High-Performance Whole-Cell Simulation Exploiting Modular Cell Biology Principles

2021 ◽  
Author(s):  
Barnali Das ◽  
Pralay Mitra
Keyword(s):  
Cell Biology ◽  
High Performance ◽  
Whole Cell ◽  
Cell Simulation

scholarly journals BiPSim: a flexible and generic stochastic simulator for polymerization processes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Stephan Fischer ◽  
Marc Dinh ◽  
Vincent Henry ◽  
Philippe Robert ◽  
Anne Goelzer ◽  
...  
Keyword(s):  
Large Scale ◽  
Stochastic Simulation Algorithm ◽  
Specific Information ◽  
Whole Cell ◽  
Simulation Speed ◽  
Genome Wide ◽  
Cell Simulation ◽  
Stochastic Simulator ◽  
Modeling Formalisms ◽  
Stochastic Phenomena

AbstractDetailed whole-cell modeling requires an integration of heterogeneous cell processes having different modeling formalisms, for which whole-cell simulation could remain tractable. Here, we introduce BiPSim, an open-source stochastic simulator of template-based polymerization processes, such as replication, transcription and translation. BiPSim combines an efficient abstract representation of reactions and a constant-time implementation of the Gillespie’s Stochastic Simulation Algorithm (SSA) with respect to reactions, which makes it highly efficient to simulate large-scale polymerization processes stochastically. Moreover, multi-level descriptions of polymerization processes can be handled simultaneously, allowing the user to tune a trade-off between simulation speed and model granularity. We evaluated the performance of BiPSim by simulating genome-wide gene expression in bacteria for multiple levels of granularity. Finally, since no cell-type specific information is hard-coded in the simulator, models can easily be adapted to other organismal species. We expect that BiPSim should open new perspectives for the genome-wide simulation of stochastic phenomena in biology.

scholarly journals An integrated multiscale, multicellular skin model

2019 ◽  
Author(s):  
Ryan Tasseff ◽  
Boris Aguilar ◽  
Simon Kahan ◽  
Seunghwa Kang ◽  
Charles C. Bascom ◽  
...  
Keyword(s):  
Differential Equations ◽  
Cell Biology ◽  
High Performance ◽  
Skin Barrier ◽  
Skin Barrier Function ◽  
Emergent Properties ◽  
Skin Model ◽  
Environmental Chemical ◽  
Software Models

ABSTRACTSkin is our primary barrier to the outside world, protecting us from physical, biological and chemical threats. Developing innovative products that preserve and improve skin barrier function requires a thorough understanding of the mechanisms underlying barrier response to topical applications. In many fields, computer simulations already facilitate understanding, thus accelerating innovation. Simulations of software models allow scientists to test hypothesized mechanisms by comparing predicted results to physical observations. They also enable virtual product optimization, without physical experiments, once mechanisms have been validated. The physical accessibility and abundant knowledge of skin structure makes it a prime candidate for computational modeling. In this article, we describe a computational multiscale multicellular skin model used to simulate growth and response of the epidermal barrier. The model integrates several modeling styles and mathematical frameworks including ordinary differential equations, partial differential equations, discrete agent-based modeling and discrete element methods. Specifically, to capture cell biology and physical transport, we combined four distinct sub-models from existing literature. We also implemented methods for elastic biomechanics. Our software implementation of the model is compatible with the high-performance computing simulation platform Biocellion. The integrated model recapitulates barrier formation, homeostasis and response to environmental, chemical and mechanical perturbation. This work exemplifies methodology for integrating models of vastly different styles. The methodology enables us to effectively build on existing knowledge and produce “whole-system” tissue models capable of displaying emergent properties. It also illustrates the inherent technical difficulties associated with the mounting complexity of describing biological systems at high fidelity. Among the challenges are validation of the science, the mathematical representations approximating the science and the software implementing these representations. Responsibility for a discrepancy observed between in silico and in vitro results may as easily lie at one of these three levels as at another, demanding that any sustainable modeling endeavor engage expertise from biology, mathematics and computing.

