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Energy landscapes reviews

Energy Landscapes by D.J. Wales
Cambridge University Press (Cambridge) 2003
Hardback edition: ISBN 0521814154
J.A. Joseph, K. Röder, D. Chakraborty, R.G. Mantell and D.J. Wales, Chem. Commun, 53, 6974-6988 (2017)
Exploring biomolecular energy landscapes
D.J. Wales, Phil. Trans. Roy. Soc. A, 370, 2877-2899 (2012).
D.J. Wales, Curr. Op. Struct. Biol., 20, 3-10 (2010)
Energy Landscapes: Some New Horizons
K. Klenin, B. Strodel, D.J. Wales and W. Wenzel, Biochimica et Biophysica Acta, 1814, 977-1000 (2011)
Modelling Proteins: Conformational Sampling and Reconstruction of Folding Kinetics
D.J. Wales and T.V. Bogdan, J. Phys. Chem. B, 110, 20765-20776 (2006)
Feature Article: Potential Energy and Free Energy Landscapes
D.J. Wales, J.P.K. Doye, M.A. Miller, P.N. Mortenson and T.R. Walsh, Adv. Chem. Phys., 115, 1-111 (2000)
Energy Landscapes: from Clusters to Biomolecules

 

Thermodynamics of finite systems

F. Calvo, D.J. Wales, J.P.K. Doye, R.S. Berry, P. Labastie and M. Schmidt, Europhys. Lett., 82, 43003 (2008).
Comment on "Critical analysis of negative heat capacities in nanoclusters"
J.P.K. Doye and D.J. Wales, J. Chem. Phys., 102, 9673-9688, (1995)
An order parameter approach to coexistence in atomic clusters
D.J. Wales and J.P.K. Doye, J. Chem. Phys., 103, 3061-3070 (1995)
Coexistence and phase separation in clusters: From the small to the not-so-small regime
R.M. Lynden-Bell and D.J. Wales, J. Chem. Phys., 101, 1460-1476 (1994)
Free Energy Barriers to Melting in Atomic Clusters
D.J. Wales and R.S. Berry, Phys. Rev. Lett., 73, 2875-2878 (1994)
Coexistence in Finite Systems
D.J. Wales and J.P.K. Doye, J. Chem. Phys., 119, 12409-12416 (2003)
Coexistence and phase separation in clusters: From the small to the not-so-small regime

 

Growth in the number of minima (and transition states) with system size

F.H. Stillinger and T.A. Weber, Phys. Rev. A, 25, 978 (1982)
Hidden Structure in Liquids
F.H. Stillinger and T.A. Weber, Science, 225, 983-989 (1984)
Packing Structures and Transitions in Liquids and Solids
D.J. Wales and J.P.K. Doye, J. Chem. Phys., 119, 12409-12416 (2003)
Stationary Points and Dynamics in High-Dimensional Systems

Basin-hopping global optimization

F. Calvo, D. Schebarchov and D.J. Wales, J. Chem. Theory. Comput. 2, 902 (2016) (DOI: 10.1021/acs.jctc.5b00962)                                                                                                                Grand and Semigrand Canonical Basin-Hopping

Basin-hopping parallel tempering: B. Strodel, J.W.L. Lee, C.S. Whittleston and D.J. Wales, Journal of the American Chemical Society. 132, 13300 (2010).                                    Transmembrane structures for Alzheimer's Aβ(1-42) oligomers.

M.T. Oakley, R.L. Johnston and D.J. Wales, Phys. Chem. Chem. Phys., 15, 3965-3976 (2013).
Symmetrisation Schemes for Global Optimisation of Atomic Clusters
D.J. Wales and J.P.K. Doye, J. Phys. Chem. A, 101, 5111 (1997)
Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms
Z. Li and H. A. Scheraga, Proc. Natl. Acad. Sci. USA 84, 6611 (1987).
Z. Li and H. A. Scheraga, J. Mol. Struct., 179, 333 (1988)

Group rotation moves for basin-hopping global optimisation

K. Mochizuki, C.S. Whittleston, S. Somani, H. Kusumaatmaja and D.J. Wales, Phys. Chem. Chem. Phys., 16, 2842-2853, (2014). 
A Conformational Factorisation Approach for Estimating the Binding Free Energies of Macromolecules
M.T. Oakley and R.L. Johnston, J. Chem. Theory Comput. 10, 1810– 1816, (2014).
Energy landscapes and global optimization of self-assembling cyclic peptides

 

Basin-sampling and the superposition approach to thermodynamics

K. Mochizuki, C.S. Whittleston, S. Somani, H. Kusumaatmaja and D.J. Wales, Phys. Chem. Chem. Phys., 16, 2842-2853, (2014). 
A Conformational Factorisation Approach for Estimating the Binding Free Energies of Macromolecules
D.J. Wales, Chem. Phys. Lett., 584, 1-9 (2013).
Frontiers Article: Surveying a Complex Potential Energy Landscape: Overcoming Broken Ergodicity Using Basin-Sampling
T.V. Bogdan, D.J. Wales and F. Calvo, J. Chem. Phys., 124, 044102 (2006).
Equilibrium Thermodynamics from Basin-Sampling
B. Strodel and D.J. Wales, Chem. Phys. Lett., 466, 105-115 (2008).
Frontiers Article: Free Energy Surfaces from an Extended Harmonic Superposition Approach and Kinetics for Alanine Dipeptide
D. J. Wales, Mol. Phys., 78, 151-171 (1993)
Coexistence in Small Inert Gas Clusters

 

