Literature DB >> 29677468

Exploring Energy Landscapes.

David J Wales1.   

Abstract

Recent advances in the potential energy landscapes approach are highlighted, including both theoretical and computational contributions. Treating the high dimensionality of molecular and condensed matter systems of contemporary interest is important for understanding how emergent properties are encoded in the landscape and for calculating these properties while faithfully representing barriers between different morphologies. The pathways characterized in full dimensionality, which are used to construct kinetic transition networks, may prove useful in guiding such calculations. The energy landscape perspective has also produced new procedures for structure prediction and analysis of thermodynamic properties. Basin-hopping global optimization, with alternative acceptance criteria and generalizations to multiple metric spaces, has been used to treat systems ranging from biomolecules to nanoalloy clusters and condensed matter. This review also illustrates how all this methodology, developed in the context of chemical physics, can be transferred to landscapes defined by cost functions associated with machine learning.

Keywords:  energy landscapes; enhanced sampling; global optimization; machine learning; rare events

Year:  2018        PMID: 29677468     DOI: 10.1146/annurev-physchem-050317-021219

Source DB:  PubMed          Journal:  Annu Rev Phys Chem        ISSN: 0066-426X            Impact factor:   12.703


  12 in total

1.  Phase Transition in a Heterogeneous Membrane: Atomically Detailed Picture.

Authors:  Arman Fathizadeh; Mason Valentine; Carlos R Baiz; Ron Elber
Journal:  J Phys Chem Lett       Date:  2020-06-18       Impact factor: 6.475

2.  Characterizing key features in the formation of ice and gas hydrate systems.

Authors:  Shuai Liang; Kyle Wm Hall; Aatto Laaksonen; Zhengcai Zhang; Peter G Kusalik
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2019-06-03       Impact factor: 4.226

3.  Archetypal landscapes for deep neural networks.

Authors:  Philipp C Verpoort; Alpha A Lee; David J Wales
Journal:  Proc Natl Acad Sci U S A       Date:  2020-08-25       Impact factor: 11.205

4.  Emerging Diversity in Lipid-Protein Interactions.

Authors:  Valentina Corradi; Besian I Sejdiu; Haydee Mesa-Galloso; Haleh Abdizadeh; Sergei Yu Noskov; Siewert J Marrink; D Peter Tieleman
Journal:  Chem Rev       Date:  2019-02-13       Impact factor: 60.622

5.  Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools.

Authors:  Balaji Nagarajan; Nehru Viji Sankaranarayanan; Umesh R Desai
Journal:  Glycobiology       Date:  2020-07-16       Impact factor: 4.313

6.  Exact Topology of the Dynamic Probability Surface of an Activated Process by Persistent Homology.

Authors:  Farid Manuchehrfar; Huiyu Li; Wei Tian; Ao Ma; Jie Liang
Journal:  J Phys Chem B       Date:  2021-05-03       Impact factor: 2.991

7.  Direct detection of molecular intermediates from first-passage times.

Authors:  Alice L Thorneywork; Jannes Gladrow; Yujia Qing; Marc Rico-Pasto; Felix Ritort; Hagan Bayley; Anatoly B Kolomeisky; Ulrich F Keyser
Journal:  Sci Adv       Date:  2020-05-01       Impact factor: 14.136

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

Authors:  Konstantin Röder; David J Wales
Journal:  Front Mol Biosci       Date:  2022-01-27

9.  Calculation of absolute molecular entropies and heat capacities made simple.

Authors:  Philipp Pracht; Stefan Grimme
Journal:  Chem Sci       Date:  2021-03-25       Impact factor: 9.825

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

Authors:  Daniel J Sharpe; Konstantin Röder; David J Wales
Journal:  J Phys Chem B       Date:  2020-05-06       Impact factor: 2.991

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.