Element Library Research Articles

Synthetic Gene Circuits Enable Escherichia coli To Use Endogenous H2S as a Signaling Molecule for Quorum Sensing.

Microorganisms often use specific autoinducers other than common metabolites for quorum sensing (QS). Herein, we demonstrated that Escherichia coli produced sulfide (H2S, HS-, and S2-) with the concentrations proportionally correlated to its cell density. We then designed synthetic gene circuits that used H2S as an autoinducer for quorum sensing. A sulfide/quinone oxidoreductase converted diffusible H2S to indiffusible hydrogen polysulfide (HSnH, n ≥ 2), and a gene regulator CstR sensed the latter to turn on the gene expression. We constructed three element libraries, with which 24 different circuits could be assembled for adjustable sensitivity to cell density. The H2S-mediated gene circuits endowed E. coli cells within the same batch or microcolony with highly synchronous behaviors. Using them we successfully constructed cell factories capable of an autonomous switch from growth phase to production phase. Thus, these circuits provide a new tool-kit for metabolic engineering and synthetic biology.

Solving inverse electromagnetic scattering problems via domain derivatives††This paper is dedicated to the memory of our friend and colleague Armin Lechleiter.

We employ domain derivatives to solve inverse electromagnetic scattering problems for perfect conducting or for penetrable obstacles. Using a variational approach, the derivative of the scattered field with respect to boundary variations is characterized as the solution of a boundary value problem of the same type as the original scattering problem. The inverse scattering problem of reconstructing the scatterer from far field measurements for a single incident field can thus be solved via a regularized iterative Newton scheme. Both the original forward problem and the problem characterizing the domain derivative are formulated as boundary integral equations and we carefully describe how these formulations are obtained in the case of Lipschitz domains. The integral equations are solved using the boundary element library Bempp. A number of numerical examples of shape reconstructions are presented.

THREE-PHASE MATHEMATICAL MODEL OF THE PROCESS OF DEHYDRATION AND GRANULATION IN THE FLUIDIZED BED

A mathematical model is developed which takes into account the hydrodynamics of a fluidized bed, the contact of droplets with particles and their adhesion to the surface, as well as the kinetics of drying the solution on the surface of the particles. In developing the model, the following assumptions were made: the change in the parameters of the fluidized bed occurs in time, without taking into account the radial component and changes in height; heat exchange between air, particles and droplets is convective; particles are monodispersed, non-porous, agglomeration is absent. The intensity of the mixing of particles between the layers is described by the coefficient of the axial dispersion r, which depends on the velocity of the gas phase, as well as the properties of the particles. The droplets obtained with the pneumatic nozzle have a narrow size distribution, which allows them to be considered as a mono-dispersed phase. Between the drops there are no collisions and sticking, no sticking on the walls of the device. The droplets move through the fluidized bed, aligned with the air flow. When creating the model, the process of dehydration and granulation in the fluidized bed is considered as a heterogeneous three-phase process, during which they interact with three separate phases: the particles are the centers of granulation, the source material is ammonium sulfate in the form of droplets and the carrier - air. The system of equations is designed taking into account the empirical correlations for calculating the specific drying rate, the specific speed of droplet settling on the particles as a result of adhesion, the coefficient of the axial dispersion of the particles, the coefficients of heat transfer, the ratios for calculating the material losses and the thickness of the coating layer, as well as the initial conditions. To get the dynamic characteristics of the developed system, the Simulink library of the Matlab software package is used. Using the built-in library elements, we obtain a scheme of differential equations describing the model of the control object. In order to maintain the stable operation of devices with a fluidized bed and the necessary hydrodynamic regime inside the apparatus, it is necessary to develop an efficient system for controlling dewatering and granulation processes. The quality of management of the developed system directly depends on the accuracy of the object model. The results of the research allow to specify the model of the control object and become a reliable ground for developing an effective control system.

The deal.II library, Version 9.1

Abstract This paper provides an overview of the new features of the finite element library deal.II, version 9.1.

Covariance Similarity Approach for Semiblind Unmixing of Hyperspectral Image

Hyperspectral sparse unmixing methods estimate abundance of endmembers, assuming spectral library as an overcomplete set of endmembers. In this letter, we present a novel, fast and efficient dictionary pruning approach for hyperspectral unmixing. We quantify the change in the latent structure of data due to augmentation of spectral library element using covariance similarity measure. Since the covariance matrices form a nonlinear manifold, choosing an appropriate similarity measure is a nontrivial task. We explored prevalent similarity measures, which motivated us to employ Jeffrey’s Kullback–Leibler divergence measure due to its tighter bounds and better noise performance. We also present analytical formulations for faster implementation of covariance similarity. We evaluate the performance of dictionary pruning algorithms on several synthetic and real hyperspectral images and demonstrate the proficiency of our proposed work in diverse scenarios.

