Tight-binding Hamiltonian
Tight-binding Hamiltonian - Related Videos
01:29
Tight Junctions
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2023
Tight junctions are molecular seals between cells that prevent the leaking of fluids, ions, and other small solutes across cavities and compartments in multicellular organisms. They are mainly composed of claudin and occludin transmembrane proteins, and other proteins such as tricellulin and JAM (junctional adhesion molecule). All these proteins are 4-pass transmembrane proteins, except JAM, which is a single-pass transmembrane protein belonging to the immunoglobulin superfamily. The...
04:15
Fluorescence Localization of Tight Junction Proteins and Stress Fibers in Endothelial Cells
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2025
Source: Alluri, H., et al. Oxygen-Glucose Deprivation and Reoxygenation as an In Vitro Ischemia-Reperfusion Injury Model for Studying Blood-Brain Barrier Dysfunction. J. Vis. Exp. (2015).The video demonstrates the fluorescent localization of tight junction proteins and stress fibers in rat brain microvascular endothelial cells (RBMECs). In the stressed monolayer, fluorescently labeled antibodies are used to tag the tight junction proteins, while fluorophore-tagged phalloidin labels the stress...
02:18
The Equilibrium Binding Constant and Binding Strength
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2020
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium: where P and L are the unbound protein and ligand, respectively, and PL is the protein-ligand complex. As the amount of bound ligand is also related to the rate of ligand binding, experiments can also determine Kb by examining the rates of protein-ligand association (kon) and dissociation (koff) using the following ratio: Thus,...
02:13
Cooperative Binding of Transcription Regulators
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2020
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
08:09
Vasodilation of Isolated Vessels and the Isolation of the Extracellular Matrix of Tight-skin Mice
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Cited by 1 •
2017
We describe the isolation of cardiac extracellular matrix from C57Bl/6J control mice, tight-skin mice, and tight-skin mice treated with the IRF5 inhibitory peptide. We also describe the vasodilation studies on the isolated vessels from C57Bl/6J, tight-skin mice and tight-skin mice treated with the IRF5 inhibitory peptide.
FAQs
On-site energies set the reference energy for electrons associated with individual atomic orbitals. Hopping or resonance integrals occupy the connections that couple orbitals on neighboring sites. Changing either term alters the Hamiltonian matrix and therefore the calculated molecular or electronic levels. This separation lets chemists relate local atomic environments and orbital interactions to bonding patterns in molecules or solids.
When neighboring orbitals are connected by nonzero hopping or resonance integrals, their interaction changes the energy levels relative to isolated on-site values. In a molecule, this coupling provides a compact way to represent covalent bonding and conjugation. Repeated coupling across an extended structure can instead produce a set of closely related levels associated with band formation, linking local interactions to bulk electronic behavior.
The same matrix framework can describe molecular and solid-state systems, but the resulting level patterns differ with the number and arrangement of coupled sites. A molecule is represented through discrete molecular energy levels arising from its atomic orbitals and interactions. In an extended solid, many connected sites generate electronic levels associated with band formation, supporting analysis of broader electronic behavior.
A basic calculation begins by identifying the atomic orbitals used to represent the relevant sites. On-site energies are then assigned, followed by hopping or resonance integrals for neighboring orbital connections. These values form the Hamiltonian matrix, which is solved to obtain molecular or electronic energy levels. The calculated levels can then be related to structure and orbital interactions.
Chemists can apply this approach to examine covalent bonding, conjugated systems, and aromaticity without treating every electronic detail with the same level of complexity. It is also useful for extended solids, where the model connects orbital interactions with band formation and conductivity. More broadly, the calculated levels help relate molecular structure to electronic properties and reactivity.
Calculated energy levels show how the selected atomic orbitals and their couplings combine into molecular or electronic states. Comparing level patterns for different structures can reveal how changes in molecular arrangement or orbital interaction affect the electronic description. In chemistry, those relationships provide context for discussing bonding, conjugation, aromaticity, conductivity, and reactivity within the model.