scholarly journals A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

GigaScience ◽  
2020 ◽  
Vol 9 (10) ◽  
Author(s):  
Mehmet Tekman ◽  
Bérénice Batut ◽  
Alexander Ostrovsky ◽  
Christophe Antoniewski ◽  
Dave Clements ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cell Biology ◽  
High Performance ◽  
Learning Experience ◽  
Sequencing Analysis ◽  
Teaching Resources ◽  
Single Cell Rna Sequencing ◽  
The Galaxy ◽  
Downstream Analysis

Abstract Background The vast ecosystem of single-cell RNA-sequencing tools has until recently been plagued by an excess of diverging analysis strategies, inconsistent file formats, and compatibility issues between different software suites. The uptake of 10x Genomics datasets has begun to calm this diversity, and the bioinformatics community leans once more towards the large computing requirements and the statistically driven methods needed to process and understand these ever-growing datasets. Results Here we outline several Galaxy workflows and learning resources for single-cell RNA-sequencing, with the aim of providing a comprehensive analysis environment paired with a thorough user learning experience that bridges the knowledge gap between the computational methods and the underlying cell biology. The Galaxy reproducible bioinformatics framework provides tools, workflows, and trainings that not only enable users to perform 1-click 10x preprocessing but also empower them to demultiplex raw sequencing from custom tagged and full-length sequencing protocols. The downstream analysis supports a range of high-quality interoperable suites separated into common stages of analysis: inspection, filtering, normalization, confounder removal, and clustering. The teaching resources cover concepts from computer science to cell biology. Access to all resources is provided at the singlecell.usegalaxy.eu portal. Conclusions The reproducible and training-oriented Galaxy framework provides a sustainable high-performance computing environment for users to run flexible analyses on both 10x and alternative platforms. The tutorials from the Galaxy Training Network along with the frequent training workshops hosted by the Galaxy community provide a means for users to learn, publish, and teach single-cell RNA-sequencing analysis.

scholarly journals Study on Topology and Control Strategy of High-Precision and Wide-Range Hybrid Converter for Photovoltaic Cell Simulator

Energies ◽  
2018 ◽  
Vol 12 (1) ◽  
pp. 39
Author(s):  
Jianfei Zhao ◽  
Minqi Hua ◽  
Tingzhang Liu ◽  
Tao Yu
Keyword(s):  
Control Strategy ◽  
Power Supply ◽  
High Performance ◽  
Photovoltaic Cell ◽  
Programmable Logic ◽  
Motor Simulation ◽  
Hybrid Topology ◽  
Wide Range ◽  
Cell Simulation ◽  
And Control

Aiming at the function and technical requirements of high-power photovoltaic cell simulation, high-performance programmable logic power supply and dc motor simulation, a high frequency isolation hybrid topology and control strategy based on current-source/voltage-source converter was studied and proposed. Firstly, according to the performance requirements of photovoltaic cell analog power supply, the control strategy requirements of the high-precision wide-range hybrid topology were proposed. Secondly, the working principle of the new hybrid topology was analyzed. At the same time, the equivalent model of the new hybrid topology was simplified and established, and the overall control strategy of the hybrid topology based on current compensation and sliding mode variable structure was proposed. Finally, simulation and experimental research on the hybrid topology was carried out, and the experimental test of photovoltaic cell simulation was completed. The simulation and experimental results show that the hybrid topology and control strategy proposed in this paper has the characteristics of wide-range output regulation, fast dynamic response, high efficiency and high power factor, and can be used for high performance photovoltaic cell simulation, programmable logic power supply and DC motor simulation.

Kinematics of Cytoplasmic Deformation in Neutrophils During Active Motion

1990 ◽  
Vol 112 (3) ◽  
pp. 303-310 ◽  
Author(s):  
S. I. Simon ◽  
G. W. Schmid-Scho¨nbein
Keyword(s):  
Cell Biology ◽  
Random Motion ◽  
Large Strains ◽  
Strain Rates ◽  
Local Motion ◽  
Active Motion ◽  
Whole Cell ◽  
Wide Range ◽  
Freely Suspended ◽  
High Degree

