Multi-behaviors coordination controller design with enzymatic numerical P systems for robots

Membrane computing models are parallel and distributed natural computing models. These models are often referred to as P systems. This paper proposes a novel multi-behaviors coordination controller model using enzymatic numerical P systems for autonomous mobile robots navigation in unknown environments. An environment classifier is constructed to identify different environment patterns in the maze-like environment and the multi-behavior coordination controller is constructed to coordinate the behaviors of the robots in different environments. Eleven sensory prototypes of local environments are presented to design the environment classifier, which needs to memorize only rough information , for solving the problems of poor obstacle clearance and sensor noise. A switching control strategy and multi-behaviors coordinator are developed without detailed environmental knowledge and heavy computation burden, for avoiding the local minimum traps or oscillation problems and adapt to the unknown environments. Also, a serial behaviors control law is constructed on the basis of Lyapunov stability theory aiming at the specialized environment, for realizing stable navigation and avoiding actuator saturation. Moreover, both environment classifier and multi-behavior coordination controller are amenable to the addition of new environment models or new behaviors due to the modularity of the hierarchical architecture of P systems. The simulation of wheeled mobile robots shows the effectiveness of this approach

QSpike tools: a generic framework for parallel batch preprocessing of extracellular neuronal signals recorded by substrate microelectrode arrays

Micro-Electrode Arrays (MEAs) have emerged as a mature technique to investigate brain (dys)functions in vivo and in in vitro animal models. Often referred to as “smart” Petri dishes, MEAs have demonstrated a great potential particularly for medium-throughput studies in vitro, both in academic and pharmaceutical industrial contexts. Enabling rapid comparison of ionic/pharmacological/genetic manipulations with control conditions, MEAs are employed to screen compounds by monitoring non-invasively the spontaneous and evoked neuronal electrical activity in longitudinal studies, with relatively inexpensive equipment. However, in order to acquire sufficient statistical significance, recordings last up to tens of minutes and generate large amount of raw data (e.g., 60 channels/MEA, 16 bits A/D conversion, 20 kHz sampling rate: approximately 8 GB/MEA,h uncompressed). Thus, when the experimental conditions to be tested are numerous, the availability of fast, standardized, and automated signal preprocessing becomes pivotal for any subsequent analysis and data archiving. To this aim, we developed an in-house cloud-computing system, named QSpike Tools, where CPU-intensive operations, required for preprocessing of each recorded channel (e.g., filtering, multi-unit activity detection, spike-sorting, etc.), are decomposed and batch-queued to a multi-core architecture or to a computers cluster. With the commercial availability of new and inexpensive high-density MEAs, we believe that disseminating QSpike Tools might facilitate its wide adoption and customization, and inspire the creation of community-supported cloud-computing facilities for MEAs users

A Comprehensive Study Of Esterification Of Free Fatty Acid To Biodiesel In a Simulated Moving Bed System

Simulated Moving Bed (SMB) systems are used for separations that are difficult using traditional separation techniques. Due to the advantage of adsorption-based chromatographic separation, SMB has shown promising application in petrochemical and sugar industries, and of late, for chiral drug separations. In recent years, the concept of integration of reaction and in-situ separation in a single unit has achieved considerable attention. The simulated moving bed reactor (SMBR) couples both these unit operations bringing down the operation costs while improving the process performance, particularly for products that require mild operating conditions. However, its application has been limited due to complexity of the SMBR process. Hence, to successfully implement a reaction in SMB, a detailed understanding of the design and operating conditions of the SMBR corresponding to that particular reaction process is necessary. Biodiesel has emerged has a viable alternative to petroleum-based diesel as a renewable energy source in recent years. Biodiesel can be produced by esterification of free fatty acids (present in large amounts in waste oil) with alcohol. The reaction is equilibrium-limited, and hence, to achieve high purity, additional purification steps increases the production cost. Therefore, combining reaction and separation in SMBR to produce high purity biodiesel is quite promising in terms of bringing down the production cost. In this work, the reversible esterification reaction of oleic acid with methanol catalyzed by Amberlyst 15 resin to form methyl oleate (biodiesel) in SMBR has been investigated both theoretically and experimentally. First, the adsorption and kinetic constants were determined for the biodiesel synthesis reaction by performing experiments in a single column packed with Amberlyst 15, which acts as both adsorbent and catalyst. Thereafter, a rigorous model was used to describe the dynamic behaviour of multi-column SMBR followed by experimental verification of the mathematical model. Sensitivity analysis is done to determine robustness of the model. Finally, a few simple multi-objective optimization problems were solved that included both existing and design-stage SMBRs using non-dominated sorting genetic algorithm (NSGA). Pareto-optimal solutions were obtained in both cases, and moreover, it was found that the performance of the SMBR could be improved significantly under optimal operating conditions

