again reduces heterogeneity, now in the case of cell stiffness values. It is further found analytically that a postulated Gaussian distribution of power-law exponent values leads naturally to the log-normal distribution of cell stiffness values that is widely observed. Based on these connections, a framework is presented to improve our understanding of the appearance of mechanical heterogeneity in successively more complex assemblies of cell components. Two case studies are described to explore the implications of unavoidable intrinsic variation of cell stiffness in diagnostic and therapeutic applications. Finally, all the single-cell mechanical parameters studied so far (stiffness during creep and recovery, stiffness heterogeneity among cells, and power-law exponents in creep and recovery) are characterized in mesenchymal stem cells during twenty population doublings with the aim of developing a high-throughput sorting tool. How- ever, mechanical and structural changes that are observed in the attached state during this culture time are not observed after cell detachment from the substratum. The absence in the suspended state of these alterations indicates that they manifest themselves through stress fiber arrangement rather than cortical network arrangement. While optical stretching under the present approach does not detect mechanical markers of extended passaging that are correlated with decreased differentiation propensity, the technique is nevertheless found capable of investigating another structural transition: mechanical stiffening over tens of minutes after adherent cells are suspended. This previously unquantified transition is correlated with membrane resorption and reattachment to the cortex as the cell "remodels" after substratum detachment. Together, these quantitative studies and models of attached and suspended cells de- fine the extremes of the extracellular environment while probing mechanisms that con- tribute to cellular chemomechanical response. An integration of the results described above shows that no one existing model can describe cell chemomechanics. However, the cell can be usefully described as a material -- one in which animate mechanisms such as active contraction will generally, but not invariably, need to be considered as augmenting existing viscoelastic theories of inanimate matter.by John Mapes Maloney.Ph.D