A procedure is proposed to measure the cytoplasmic deformation in active motile neutrophils in the form of cytoplasmic strains and strain rates. Three neighboring microspheres in a local region of the cytoplasm serve as markers for local motion. Their positions are tracked by means of a high resolution light microscope and serve to compute nonlinear measures of strains and strain rates together with the principal strains and principal directions. Active neutrophils exhibit large cytoplasmic strains both during periodic pseudopod projections and during continuous locomotion in a polarized shape. The cytoplasmic motion is often synchronized with the whole cell deformation. The local cytoplasmic strains exceed the strains estimated for the whole cell and are not reversible except in some cases of single pseudopod projections. Large strains are observed both in attached and freely suspended cells. Strain rates are relatively constant but show an increase during the pseudopod retraction phase. Local cytoplasmic strains in neutrophils are inhomogeneous and reach large values during passage of the contraction rings. Neutrophils rendered passive by treatment with cytochalasin or EDTA show a random motion of microspheres with much smaller displacements. These observations suggest that the cytoplasm of active neutrophil exhibits large cytoplasmic strains and strain rates in the absence of an external stress resulting in a high degree of intracellular mixing. The proposed technique may be applied to a wide range of problems in cell biology.

scholarly journals Digital Spindle: A New Way to Explore Mitotic Functions by Whole Cell Data Collection and a Computational Approach

Cells ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 1255
Author(s):  
Norio Yamashita ◽  
Masahiko Morita ◽  
Hideo Yokota ◽  
Yuko Mimori-Kiyosue
Keyword(s):  
Cell Biology ◽  
Information Science ◽  
Three Dimensional ◽  
Light Sheet ◽  
Live Imaging ◽  
Three Dimensions ◽  
Complex Data ◽  
Spatiotemporal Resolution ◽  
Whole Cell ◽  
Light Sheet Microscopy

From cells to organisms, every living system is three-dimensional (3D), but the performance of fluorescence microscopy has been largely limited when attempting to obtain an overview of systems’ dynamic processes in three dimensions. Recently, advanced light-sheet illumination technologies, allowing drastic improvement in spatial discrimination, volumetric imaging times, and phototoxicity/photobleaching, have been making live imaging to collect precise and reliable 3D information increasingly feasible. In particular, lattice light-sheet microscopy (LLSM), using an ultrathin light-sheet, enables whole-cell 3D live imaging of cellular processes, including mitosis, at unprecedented spatiotemporal resolution for extended periods of time. This technology produces immense and complex data, including a significant amount of information, raising new challenges for big image data analysis and new possibilities for data utilization. Once the data are digitally archived in a computer, the data can be reused for various purposes by anyone at any time. Such an information science approach has the potential to revolutionize the use of bioimage data, and provides an alternative method for cell biology research in a data-driven manner. In this article, we introduce examples of analyzing digital mitotic spindles and discuss future perspectives in cell biology.

scholarly journals Long-term tracking of budding yeast cells in brightfield microscopy: CellStar and the Evaluation Platform

2017 ◽  
Vol 14 (127) ◽  
pp. 20160705 ◽  
Author(s):  
Cristian Versari ◽  
Szymon Stoma ◽  
Kirill Batmanov ◽  
Artémis Llamosi ◽  
Filip Mroz ◽  
...  
Keyword(s):  
Cell Biology ◽  
High Performance ◽  
Yeast Cells ◽  
Additional Information ◽  
New Variant ◽  
Long Term Experiments ◽  
Community Effort ◽  
Set Up ◽  
Evaluation Platform

With the continuous expansion of single cell biology, the observation of the behaviour of individual cells over extended durations and with high accuracy has become a problem of central importance. Surprisingly, even for yeast cells that have relatively regular shapes, no solution has been proposed that reaches the high quality required for long-term experiments for segmentation and tracking (S&T) based on brightfield images. Here, we present CellStar , a tool chain designed to achieve good performance in long-term experiments. The key features are the use of a new variant of parametrized active rays for segmentation, a neighbourhood-preserving criterion for tracking, and the use of an iterative approach that incrementally improves S&T quality. A graphical user interface enables manual corrections of S&T errors and their use for the automated correction of other, related errors and for parameter learning. We created a benchmark dataset with manually analysed images and compared CellStar with six other tools, showing its high performance, notably in long-term tracking. As a community effort, we set up a website, the Yeast Image Toolkit, with the benchmark and the Evaluation Platform to gather this and additional information provided by others.

