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Related Concept Videos

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving01:29

Mechanistic Models: Compartment Models in Algorithms for Numerical Problem Solving

Mechanistic models play a crucial role in algorithms for numerical problem-solving, particularly in nonlinear mixed effects modeling (NMEM). These models aim to minimize specific objective functions by evaluating various parameter estimates, leading to the development of systematic algorithms. In some cases, linearization techniques approximate the model using linear equations.
In individual population analyses, different algorithms are employed, such as Cauchy's method, which uses a...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation01:24

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation

This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
On...
Modeling and Similitude01:12

Modeling and Similitude

Scaled modeling is a fundamental technique in engineering, enabling the study of large and complex systems by creating smaller, manageable replicas that recreate critical characteristics of the original. In hydrology and civil infrastructure, for example, scaled models of dams help analyze water flow, turbulence, and pressure. This method allows for accurate predictions of real-world behavior within a controlled environment, significantly reducing the cost and time involved in full-scale...
Per-Unit Sequence Models01:26

Per-Unit Sequence Models

An ideal Y-Y transformer, grounded through neutral impedances, displays per-unit sequence networks akin to those of a single-phase ideal transformer when subjected to balanced positive- or negative-sequence currents. These currents do not produce neutral currents, and their associated voltage drops.
Zero-sequence currents, which are identical in magnitude and phase, generate a neutral current, resulting in voltage drops across the neutral impedance and the low-voltage winding. If the...

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Related Experiment Video

Updated: Jul 5, 2026

Constructing and Visualizing Models using Mime-based Machine-learning Framework
06:19

Constructing and Visualizing Models using Mime-based Machine-learning Framework

Published on: July 22, 2025

Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias.

Thomas C Terwilliger1, Ralf W Grosse-Kunstleve, Pavel V Afonine

  • 1Los Alamos National Laboratory, Los Alamos, NM 87545, USA. terwilliger@lanl.gov

Acta Crystallographica. Section D, Biological Crystallography
|May 6, 2008
PubMed
Summary

This study introduces a novel iterative OMIT map procedure to create unbiased atomic models. This method enhances structural biology by improving model validation and accuracy.

Related Experiment Videos

Last Updated: Jul 5, 2026

Constructing and Visualizing Models using Mime-based Machine-learning Framework
06:19

Constructing and Visualizing Models using Mime-based Machine-learning Framework

Published on: July 22, 2025

Area of Science:

  • Crystallography
  • Structural Biology
  • Computational Biology

Background:

  • Atomic model refinement in structural biology can introduce bias.
  • Accurate validation of atomic models is crucial for reliable structural data.

Purpose of the Study:

  • To present a procedure for generating unbiased OMIT maps for iterative model building.
  • To enhance the validation of atomic models in crystallography.

Main Methods:

  • Developing a procedure for iterative model building and density modification.
  • Creating composite iterative-build OMIT maps from overlapping OMIT regions.
  • Applying the method to molecular replacement and experimentally phased structures.

Main Results:

  • The iterative-build OMIT map is unbiased by the atomic model.
  • The map benefits from model-based information elsewhere in the unit cell.
  • Demonstrated successful application to PDB structures, removing model bias.

Conclusions:

  • The presented procedure offers a robust method for atomic model validation.
  • This technique can improve the accuracy and reliability of structural models.
  • Potential applications in validating specific features and overall model integrity.