MANET: tracing evolution of protein architecture in metabolic networks

BACKGROUND: Cellular metabolism can be characterized by networks of enzymatic reactions and transport processes capable of supporting cellular life. Our aim is to find evolutionary patterns and processes embedded in the architecture and function of modern metabolism, using information derived from structural genomics. DESCRIPTION: The Molecular Ancestry Network (MANET) project traces evolution of protein architecture in biomolecular networks. We describe metabolic MANET, a database that links information in the Structural Classification of Proteins (SCOP), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and phylogenetic reconstructions depicting the evolution of protein fold architecture. Metabolic MANET literally 'paints' the ancestries of enzymes derived from rooted phylogenomic trees directly onto over one hundred metabolic subnetworks, enabling the study of evolutionary patterns at global and local levels. An initial analysis of painted subnetworks reveals widespread enzymatic recruitment and an early origin of amino acid metabolism. CONCLUSION: MANET maps evolutionary relationships directly and globally onto biological networks, and can generate and test hypotheses related to evolution of metabolism. We anticipate its use in the study of other networks, such as signaling and other protein-protein interaction networks

Frontiers of Membrane Computing: Open Problems and Research Topics

This is a list of open problems and research topics collected after the Twelfth Conference on Membrane Computing, CMC 2012 (Fontainebleau, France (23 - 26 August 2011), meant initially to be a working material for Tenth Brainstorming Week on Membrane Computing, Sevilla, Spain (January 30 - February 3, 2012). The result was circulated in several versions before the brainstorming and then modified according to the discussions held in Sevilla and according to the progresses made during the meeting. In the present form, the list gives an image about key research directions currently active in membrane computing

A centrifugal microfluidic platform for capturing, assaying and manipulation of beads and biological cells

Microfluidics is deemed a field with great opportunities, especially for applications in medical diagnostics. The vision is to miniaturize processes typically performed in a central clinical lab into small, simple to use devices - so called lab-on-a-chip (LOC) systems. A wide variety of concepts for liquid actuation have been developed, including pressure driven flow, electro-osmotic actuation or capillary driven methods. This work is based on the centrifugal platform (lab-on-a-disc). Fluid actuation is performed by the forces induced due to the rotation of the disc, thus eliminating the need for external pumps since only a spindle motor is necessary to rotate the disc and propel the liquids inside of the micro structures. Lab-on-a-disc systems are especially promising for point-of-care applications involving particles or cells due to the centrifugal force present in a rotating system. Capturing, assaying and identification of biological cells and microparticles are important operations for lab-on-a-disc platforms, and the focus of this work is to provide novel building blocks towards an integrated system for cell and particle based assays. As a main outcome of my work, a novel particle capturing and manipulation scheme on a centrifugal microfluidic platform has been developed. To capture particles (biological cells or micro-beads) I designed an array of V-shaped micro cups and characterized it. Particles sediment under stagnant flow conditions into the array where they are then mechanically trapped in spatially well-defined locations. Due to the absence of flow during the capturing process, i.e. particle sedimentation is driven by the artificial gravity field on the centrifugal platform, the capture efficiency of this approach is close to 100% which is notably higher than values reported for typical pressure driven systems. After capturing the particles, the surrounding medium can easily be exchanged to expose them to various conditions such as staining solutions or washing buffers, and thus perform assays on the captured particles. By scale matching the size of the capturing elements to the size of the particles, sharply peaked single occupancy can be achieved. Since all particles are arrayed in the same focal plane in spatially well defined locations, operations such as counting or fluorescent detection can be performed easily. The application of this platform to perform multiplexed bead-based immunoassays as well as the discrimination of various cell types based on intra cellular and membrane based markers using fluorescently tagged antibodies is demonstrated. Additionally, methods to manipulate captured particles either in batch mode or on an individual particle level have been developed and characterized. Batch release of captured particles is performed by a novel magnetic actuator which is solely controlled by the rotation frequency of the disc. Furthermore, the application of this actuator to rapidly mix liquids is shown. Manipulation of individual particles is performed using an optical tweezers setup which has been developed as part of this work. Additionally, this optical module also provides fluorescence detection capabilities. This is the first time that optical tweezers have been combined with a centrifugal microfluidic system. This work presents the core technology for an integrated centrifugal platform to perform cell and particle based assays for fundamental research as well as for point-of- care applications. The key outputs of my specific work are: 1. Design, fabrication and characterization of a novel particle capturing scheme on a centrifugal microfluidic platform (V-cups) with very high capture efficiency (close to 100%) and sharply peaked single occupancy (up to 99.7% single occupancy). 2. A novel rotation frequency controlled magnetic actuator for releasing captured particles as well as for rapidly mixing liquids has been developed, manufactured and characterized. 3. The V-cup platform has successfully been employed to capture cells and perform multi-step antibody staining assays for cell discrimination. 4. An optical tweezers setup has been built and integrated into a centrifugal teststand, and successful manipulation of individual particles trapped in the V-cup array is demonstrated

