Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Hybrid Zones02:29

Hybrid Zones

22.0K
Hybrid zones are narrow regions where two closely related species interact, mate, and produce hybrids. Relative to either parent species, hybrids may possess distinct phenotypic or genetic differences that impact their survival and reproductive success. The genetic variances introduced by hybridization influence species diversity and speciation processes within the hybrid zone.
22.0K
Zones of Protection01:16

Zones of Protection

808
In power systems, the entire setup is divided into protective zones to isolate faults and protect the rest of the network. These zones include generators, transformers, buses, transmission lines, distribution lines, and motors. Each zone can be visualized as a separate room in a house, with each room protected by its own circuit breaker.
Protective zones are defined by closed dashed lines, containing one or more components. A key characteristic of these zones is the strategic placement of...
808
Protein Networks02:26

Protein Networks

4.6K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.6K
Parallel Resonance01:23

Parallel Resonance

589
The parallel RLC circuit is an arrangement where the resistor (R), inductor (L), and capacitor (C) are all connected to the same nodes and, as a result, share the same voltage across them. The parallel RLC circuit is analyzed in terms of admittance (Y), which reflects the ease with which current can flow. The admittance is given by:
589
Transition Zone01:28

Transition Zone

395
The transition zone in concrete is a critical area where aggregate meets cement paste, marked by a distinct porosity and weakness compared to the surrounding material. The adhesion around the aggregates is primarily due to Van Der Waals forces. The voids within this zone influence its robustness; initially, it is less durable than the surrounding bulk mortar due to larger voids. Initially, when concrete is compacted, a higher water-cement ratio near the aggregates leads to the formation of...
395
Parallel Processing01:20

Parallel Processing

740
The brain processes sensory information rapidly due to parallel processing, which involves sending data across multiple neural pathways at the same time. This method allows the brain to manage various sensory qualities, such as shapes, colors, movements, and locations, all concurrently. For instance, when observing a forest landscape, the brain simultaneously processes the movement of leaves, the shapes of trees, the depth between them, and the various shades of green. This enables a quick and...
740

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Leveraging an Explainable Machine Learning Model for Early Identification of Acute Kidney Injury: A Retrospective Study.

The journal of applied laboratory medicine·2026
Same author

Proteomic signatures as biomarkers of atherosclerosis burden.

Cardiovascular research·2026
Same author

Clinical Validation and Comparative Study Between the KDIGO 2012 AKI Criteria and the AACC Guidance Document 2020.

Indian journal of clinical biochemistry : IJCB·2026
Same author

Urine Proteins Stratify Patient Symptom Severity Phenotypes in Urologic Chronic Pelvic Pain Syndrome: A Multidisciplinary Approach to the Study of Chronic Pelvic Pain Research Network Study.

Urology·2026
Same author

Integrated transcriptomic and proteomic analyses identify novel biomarkers of bladder outlet obstruction.

bioRxiv : the preprint server for biology·2026
Same author

Targeting of HSP27 and MMP-2/9 Crosstalk by High-Throughput Drug Repurposing Strategies Identifies Paroxetine as a Potential Candidate in Glioblastoma.

Journal of medicinal chemistry·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Feb 8, 2026

The Subventricular Zone En-face: Wholemount Staining and Ependymal Flow
14:33

The Subventricular Zone En-face: Wholemount Staining and Ependymal Flow

Published on: May 6, 2010

43.0K

A network-based zoning for parallel whole-cell simulation.

Barnali Das1, Abhijeet Rajendra Patil1, Pralay Mitra1

  • 1Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, West Bengal, India.

Bioinformatics (Oxford, England)
|June 30, 2018
PubMed
Summary
This summary is machine-generated.

We developed a network-based zoning method to parallelize whole-cell simulations, reducing computational demands. This approach partitions cells into sub-cells for High-Performance Computing (HPC), enabling efficient whole-cell modeling.

More Related Videos

Culturing Lymphocytes in Simulated Microgravity Using a Rotary Cell Culture System
09:28

Culturing Lymphocytes in Simulated Microgravity Using a Rotary Cell Culture System

Published on: August 25, 2022

3.6K
Isolation and Culture of Cells from the Nephrogenic Zone of the Embryonic Mouse Kidney
08:06

Isolation and Culture of Cells from the Nephrogenic Zone of the Embryonic Mouse Kidney

Published on: April 22, 2011

18.5K

Related Experiment Videos

Last Updated: Feb 8, 2026

The Subventricular Zone En-face: Wholemount Staining and Ependymal Flow
14:33

The Subventricular Zone En-face: Wholemount Staining and Ependymal Flow

Published on: May 6, 2010

43.0K
Culturing Lymphocytes in Simulated Microgravity Using a Rotary Cell Culture System
09:28

Culturing Lymphocytes in Simulated Microgravity Using a Rotary Cell Culture System

Published on: August 25, 2022

3.6K
Isolation and Culture of Cells from the Nephrogenic Zone of the Embryonic Mouse Kidney
08:06

Isolation and Culture of Cells from the Nephrogenic Zone of the Embryonic Mouse Kidney

Published on: April 22, 2011

18.5K

Area of Science:

  • Computational Cell Biology
  • Systems Biology
  • Bioinformatics

Background:

  • Whole-cell modeling is crucial for understanding cellular processes but is computationally intensive.
  • Existing methods lack efficient strategies to manage the computational overhead of whole-cell simulations.

Purpose of the Study:

  • To present a novel network-based zoning approach for parallelizing whole-cell simulations.
  • To reduce the computational burden of whole-cell modeling and enable its application on High-Performance Computing (HPC) systems.

Main Methods:

  • Constructed protein-protein interaction graphs from experimental data.
  • Predicted protein locality and interaction confidence scores.
  • Identified spatially and functionally localized protein clusters using graph clustering and Gene Ontology analysis.
  • Applied Principal Coordinates Analysis to predict cluster distribution in simulation space.
  • Developed automated techniques to partition the cell into simulation sub-cells for parallel processing.

Main Results:

  • Identified 188 spatially localized and functionally proximate protein clusters in Escherichia coli K12.
  • Demonstrated the potential for partitioning the entire simulation space into manageable sub-cells.
  • Validated the method's applicability for parallel simulation on HPC systems.
  • Showcased the extensibility of the method to include other cellular components like DNA, RNA, and metabolites.

Conclusions:

  • The network-based zoning approach effectively partitions whole-cell simulations for parallel processing.
  • This method significantly reduces computational overhead, facilitating large-scale whole-cell modeling.
  • The approach offers a scalable solution for advancing computational cell biology research.