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Related Concept Videos

Reaction Mechanisms03:06

Reaction Mechanisms

Chemical reactions often occur in a stepwise fashion, involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs.
For instance, the decomposition of ozone appears to follow a mechanism with two steps:
Reaction Mechanisms: The Steady-State Approximation01:26

Reaction Mechanisms: The Steady-State Approximation

The steady-state approximation, also referred to as the quasi-steady-state approximation to differentiate it from a true steady state, is a widely used method for simplifying calculations in complex reaction mechanisms. This approach is particularly useful when dealing with multi-step reactions that involve reverse reactions or several steps, which can significantly increase mathematical complexity and make the reactions nearly unsolvable analytically.The steady-state approximation operates on...
Entropy02:39

Entropy

Salt particles that have dissolved in water never spontaneously come back together in solution to reform solid particles. Moreover, a gas that has expanded in a vacuum remains dispersed and never spontaneously reassembles. The unidirectional nature of these phenomena is the result of a thermodynamic state function called entropy (S). Entropy is the measure of the extent to which the energy is dispersed throughout a system, or in other words, it is proportional to the degree of disorder of a...
Multi-Step Reactions02:31

Multi-Step Reactions

Chemical reactions often occur in a stepwise fashion involving two or more distinct reactions taking place in a sequence. A balanced equation indicates the reacting species and the product species, but it reveals no details about how the reaction occurs at the molecular level. The reaction mechanism (or reaction path) provides details regarding the precise, step-by-step process by which a reaction occurs. Each of the steps in a reaction mechanism is called an elementary reaction. These...
Second Law of Thermodynamics02:49

Second Law of Thermodynamics

In the quest to identify a property that may reliably predict the spontaneity of a process, a promising candidate has been identified: entropy. Processes that involve an increase in entropy of the system (ΔS > 0) are very often spontaneous; however, examples to the contrary are plentiful. By expanding consideration of entropy changes to include the surroundings, a significant conclusion regarding the relation between this property and spontaneity may be reached. In thermodynamic models, the...
Molecular Spectroscopy: Absorption and Emission01:14

Molecular Spectroscopy: Absorption and Emission

Molecules possess discrete energy levels called quantum states. Unlike atoms, which have simpler energy levels, molecules possess additional rotational and vibrational energy levels. Each energy level is separated by an energy gap, with the gaps between adjacent electronic, vibrational, and rotational levels varying significantly. The three types of energy levels in a diatomic molecule are shown in Figure 1.

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Related Experiment Video

Updated: May 18, 2026

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
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Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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What do molecules do when we are not looking? State sequence analysis for stochastic chemical systems.

Pavel Levin1, Jérémie Lefebvre, Theodore J Perkins

  • 1Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, Ontario, Canada, K1H 8L6.

Journal of the Royal Society, Interface
|September 15, 2012
PubMed
Summary

We introduce state sequence analysis to predict stochastic molecular system behavior. This method reveals novel insights into complex biological processes like drug resistance and ion channel dynamics.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology
  • Biophysics

Background:

  • Biomolecular systems rely on ordered chemical transformations.
  • Single-molecule and small-copy-number systems exhibit significant stochastic dynamics.
  • Understanding these stochastic behaviors is crucial for many biological processes.

Purpose of the Study:

  • To propose a novel computational approach, state sequence analysis, for predicting and visualizing the behavior of stochastic molecular systems.
  • To apply this method to real-world biological examples, demonstrating its utility and advantages over existing techniques.

Main Methods:

  • State sequence analysis involves computing maximum probability state sequences.
  • The approach utilizes initial or boundary conditions to guide predictions.
  • Applied to human immunodeficiency virus (HIV) drug resistance mutation acquisition and sodium ion channel gating dynamics.

Main Results:

  • State sequence analysis provides novel insights into the stochastic dynamics of the studied systems.
  • The method accurately captures rare events occurring over long timescales (HIV drug resistance).
  • It effectively models fast, stochastic events like ion channel opening and closing.

Conclusions:

  • State sequence analysis offers a powerful new tool for analyzing complex stochastic molecular systems.
  • This approach surpasses standard time-discretization methods in reproducing system dynamics.
  • It has broad applicability in understanding diverse biomolecular processes governed by stochasticity.