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Related Concept Videos

Kinetic Energy00:23

Kinetic Energy

42.9K
Kinetic energy is the ability of an object in motion to do work or enact change. It can take on many forms. For instance, water flowing down a waterfall has kinetic energy. In biological systems, particles of light travel and are absorbed by plants to create chemical energy. Animals consume the chemical energy and give off molecules that carry their scent through the air. They also generate kinetic energy when they run away from predators. Entire systems also possess kinetic energy, like the...
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Kinematic Equations: Problem Solving01:15

Kinematic Equations: Problem Solving

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When analyzing one-dimensional motion with constant acceleration, the problem-solving strategy involves identifying the known quantities and choosing the appropriate kinematic equations to solve for the unknowns. Either one or two kinematic equations are needed to solve for the unknowns, depending on the known and unknown quantities. Generally, the number of equations required is the same as the number of unknown quantities in the given example. Two-body pursuit problems always require two...
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Kinematic Equations - II01:17

Kinematic Equations - II

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The second kinematic equation expresses the final position of an object in terms of its initial position, the distance traveled with the initial constant velocity, and the distance traveled due to a change in velocity. Similar to the first kinematic equation, this equation is also only valid when the acceleration is constant throughout the motion of an object.
Suppose a car merges into freeway traffic on a 200 m long ramp. If its initial velocity is 10 m/s and it accelerates at 2 m/s2, then the...
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Kinetic Energy for a Rigid Body01:13

Kinetic Energy for a Rigid Body

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Imagine a solid object involved in a general planar movement, with its center of mass pinpointed at a spot labeled G. The object's kinetic energy relative to an arbitrary point A can be quantified for each of its particles - the ith particle in this case. This measurement is achieved through the employment of the relative velocity definition. The position vector, known as rA, extends from point A to the mass element i.
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Kinematic Equations - III01:18

Kinematic Equations - III

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The first two kinematic equations have time as a variable, but the third kinematic equation is independent of time. This equation expresses final velocity as a function of the acceleration and distance over which it acts. The fourth kinematic equation does not have an acceleration term and provides the final position of the object at time t in terms of the initial and final velocities. This equation is useful when the value of the constant acceleration is unknown.
Using the kinematic equations,...
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Kinematic Equations - I01:26

Kinematic Equations - I

13.9K
When an object moves with constant acceleration, the velocity of the object changes at a constant rate throughout the motion. The kinematic equations of motions are derived for such cases where the acceleration of the object is constant. The first kinematic equation gives an insight into the relationship between velocity, acceleration, and time. We can see, for example:
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Subject-specific Musculoskeletal Model for Studying Bone Strain During Dynamic Motion
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Subject-specific Musculoskeletal Model for Studying Bone Strain During Dynamic Motion

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Publishing reproducible dynamic kinetic models.

Veronica Porubsky1, Lucian Smith1, Herbert M Sauro1

  • 1Department of Bioengineering, University of Washington, Seattle, 98105,USA.

Briefings in Bioinformatics
|August 15, 2020
PubMed
Summary
This summary is machine-generated.

Publishing reproducible computational models is vital but often neglected in systems biology. This review highlights tools and practices to improve repeatability and reproducibility of kinetic models.

Keywords:
SBMLkinetic modelingreproducibilitystandardssystems biology

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Area of Science:

  • Computational Biology
  • Systems Biology
  • Scientific Computing

Background:

  • Reproducibility and repeatability are critical for the scientific method in computational biology.
  • Current academic pressures and reward systems often hinder the publication of reproducible science.
  • Many published models in systems biology lack sufficient detail for replication.

Purpose of the Study:

  • To review the current landscape of tools, repositories, standards, and best practices for publishing repeatable and reproducible kinetic models.
  • To identify challenges and propose solutions for improving model reproducibility in systems biology.

Main Methods:

  • Literature review of software tooling for computational models.
  • Analysis of existing model repositories and standards.
  • Examination of best practices for publishing kinetic models.
  • Discussion of potential future remedies and journal involvement.

Main Results:

  • A significant gap exists between the need for and the practice of publishing reproducible computational models.
  • Various software tools, model repositories, and emerging standards can aid in reproducibility.
  • There is a need for enhanced collaboration with journals to ensure minimum standards for model repeatability.

Conclusions:

  • Improving the repeatability and reproducibility of kinetic models is essential for advancing systems biology.
  • Adoption of standardized practices and better tooling can enhance scientific rigor.
  • Closer collaboration between researchers, journals, and institutions is necessary to foster a culture of reproducible science.