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Literature DB >> 24374625

Observation time scale, free-energy landscapes, and molecular symmetry.

Abstract

When structures that interconvert on a given time scale are lumped together, the corresponding free-energy surface becomes a function of the observation time. This view is equivalent to grouping structures that are connected by free-energy barriers below a certain threshold. We illustrate this time dependence for some benchmark systems, namely atomic clusters and alanine dipeptide, highlighting the connections to broken ergodicity, local equilibrium, and "feasible" symmetry operations of the molecular Hamiltonian.

Entities: Chemical

Mesh：

Substances：
Alanine

Year: 2013 PMID： 24374625 PMCID： PMC3896148 DOI： 10.1073/pnas.1319599111

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

27 in total

1. Protein conformational dynamics probed by single-molecule electron transfer.

Authors: Haw Yang; Guobin Luo; Pallop Karnchanaphanurach; Tai-Man Louie; Ivan Rech; Sergio Cova; Luying Xun; X Sunney Xie
Journal: Science Date: 2003-10-10 Impact factor: 47.728

2. Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms.

Authors: Florent Calvo; Jonathan P K Doye; David J Wales
Journal: Nanoscale Date: 2011-10-06 Impact factor: 7.790

3. Materials science. Turning away from high symmetry.

Authors: John C Crocker
Journal: Science Date: 2010-01-29 Impact factor: 47.728

4. Energy landscapes of clusters bound by short-ranged potentials.

Authors: David J Wales
Journal: Chemphyschem Date: 2010-08-23 Impact factor: 3.102

5. Comparison of multiple Amber force fields and development of improved protein backbone parameters.

Authors: Viktor Hornak; Robert Abel; Asim Okur; Bentley Strockbine; Adrian Roitberg; Carlos Simmerling
Journal: Proteins Date: 2006-11-15

6. Refined kinetic transition networks for the GB1 hairpin peptide.

Authors: Joanne M Carr; David J Wales
Journal: Phys Chem Chem Phys Date: 2009-03-17 Impact factor: 3.676

Review 7. Energy landscapes: some new horizons.

Authors: David J Wales
Journal: Curr Opin Struct Biol Date: 2010-01-22 Impact factor: 6.809

8. Diffusive reaction dynamics on invariant free energy profiles.

Authors: Sergei V Krivov; Martin Karplus
Journal: Proc Natl Acad Sci U S A Date: 2008-09-04 Impact factor: 11.205

9. Relaxation of caloric curves on complex potential energy surfaces.

Authors: F Calvo; D J Wales
Journal: J Chem Phys Date: 2008-04-21 Impact factor: 3.488

10. Colloidal self-assembly: designed to yield.

Authors: Daan Frenkel; David J Wales
Journal: Nat Mater Date: 2011-06 Impact factor: 43.841

8 in total

1. RNA Modeling with the Computational Energy Landscape Framework.

Authors: Konstantin Röder; Samuela Pasquali
Journal: Methods Mol Biol Date: 2021

2. A Statistical Physics Characterization of the Complex Systems Dynamics: Quantifying Complexity from Spatio-Temporal Interactions.

Authors: Hana Koorehdavoudi; Paul Bogdan
Journal: Sci Rep Date: 2016-06-14 Impact factor: 4.379

Observation time scale, free-energy landscapes, and molecular symmetry.

1. Protein conformational dynamics probed by single-molecule electron transfer.

2. Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms.

3. Materials science. Turning away from high symmetry.

4. Energy landscapes of clusters bound by short-ranged potentials.

5. Comparison of multiple Amber force fields and development of improved protein backbone parameters.

6. Refined kinetic transition networks for the GB1 hairpin peptide.

Review 7. Energy landscapes: some new horizons.

8. Diffusive reaction dynamics on invariant free energy profiles.

9. Relaxation of caloric curves on complex potential energy surfaces.

10. Colloidal self-assembly: designed to yield.

1. RNA Modeling with the Computational Energy Landscape Framework.

2. A Statistical Physics Characterization of the Complex Systems Dynamics: Quantifying Complexity from Spatio-Temporal Interactions.

3. Intrinsically disordered energy landscapes.

4. The Energy Landscape Perspective: Encoding Structure and Function for Biomolecules.

Review 5. Dynamical Signatures of Multifunnel Energy Landscapes.

6. Strain and the optoelectronic properties of nonplanar phosphorene monolayers.

7. Computational investigation of RNA CUG repeats responsible for myotonic dystrophy 1.

8. Energy Landscapes of Deoxyxylo- and Xylo-Nucleic Acid Octamers.