Modeling and simulation of Ultrasonic Guided Waves propagation in the fluid-structure domain by a monolithic approach

The present study introduces the coupled multiphysics model as part of the structural health monitoring (SHM) system. In particular, the Ultrasonic Guided Waves (UGWs) propagation is tracked in order to identify the damage to the structure. For this purpose, a multiphysics mathematical model is proposed. The model constitutes a monolithically coupled system of acoustic and elastic wave equations (WpFSI problem) where the wave signal displacement measurements are analyzed as the UGWs propagates in the solid, fluid and their interface. The ultimate goal of this paper is to explore and develop the efficient numerical solution of the WpFSI problem using the finite element method. A detailed description of the modeling framework and conditions that facilitate the coupling is provided. To couple the displacement-based acoustic wave equations for the isothermal fluid with elastic wave equations for the Saint Venant-Kirchhoff material model, the present study uses a monolithic solution algorithm. In particular, at each time step, wave equations are transformed to a fixed reference configuration via the arbitrary Lagrangian-Eulerian (ALE) mapping and automatically adopt the boundary conditions from the previous time step. The implementation is accomplished via the finite element library deal.II (Goll et al., 2017) based software toolbox DOpElib (Bangerth et al., 2007) which provides modularized higher level algorithms. Beyond SHM systems, the model is relevant for problems from biomechanics and biomedicine, vibromechanics, poroelasticity as well as subsurface and porous media flow. The model developed here serves as a first step towards the on-line SHM system modeling, where structural dynamics are accounted for.

Accelerating magnetic induction tomography‐based imaging through heterogeneous parallel computing

SummaryMagnetic Induction Tomography (MIT) is a non‐invasive imaging technique, which has applications in both industrial and clinical settings. In essence, it is capable of reconstructing the electromagnetic parameters of an object from measurements made on its surface. With the exploitation of parallelism, it is possible to achieve high quality inexpensive MIT images for biomedical applications on clinically relevant time scales. In this paper we investigate the performance of different parallel implementations of the forward eddy current problem, which is the main computational component of the inverse problem through which measured voltages are converted into images. We show that a heterogeneous parallel method that exploits multiple CPUs and GPUs can provide a high level of parallel scaling, leading to considerably improved runtimes. We also show how multiple GPUs can be used in conjunction with deal.II, a widely‐used open source finite element library.

Optimization of Cell Free Protein Synthesis: Development of a Fusion Protein Fitness Strategy

Our undergraduate researchers work in the field of metabolic engineering to harness metabolic pathways for the production of useful metabolites with applications in the biofuel, pharmaceutical, or industrial chemical industries. We published a metabolic engineering approach called programmed evolution that introduces variation in regulatory elements for the expression of enzymes that control orthogonal metabolic pathways. Programmed evolution employs a riboswitch‐based fitness module to transduce the production of a desired metabolite into antibiotic resistance. We validated programmed evolution by optimizing the conversion of caffeine to theophylline by caffeine demethylase, but we recognized several limitations to the widespread use of our approach, including crosstalk between orthogonal and native bacterial metabolism, potential toxicity of metabolites, and poor representation of large variation spaces. To avoid these limitations, we are developing an in vitro approach to programmed evolution. For cell‐free protein synthesis (CFPS), we found supercoiled plasmid was a much better template than linear PCR amplicon. We designed, constructed, and have begun testing a novel fitness module that responds to the production of theophylline produced by the action of caffeine demethylase produced by CFPS. The fitness module encodes a fusion protein composed of three functional units. The amino portion contains a Gal4 DNA binding domain that will target binding sites on a library of DNA regulatory elements for the expression of caffeine demethylase. The carboxyl terminus includes streptavidin which will bind to avidin beads for physical separation of selected DNA regulatory elements. Sandwiched in between these two domains is GFP, which serves as a biosensor. Using this in vitro selection strategy, we plan to pursue the optimization of CFPS for the discovery of efficient metabolic pathways of interest.Support or Funding InformationNSF RUI grant MCB‐1613203 to Davidson College and MCB‐1613281 to Missouri Western State University, Davidson College Martin Genomics ProgramThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

ISeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast.

