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Related Concept Videos

Shape and Texture of Coarse Aggregate01:25

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Aggregate shape is classified based on the relative sharpness or roundness of the edges and corners. This classification includes categories like rounded, angular, elongated, and flaky, each with specific characteristics. Rounded aggregates, fully shaped by attrition, are typical of river or seashore gravel, while angular aggregates, such as crushed rock, have well-defined edges. Aggregates that are elongated and flaky are less desirable, as they can reduce the workability and strength of...
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A polyprotic acid contains more than one ionizable hydrogen and undergoes a stepwise ionization process.  If the acid dissociation constants of the ionizable protons differ sufficiently from each other, then the titration curve for such polyprotic acid generates a distinct equivalence point for each of its ionizable hydrogens. Therefore, titration of a diprotic acid results in the formation of two equivalence points, whereas the titration of a triprotic acid results in the formation of three...
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Acid-Base Titration Curves02:23

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A titration curve is a plot of some solution property versus the amount of added titrant. For acid-base titrations, solution pH is a useful property to monitor because it varies predictably with the solution composition and, therefore, may be used to monitor the titration’s progress and detect its endpoint. Acid-base titration can be performed with a strong acid and a strong base, a strong acid and a weak base, or a strong base and a weak acid.
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Titration Calculations: Weak Acid - Strong Base03:55

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Titration Calculations: Strong Acid - Strong Base02:28

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Calculating pH for Titration Solutions: Strong Acid/Strong Base
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Redox titration is a chemical analysis technique used to determine the concentration of an unknown substance by measuring the electron transfer in a redox (reduction-oxidation) reaction. The process involves gradually adding a titrant with a known concentration of an oxidizing or reducing agent, to the analyte, the solution with an unknown concentration, until reaching the endpoint, which indicates the completion of the reaction between the two substances. Ensuring the analyte is in a single...
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Updated: Jan 25, 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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Coarse-grained dynamic RNA titration simulations.

S Pasquali1, E Frezza1, F L Barroso da Silva2,3

  • 1Laboratoire de Cristallographie et RMN Biologiques, CNRS UMR 8015, Université Paris Descartes, Paris 75006, France.

Interface Focus
|May 9, 2019
PubMed
Summary
This summary is machine-generated.

Investigating RNA

Keywords:
RNAcoarse-grained modelpHtitration

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Area of Science:

  • Biochemistry and Molecular Biology
  • Computational Biology and Biophysics

Background:

  • Electrostatic interactions are crucial for biomolecular processes and RNA structure.
  • RNA's negative charge amplifies electrostatic effects, influencing its organization and function.
  • Solution pH critically affects RNA's charge, structure, and behavior by regulating base protonation.

Purpose of the Study:

  • To explore RNA conformational plasticity across different pH values.
  • To compute electrostatic properties and local pKa values for RNA nucleotides.
  • To understand the influence of pH on RNA structure and dynamics.

Main Methods:

  • Utilized constant-pH Monte Carlo simulations with a fast proton titration scheme.
  • Employed the coarse-grained model HiRE-RNA for molecular dynamics simulations.
  • Simulated RNA molecules at constant pH to analyze structural and electrostatic properties.

Main Results:

  • Demonstrated RNA's conformational plasticity in response to varying pH conditions.
  • Successfully computed local pKa values for individual nucleotides within the RNA structure.
  • Provided insights into the electrostatic properties of RNA as a function of pH.

Conclusions:

  • Constant-pH simulations offer a powerful approach to study RNA behavior.
  • pH is a critical determinant of RNA structure, dynamics, and electrostatic interactions.
  • This study enhances our understanding of RNA's environmental sensitivity and molecular mechanisms.