Droplet Microfluidics

Droplet microfluidics has dramatically developed in the past decade and has been established as a microfluidic technology that can translate into commercial products. Its rapid development and adoption have relied not only on an efficient stabilizing system (oil and surfactant), but also on a library of modules that can manipulate droplets at a high-throughput. Droplet microfluidics is a vibrant field that keeps evolving, with advances that span technology development and applications. Recent examples include innovative methods to generate droplets, to perform single-cell encapsulation, magnetic extraction, or sorting at an even higher throughput. The trend consists of improving parameters such as robustness, throughput, or ease of use. These developments rely on a firm understanding of the physics and chemistry involved in hydrodynamic flow at a small scale. Finally, droplet microfluidics has played a pivotal role in biological applications, such as single-cell genomics or high-throughput microbial screening, and chemical applications. This Special Issue will showcase all aspects of the exciting field of droplet microfluidics, including, but not limited to, technology development, applications, and open-source systems

Optimization of Chiral Separation of Nadolol by Simulated Moving Bed Technology

Simulated Moving Bed (SMB) technology has gained increasing attention as one of the most powerful techniques for chromatographic separations due to its cost-effectiveness and efficiency. Application of SMB technology is especially important in the pharmaceutical industry for production of enantiopure drugs, as required under strict FDA regulations, to avoid possible adverse effects of racemic drugs. In this study, the performance of the SMB process in separation of racemic nadolol on a perphenyl carbamoylated beta cyclodextrin (β-CD) stationary phase was investigated. The equilibrium dispersive model coupled with bi-Langmuir adsorption isotherm and lumped kinetic approximation, constitute the mathematical model used to simulate the dynamic behavior of SMB. Multi-objective optimization was carried out using a robust state-of-the-art optimization technique, non-dominated sorting genetic algorithm (NSGA). Two optimization problems were solved to simultaneously maximize productivity and purity of the product and minimize consumption of desorbent. The generated Pareto optimal solutions showed that selection of operating conditions can significantly affects the performance of SMB to meet the desired objectives

Genetic Analysis and Cell Manipulation on Microfluidic Surfaces

Personalized cancer medicine is a cancer care paradigm in which diagnostic and therapeutic strategies are customized for individual patients. Microsystems that are created by Micro-Electro-Mechanical Systems (MEMS) technology and integrate various diagnostic and therapeutic methods on a single chip hold great potential to enable personalized cancer medicine. Toward ultimate realization of such microsystems, this thesis focuses on developing critical functional building blocks that perform genetic variation identification (single-nucleotide polymorphism (SNP) genotyping) and specific, efficient and flexible cell manipulation on microfluidic surfaces. For the identification of genetic variations, we first present a bead-based approach to detect single-base mutations by performing single-base extension (SBE) of SNP specific primers on solid surfaces. Successful genotyping of the SNP on exon 1 of HBB gene demonstrates the potential of the device for simple, rapid, and accurate detection of SNPs. In addition, a multi-step solution-based approach, which integrates SBE with mass-tagged dideoxynucleotides and solid-phase purification of extension products, is also presented. Rapid, accurate and simultaneous detection of 4 loci on a synthetic template demonstrates the capability of multiplex genotyping with reduced consumption of samples and reagents. For cell manipulation, we first present a microfluidic device for cell purification with surface-immobilized aptamers, exploiting the strong temperature dependence of the affinity binding between aptamers and cells. Further, we demonstrate the feasibility of using aptamers to specifically separate target cells from a heterogeneous solution and employing environmental changes to retrieve purified cells. Moreover, spatially specific capture and selective temperature-mediated release of cells on design-specified areas is presented, which demonstrates the ability to establish cell arrays on pre-defined regions and to collect only specifically selected cell groups for downstream analysis. We also investigate tunable microfluidic trapping of cells by exploiting the large compliance of elastomers to create an array of cell-trapping microstructures, whose dimensions can be mechanically modulated by inducing uniform strain via the application of external force. Cell trapping under different strain modulations has been studied, and capture of a predetermined number of cells, from single cells to multiple cells, has been achieved. In addition, to address the lack of aptamers for targets of interest, which is a major hindrance to aptamer-based cell manipulation, we present a microfluidic device for synthetically isolating cell-targeting aptamers from a randomized single-strand DNA (ssDNA) library, integrating cell culturing with affinity selection and amplification of cell-binding ssDNA. Multi-round aptamer isolation on a single chip has also been realized by using pressure-driven flow. Finally, some perspectives on future work are presented, and strategies and notable issues are discussed for further development of MEMS/microfluidics-based devices for personalized cancer medicine