We developed a flexible toolkit for combinatorial screening in Saccharomyces cerevisiae, which generates large libraries of cells, each uniquely barcoded to mark a combination of DNA elements. This interaction sequencing platform (iSeq 2.0) includes genomic landing pads that assemble combinations through sequential integration of plasmids or yeast mating,15barcoded plasmid libraries containing split selectable markers (URA3AI, KanMXAI, HphMXAI, and NatMXAI), and an array of ∼24,000 "double-barcoder" strains that can make existing yeast libraries iSeq compatible. Various DNA elements are compatible with iSeq: DNA introduced on integrating plasmids, engineered genomic modifications, or entire genetic backgrounds. DNA element libraries are modular and interchangeable, and any two libraries can be combined, making iSeq capable of performingmany new combinatorial screens by short-read sequencing.

Application of the Monte Carlo Library Least-Squares (MCLLS) approach for chromium quantitative analysis in aqueous solution

In the present work, a new in-situ prompt gamma-ray neutron activation analysis (PGNAA) setup was developed for the quantitative measurement of chromium (Cr) in aqueous solutions which consists of a 4" × 4″ inch Bismuth Germanate detector and a 300 mCi 241Americium-beryllium neutron source. A series of standard samples were prepared by dissolving Cr compounds in deionized water of analytical pure grade and measured using the in situ PGNAA setup. Quantitative spectrum analysis was conducted using Monte Carlo Library Least-Squares approach (MCLLS). Simulates of elemental library spectra were in silico modeled using the CEARCPG code, which was developed by Prof. Robin Gardner research group in North Carolina State University. The fitted spectra presented were in excellent agreement with the total experimental spectrum, and the correlation coefficients were all nearly 1. After applying the MCLLS approach, the minimum detectable concentration of Cr was 301.5 mg/L, better than that obtained with other setups, and the relative deviation of the Cr quantitative analysis accuracy was less than 4.09%.

On implementation aspects of finite element method and its application

This paper describes the usage of the finite element library CFEM for solution of boundary value problems for partial differential equations. The application of the finite element method is shown based on the weak formulation of a boundary value problem. A unified approach for solution of linear scalar, linear vector, and nonlinear vector problems is presented. A direct link between the mathematical formulation and the design of the computer code is shown. Several examples and results are shown.

Composable block solvers for the four-field double porosity/permeability model

The objective of this paper is twofold. First, we propose two composable block solver methodologies to solve the discrete systems that arise from finite element discretizations of the double porosity/permeability (DPP) model. The DPP model, which is a four-field mathematical model, describes the flow of a single-phase incompressible fluid in a porous medium with two distinct pore-networks and with a possibility of mass transfer between them. Using the composable solvers feature available in PETSc and the finite element libraries available under the Firedrake Project, we illustrate two different ways by which one can effectively precondition these large systems of equations. Second, we employ the recently developed performance model called the Time-Accuracy-Size (TAS) spectrum to demonstrate that the proposed composable block solvers are scalable in both the parallel and algorithmic sense. Moreover, we utilize this spectrum analysis to compare the performance of three different finite element discretizations (classical mixed formulation with H(div) elements, stabilized continuous Galerkin mixed formulation, and stabilized discontinuous Galerkin mixed formulation) for the DPP model. Our performance spectrum analysis demonstrates that the composable block solvers are fine choices for any of these three finite element discretizations. Sample computer codes are provided to illustrate how one can easily implement the proposed block solver methodologies through PETSc command line options.

The DTEQ Code for Toroidal MHD Equilibria with Diamagnetic Current Modeling Using the deal.II Finite Element Library

The Deal Two Equilibrium (DTEQ) code solves the Grad-Shafranov (GS) equation for magnetohydrodynamics equilibrium in the axisymmetric toroidal geometry using the deal.II finite element library. In this paper, we introduce DTEQ that can solve the GS equation both linearly and nonlinearly. The linear solution obtained from this code is verified by comparing with a known analytic solution of the linear GS equation. For the nonlinear solution, DTEQ requires two input profiles, p(ψ) and F(ψ), to be specified as a function of the normalized minor radius ρ. The pressure profile p(ψ) is specified based on Thomson scattering, charge exchange spectroscopy data, and an energetic particle pressure model. The toroidal field profile F(ψ) is obtained from our model that makes the diamagnetic current play a significant role when the poloidal beta βp is greater than one. With these two input profiles, the nonlinear GS equation can be solved using Picard iteration within the plasma boundary from EFIT. Using this newly developed code, we obtain several meaningful results that show its validity. The calculated poloidal current density is very large in the transport barrier due to the diamagnetic current, and the characteristics of the Pfirsch-Schlüter current appear in the toroidal current density. In addition, the results obtained from this code agree well with those from EFIT, and the calculated safety factor values in the center are well correlated with the sawtooth activity in the discharge.

