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Related Concept Videos

Chemical Equilibria: Systematic Approach to Equilibrium Calculations01:21

Chemical Equilibria: Systematic Approach to Equilibrium Calculations

Equilibrium calculations for systems involving multiple equilibria are often complex. For example, to calculate the solubility of a sparingly soluble salt in an aqueous solution in the presence of a common ion, one must consider all the equilibria in this solution. Calculations for these systems can be complicated and tedious, so a systematic approach with a series of steps is often helpful. The process is detailed below.
The first step is to identify all the chemical reactions involved, The...
Constant Pressure Calorimetry03:02

Constant Pressure Calorimetry

Calorimetry is a technique used to measure the amount of heat involved in a chemical or physical process or to measure the heat transferred to or from a substance. The heat is exchanged with a calibrated and insulated device called the calorimeter. Calorimetry experiments are based on the assumption that there is no heat exchange between the insulated calorimeter and the external environment. The well-insulated calorimeters prevent the transfer of heat between the calorimeter and its external...
Le Chatelier's Principle: Changing Temperature02:19

Le Chatelier's Principle: Changing Temperature

Consistent with the law of mass action, an equilibrium stressed by a change in concentration will shift to re-establish equilibrium without any change in the value of the equilibrium constant, K. When an equilibrium shifts in response to a temperature change, however, it is re-established with a different relative composition that exhibits a different value for the equilibrium constant.
To understand this phenomenon, consider the elementary reaction:
Constant Volume Calorimetry02:41

Constant Volume Calorimetry

Calorimeters are useful to determine the heat released or absorbed by a chemical reaction. Coffee cup calorimeters are designed to operate at constant (atmospheric) pressure and are convenient to measure heat flow (or enthalpy change) accompanying processes that occur in solution at constant pressure. A different type of calorimeter that operates at constant volume, colloquially known as a bomb calorimeter, is used to measure the energy produced by reactions that yield large amounts of heat and...
Chemical Equilibria: Redefining Equilibrium Constant01:20

Chemical Equilibria: Redefining Equilibrium Constant

The effect of an inert salt on the solubility of a sparingly soluble salt is known as the salt effect. The degree of the salt effect varies with the ionic strength of the solution, which in turn depends on the activity of the species in the solution. The activity is expressed as the product of concentration and the activity coefficient of the species.
To calculate the equilibrium constants of solutions of moderately high ionic strength, one must account for the salt effect. This redefined...
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...

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Updated: Jun 2, 2026

Hot Biological Catalysis: Isothermal Titration Calorimetry to Characterize Enzymatic Reactions
13:00

Hot Biological Catalysis: Isothermal Titration Calorimetry to Characterize Enzymatic Reactions

Published on: April 4, 2014

Thermodynamically consistent model calibration in chemical kinetics.

Garrett Jenkinson1, John Goutsias

  • 1Whitaker Biomedical Engineering Institute, The Johns Hopkins University, Baltimore, MD 21218, USA. goutsias@jhu.edu

BMC Systems Biology
|May 10, 2011
PubMed
Summary
This summary is machine-generated.

We developed a method to ensure biochemical models obey thermodynamic laws, yielding accurate cellular function descriptions. This thermodynamically consistent model calibration (TCMC) method provides physically realistic parameter values for biochemical reaction systems.

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Combustion Chemistry of Fuels: Quantitative Speciation Data Obtained from an Atmospheric High-temperature Flow Reactor with Coupled Molecular-beam Mass Spectrometer
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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

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Related Experiment Videos

Last Updated: Jun 2, 2026

Hot Biological Catalysis: Isothermal Titration Calorimetry to Characterize Enzymatic Reactions
13:00

Hot Biological Catalysis: Isothermal Titration Calorimetry to Characterize Enzymatic Reactions

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Combustion Chemistry of Fuels: Quantitative Speciation Data Obtained from an Atmospheric High-temperature Flow Reactor with Coupled Molecular-beam Mass Spectrometer
07:24

Combustion Chemistry of Fuels: Quantitative Speciation Data Obtained from an Atmospheric High-temperature Flow Reactor with Coupled Molecular-beam Mass Spectrometer

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Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

Area of Science:

  • Systems biology
  • Biochemical kinetics
  • Thermodynamics

Background:

  • Biochemical reaction systems are governed by thermodynamic laws, dictating relationships between reaction rate constants.
  • Experimental data often yields parameter values violating thermodynamic constraints, leading to non-physical and inaccurate models.
  • This inaccuracy can result in erroneous descriptions of cellular functions.

Purpose of the Study:

  • To introduce a method for calibrating biochemical reaction models to satisfy thermodynamic constraints.
  • To ensure the physical realizability and accuracy of biochemical models.
  • To provide a framework for obtaining thermodynamically feasible parameter values.

Main Methods:

  • Developed a thermodynamically consistent model calibration (TCMC) method.
  • Formulated model calibration as a constrained optimization problem incorporating thermodynamic laws.
  • Applied TCMC to a model of the EGF/ERK signaling cascade.

Main Results:

  • Demonstrated TCMC's ability to yield thermodynamically feasible kinetic parameters.
  • Showcased the qualitative and quantitative significance of enforcing thermodynamic constraints.
  • Validated the effectiveness of TCMC using the EGF/ERK signaling cascade model.

Conclusions:

  • TCMC offers a simple, flexible approach for deriving physically plausible kinetic parameters for biochemical systems.
  • The method can correct existing thermodynamically infeasible models and estimate parameters for new models.
  • TCMC enhances estimation performance, reduces computational complexity, and mitigates data overfitting.