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When magnetic nuclei in a sample achieve resonance and undergo relaxation, the signal detected in NMR is an approximately exponential free induction decay. Fourier transform of an exponential decay yields a Lorentzian peak in the frequency domain. Lorentzian peaks in an NMR spectrum are defined by their amplitude, full width at half maximum, and position, where the peak width is governed by the spin-spin relaxation time alone. In real experiments, however, the applied magnetic field is rendered...
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Newtonian fluids exhibit a constant viscosity, meaning their shear stress and shear strain rate are directly proportional. This property ensures a predictable and stable response to applied forces, maintaining a linear relationship between force and flow. Examples include water, air, and light oils, consistently demonstrating this proportional behavior regardless of external conditions.
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Updated: Jun 10, 2025

An Analog Macroscopic Technique for Studying Molecular Hydrodynamic Processes in Dense Gases and Liquids
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Adaptive resolution scheme (AdResS) simulations accurately capture molecular unfolding dynamics. This method enhances computational efficiency for force probe molecular dynamics (FPMD) simulations, matching experimental timescales.

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Area of Science:

  • Computational chemistry
  • Biophysics
  • Molecular dynamics

Background:

  • Simulating molecular unfolding under mechanical force requires atomistic detail.
  • Coarse-graining methods are often necessary to match experimental timescales in force spectroscopy.

Purpose of the Study:

  • To apply the adaptive resolution scheme (AdResS) to force probe molecular dynamics (FPMD) simulations.
  • To evaluate AdResS accuracy for molecular unfolding pathways using model systems.
  • To investigate the impact of different coarse-graining methodologies on simulation results.

Main Methods:

  • Force probe molecular dynamics (FPMD) simulations.
  • Adaptive resolution scheme (AdResS) with iterative Boltzmann inversion and ideal gas approximation.
  • Analysis of unfolding pathways, characteristic forces, and hydrogen bond changes.

Main Results:

  • AdResS simulations show excellent agreement with fully atomistic FPMD simulations for both simple and complex unfolding pathways.
  • The average number of native contacts is a reliable order parameter for peptide unfolding.
  • The methodology accurately reproduces force distributions and hydrogen bond dynamics.

Conclusions:

  • AdResS is a robust and accurate method for simulating mechanical unfolding of biomolecules.
  • The approach is suitable for studying systems relevant to experimental force spectroscopy.
  • AdResS offers a computationally efficient way to achieve atomistic-level insights into molecular mechanics.