scholarly journals Mass Production of Calendering-Compatible Sulfur-Rich Secondary Particles via Hail-Inspired Nanostorm Technology for Advanced Metal-Sulfur Batteries

2020 ◽  
Author(s):  
Lanxiang Feng ◽  
Peng Yu ◽  
Xuewei Fu ◽  
Mingbo Yang ◽  
Yu Wang ◽  
...  
Keyword(s):  
Quality Control ◽  
Energy Density ◽  
Cell Biology ◽  
High Performance ◽  
Critical Role ◽  
High Energy ◽  
High Energy Density ◽  
Critical Material ◽  
Active Materials ◽  
Secondary Particles

Abstract Scalable fabrication of high-quality thick sulfur electrodes with high-energy-density and good calendering-compatibility is a prerequisite for the practical success of metal-sulfur batteries. However, this task turns out extremely challenging due to the lack of not only advanced sulfur-rich active materials via scalable approach, but also quality-control principles for thick electrodes. Here, we first develop a new hail-inspired sulfur nanostorm (HSN) technology that can efficiently produce high-performance sulfur-rich secondary particles (S-rich SPs) with applesnail-egg-like structures. This biomimetic S-rich SPs rationally integrate critical material functions and good calendering-compatibility. Meanwhile, a concept of “healthy” microenvironment as learned from cell biology is proposed, for the first time, as a key principle revealing the critical role of calendering-compatibility in the quality-control of thick sulfur electrodes. Consequently, an ultrahigh areal capacity of 12 mAh cm− 2 @ 1 mA cm− 2 is realized. Further, we successfully demonstrate a pouch cell with an exceptional energy density of 430 Wh kg− 1 or 1,004 Wh L− 1 in a quasi-lean electrolyte condition. The technology and concept of this study may bring in new insights and general principles for design of advanced thick electrodes with, but not limited to, sulfur-based active materials.

scholarly journals Optimization of the Biocatalysis for D-DIBOA Synthesis Using a Quick and Sensitive New Spectrophotometric Quantification Method

2020 ◽  
Vol 21 (22) ◽  
pp. 8523
Author(s):  
Gema Cabrera ◽  
Teresa Linares ◽  
Maria Elena de la Calle ◽  
Domingo Cantero ◽  
Antonio Valle ◽  
...  
Keyword(s):  
High Performance ◽  
Scaling Up ◽  
Microtiter Plate ◽  
High Performance Liquid Chromatographic ◽  
Coli Strain ◽  
Genetically Engineered ◽  
Whole Cell ◽  
Whole Cell Biocatalysis ◽  
Plate Reader ◽  
Liquid Chromatographic

D-DIBOA (4-hydroxy-(2H)-1,4-benzoxazin-3-(4H)-one) is an allelopathic-derived compound with interesting herbicidal, fungicidal, and insecticide properties whose production has been successfully achieved by biocatalysis using a genetically engineered Escherichia coli strain. However, improvement and scaling-up of this process are hampered by the current methodology for D-DIBOA quantification, which is based on high-performance liquid chromatographic (HPLC), a time-consuming technique that requires expensive equipment and the use of environmentally unsafe solvents. In this work, we established and validated a rapid, simple, and sensitive spectrophotometric method for the quantification of the D-DIBOA produced by whole-cell biocatalysis, with limits of detection and quantification of 0.0165 and 0.0501 µmol·mL−1 respectively. This analysis takes place in only a few seconds and can be carried out using 100 µL of the sample in a microtiter plate reader. We performed several whole-cell biocatalysis strategies to optimize the process by monitoring D-DIBOA production every hour to keep control of both precursor and D-DIBOA concentrations in the bioreactor. These experiments allowed increasing the D-DIBOA production from the previously reported 5.01 mM up to 7.17 mM (43% increase). This methodology will facilitate processes such as the optimization of the biocatalyst, the scaling up, and the downstream purification.

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