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The structure of a crystalline solid, whether a metal or not, is best described by considering its simplest repeating unit, which is referred to as its unit cell. The unit cell consists of lattice points that represent the locations of atoms or ions. The entire structure then consists of this unit cell repeating in three dimensions. The three different types of unit cells present in the cubic lattice are illustrated in Figure 1.
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An ionic compound is stable because of the electrostatic attraction between its positive and negative ions. The lattice energy of a compound is a measure of the strength of this attraction. The lattice energy (ΔHlattice) of an ionic compound is defined as the energy required to separate one mole of the solid into its component gaseous ions. For the ionic solid sodium chloride, the lattice energy is the enthalpy change of the process:
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Updated: Feb 15, 2026

Specific Labeling of Mitochondrial Nucleoids for Time-lapse Structured Illumination Microscopy
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Lattice Models of Bacterial Nucleoids.

David S Goodsell1,2, Ludovic Autin1, Arthur J Olson1

  • 1Department of Integrative Structural and Computational Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California , United States.

The Journal of Physical Chemistry. B
|January 18, 2018
PubMed
Summary

We developed a rapid lattice method to model bacterial nucleoids, integrating experimental data for genome simulations. This approach aids in understanding bacterial genome structure and function.

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Area of Science:

  • Computational biology
  • Molecular modeling
  • Genomics

Background:

  • Mesoscale molecular modeling offers insights into cellular processes.
  • Bacterial genome modeling is challenging due to size and complexity.

Purpose of the Study:

  • To present a novel lattice method for rapid bacterial nucleoid model generation.
  • To integrate diverse biophysical experimental data into these models.
  • To provide a foundation for genome simulation and hypothesis generation.

Main Methods:

  • Developed a lattice-based approach for bacterial nucleoid modeling.
  • Incorporated supercoiled plectonemes for circular bacterial genomes.
  • Generated models for Mycoplasma genitalium and Escherichia coli nucleoids.
  • Utilized models to simulate interaction data and create all-atom cell representations.

Main Results:

  • Successfully generated rapid lattice models of bacterial nucleoids.
  • Demonstrated the integration of experimental data into models.
  • Showcased the utility of models for simulating interactions and generating all-atom representations.
  • Validated the method's speed for structure/function relationship analysis.

Conclusions:

  • The lattice method enables efficient bacterial nucleoid modeling.
  • This approach facilitates simulation and hypothesis generation for bacterial genomes.
  • The method supports the creation of comprehensive cellular models.