Reactome - Pathway Context and Visualisation for Omics Data

Reactome (https://reactome.org) is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways, currently covering 2,106 Pathways; 10,712 protein coding genes; 11,302 reactions; 27,452 literature references and 1,800 small molecules. Pathways are arranged in a hierarchical structure, allowing the user to navigate from high level concepts like immune system to detailed pathway diagrams showing biomolecular events like membrane transport or phosphorylation. The Reactome curation strategy focuses on the annotation of “normal” pathways in human. However, we increasingly annotate disease-specific pathway modifications, grouped in three major classes: loss of function (typically metabolic disease phenotypes), gain of function (typically cancer phenotypes), and host-pathogen interactions. Here, we present new developments in the multi-scale Reactome visualization system that facilitate navigation through the pathway hierarchy and enable efficient reuse of Reactome visualizations for users' own research presentations and publications. For the higher levels of the hierarchy, Reactome now provides scalable, interactive textbook-style diagrams in SVG format, which are also freely downloadable and editable. Repeated diagram elements like ‘mitochondrion’ or ‘receptor’ are freely available as a library of graphic elements at https://reactome.org/icon-lib. Detailed lower-level diagrams are now downloadable in editable PPTX format as sets of interconnected objects, as well as in standard png format.

Инвестиции в сохранение и развитие культурного наследия региона: библиотека BIM-элементов памятников национальной архитектуры и градостроительства

Introduction: The paper presents a methodology for reduction of expenses within investment projects aimed at the preservation and development of cultural heritage sites, based on the combined use of methods of scientific restoration, laser scanning and information modeling, as well as creation of a library of unique BIM elements of ancient city buildings, identified at protected sites of the urban environment, using restoration of a building in the Old Tatar Quarter (Staro-Tatarskaya Sloboda) in Kazan as an example. Methods: The authors performed standard (traditional) scientific restoration activities and innovative field studies using laser scanning and built a parametric information model of the cultural heritage site for further development of a restoration plan with account for site adaptation to modern functions. Results and discussion: Point cloud processing is carried out to create an information model and a library of unique BIM elements, which can be used repeatedly in restoration and reconstruction, thus reducing costs for BIM-model development in future investment projects. The practical significance of the study lies in the creation of a public good — a library (encyclopedia) of ancient architectural elements in the form of a library of BIM elements for BIM models of architectural and urban-planning landmarks in the region, as well as in the development of recommendations (by individuals, regional and local regulatory authorities) for an efficient policy in urban planning and restoration with regard to similar historical and cultural, architectural and urban-planning landmarks.

The deal.II library, Version 9.0

Abstract This paper provides an overview of the new features of the finite element library deal.II version 9.0.

Benchmarking of two flexible multibody dynamic simulation software in engine simulations

In this paper, two different commercial multibody dynamic (MBD) simulation software cases are studied. Due to the restrictions determined in the conditions of contract, the names of the software are not revealed, instead being called Software S and Software E. The central purpose of this research was to investigate the abilities of Software S in the simulation of a large engine, as a part of the strength analysis process. The abilities were studied by comparing the program with another, here called Software E, which is designed primarily for engine simulations. The capabilities of Software E have been proven after years of usage at Wärtsilä, resulting in its essential role in the strength analysis process today. The aim was to find the shortcomings and restrictions of Software S but also advantages it could bring to the strength analysis process for Wärtsilä. Similar simulation models were also built using both programs during this research. A 16-cylinder V-engine was selected as the subject because of its size in order to obtain further information about the behavior of the program when working with extensive model files. The components of the engine were flexible and were reduced FE models, also called super elements. The forces and contact situations that occur inside the engine were modeled using elements provided by the MBD programs. Different levels of detail of the modeling elements were used to obtain information about the flexibility of the program. The results obtained from time integrations were compared to ensure the similarity of both modeling elements used. Also, this paper reports the calculation times. In addition, a small-scale study was performed for Software S to clarify the effect of the modes used in time integrations towards results accuracy and calculation times. Simulation models were built successfully in both programs, and the results obtained correlated with each other on an adequate level. Significant differences appeared in the features and usability of the programs in general. The GUI of Software S is advanced and user-friendly, whereas Software E is not focused on these features. On the other hand, the modeling element library of Software E covers all of the required features related to large engine simulations, some of which Software S is lacking. This work can be used in assistance when considering buying new software for a company as well as when investigating new development areas that could be improved with new software.

Research of evolution of the stress strain and definition of the estimated life-time of massive structure elements using of the universal finite element

Mathematical modeling of the continual fracture processes under long creep conditions on the basis of FEM is a rather complex problem. The efficiency of solving of this problem depends on the completeness of the finite element library and the algorithms for solving systems of nonlinear equations, as well as on the software organization. The main principles of the moment sheme of finite elements (MSFE) is the base for procedure of obtaining of finite-element solving relationships. In contrast to the generally accepted approaches the use of MSFE provides an independent representation of deformations in the form of Maclaurin series in addition to the choose of the law of displacements distribution. At the base of the algorithm for solving a system of nonlinear equations, the method of integration over the load parameter is adopted. It is assumed to reduce an integration step consecutively to obtain reliable results. To optimize discrete FEM models, an approach based on the initial fragmentation of the computational model was used. The accuracy of solving of a system of nonlinear equations at each step of the load parameter is determined by comparing the sum of the squares of the nodal reactions and the sum of the squares of the nodal values of the external loads. The equations of termoviscolastoplastic deformation taking into account the damage of materials are taken as initial relations. The principle of using of quasiregular fragmentation which involves constructing a general irregular finite element model based on regular finite element fragments is basis of the procedure of constructing the finite element model of objects under consideration. This make it possible to optimize substantially the total number of unknowns. When calculating of a new objects, the convergence of the results is justified by a sequential increase of the parameters of the mesh model, a decrease of integration step value due to an increase of their number within a given range of loads, and an increase of the accuracy of solving of nonlinear equations system at each step. In order to justify the reliability of the results, obtained on the basis of the universal finite element, the parameters of the stress-strain state and the damage parameter ω were compared with data calculated on the basis of finite elements of a general type with numerical integration and elements with integration in a closed form.

Genome sequencing and conservation genomics in the Scandinavian wolverine population.

Genetic approaches have proved valuable to the study and conservation of endangered populations, especially for monitoring programs, and there is potential for further developments in this direction by extending analyses to the genomic level. We assembled the genome of the wolverine (Gulo gulo), a mustelid that in Scandinavia has recently recovered from a significant population decline, and obtained a 2.42Gb draft sequence representing >85% of the genome and including >21,000protein-coding genes. We then performed whole-genome resequencing of 10Scandinavian wolverines for population genomic and demographic analyses. Genetic diversity was among the lowest detected in a red-listed population (mean genome-wide nucleotide diversity of 0.05%). Results of the demographic analyses indicated a long-term decline of the effective population size (Ne ) from 10,000well before the last glaciation to <500 after this period. Current Ne appeared even lower. The genome-wide FIS level was 0.089 (possibly signaling inbreeding), but this effect was not observed when analyzing a set of highly variable SNP markers, illustrating that such markers can give a biased picture of the overall character of genetic diversity. We found significant population structure, which has implications for population connectivity and conservation. We used an integrated microfluidic circuit chip technology to develop an SNP-array consisting of 96 highly informative markers that, together with a multiplex pre-amplification step, was successfully applied to low-quality DNA from scat samples. Our findings will inform management, conservation, and genetic monitoring of wolverines and serve as a genomic roadmap that can be applied to other endangered species. The approach used here can be generally utilized in other systems, but we acknowledge the trade-off between investing in genomic resources and direct conservation actions.

Research on part innovation design based on feature elements

Based on the mechanical manufacturing process and machining characteristics, the concept of feature elements is proposed and the feature elements are defined and classified in this paper. According to the mapping relationship between the feature elements of the mechanical parts and the geometric structure, the feature elements drawing function is developed, and the graphic library of the feature elements is constructed. By studying the combination of parts feature elements, a combination relationship model of part feature elements is established. Finally, in the condition of matching design requirements and manufacturing resources, a part innovation design platform is developed based on the combination relation model of feature elements to combine feature elements drawing function, and the efficient and innovative design of mechanical parts has been realized.