Dijkstra-based missing connection algorithm for linking (possibly distant) minima

J.M. Carr, S.A. Trygubenko and D.J. Wales, J. Chem. Phys., 122, 234903 (2005).
Finding Pathways Between Distant Local Minima

 

Multi-funnel landscapes

K. Röder and D.J. Wales, J. Phys. Chem. B, (2018)
Evolved minimal frustration in multifunctional biomolecules
F. Calvo, Phys. Rev. E, 82, 046703 (2010)
Free-energy landscapes from adaptively biased methods: Application to quantum systems
J.P.K. Doye, M.A. Miller and D.J. Wales, J. Chem. Phys., 110, 6896-6906 (1999)
The double-funnel energy landscape of the 38-atom Lennard-Jones cluster

 

Disconnectivity graphs

O.M. Becker and M. Karplus, J. Chem. Phys., 106, 1495 (1997)
The topology of multidimensional potential energy surfaces: theory and application to peptide structure and kinetics
D.J. Wales, M.A. Miller and T.R. Walsh, Nature, 394, 758-760 (1998)
Archetypal Energy Landscapes

 

Free energy disconnectivity graphs

D.A. Evans and D.J. Wales, J. Chem. Phys., 118, 3891-3897 (2003)
Free Energy Landscapes of Model Peptides and Proteins
S.V. Krivov and M.Karplus, J. Chem. Phys., 117, 10894 (2002).
Hidden complexity of free energy surfaces for peptide (protein) folding

 

Discrete path sampling

D.J. Wales, Mol. Phys., 102, 891-908 (2004)
Some Further Applications of Discrete Path Sampling to Cluster Isomerization
D.J. Wales, Mol. Phys., 100, 3285-3306 (2002)
Discrete Path Sampling

 

DIJPAIR

B. Strodel, C.S. Whittleston and D.J. Wales, J. Am. Chem. Soc., 129, 16005-16014 (2007).
Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide

 

FREEPAIRS

J.M. Carr and D.J. Wales, J. Phys. Chem. B, 112, 8760-8769 (2008).
Folding Pathways and Rates for the Three-Stranded beta-sheet Peptide Beta3s Using Discrete Path Sampling

 

SHORTCUT

J.M. Carr and D.J. Wales, J. Chem. Phys., 123, 234901 (2005).
Global Optimization and Folding Pathways of Selected alpha-Helical Proteins
B. Strodel, C.S. Whittleston and D.J. Wales, J. Am. Chem. Soc., 129, 16005-16014 (2007).
Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide

 

SHORTCUT BARRIER

B. Strodel, C.S. Whittleston and D.J. Wales, J. Am. Chem. Soc., 129, 16005-16014 (2007).
Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide

 

UNTRAP

B. Strodel, C.S. Whittleston and D.J. Wales, J. Am. Chem. Soc., 129, 16005-16014 (2007).
Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide

 

CONNECTUNC

K. Röder and D.J. Wales, J. Am. Chem. Soc., 140, 4018-4027 (2018). 
Energy Landscapes for the Aggregation of Aβ17–42

Doubly-nudged elastic band algorithm

S.A. Trygubenko and D.J. Wales, J. Chem. Phys., 120, 2082-2094 (2004)
A Doubly Nudged Elastic Band Method for Finding Transition States
S.A. Trygubenko and D.J. Wales, J. Chem. Phys., 120, 7820-7820, (2004)
Erratum: A Doubly Nudged Elastic Band Method for Finding Transition States [J. Chem. Phys. 120, 2082 (2004)]
D. Sheppard, R. Terrell and G. Henkelman, J. Chem. Phys., 128, 134106, (2008)
Optimization methods for finding minimum energy paths

 

Nudged elastic band algorithm

G. Mills and H. Jonsson, Phys. Rev. Lett., 72, 1124 (1994).
G. Mills, H. Jonsson and G. K. Schenter, Surf. Sci., 324, 305 (1995).
H. Jonsson, G. Mills, and K. W. Jacobsen, Nudged elastic band method for finding minimum energy paths of transitions, in Classical and Quantum Dynamics in Condensed Phase Simulations, edited by B. J. Berne, G. Ciccotti, and D. F. Coker, World Scientific, Singapore, (1998) p. 385.
G. Henkelman, B. P. Uberuaga and H. Jonsson, J. Chem. Phys., 113, 9901 (2000).
G. Henkelman and H. Jonsson, J. Chem. Phys., 113 , 9978 (2000).

 

Fastest-path analysis using Dijkstra's shortest path algorithm

D.A. Evans and D.J. Wales, J. Chem. Phys., 121, 1080-1090 (2004)
Folding of the GB1 Hairpin Peptide from Discrete Path Sampling
E.W. Dijkstra, Numerische Math. 1, 269 (1959).
A Note on Two Problems in Connexion with Graphs

 

Hybrid eigenvector-following

L.J. Munro and D. J. Wales, Phys. Rev. B, 59, 3969-3980 (1999).
Defect Migration in Crystalline Silicon
Y. Zeng, P. Xiao and G. Henkelman, J. Chem. Phys., 140, 044115, (2014)
Unification of algorithms for minimum mode optimization.

 

k-shortest paths analysis (recursive enumeration algorithm)

J.M. Carr and D.J. Wales, Latest Advances in Atomic Cluster Collisions: Structure and Dynamics from the Nuclear to the Biological Scale, edited by J.-P. Connerade and A. Solov'yov, Imperial College Press, London, 321-330 (2008).
The Energy Landscape as a Computational Tool
V.M. Jimenez and A.Marzal, in Algorithm Engineering: 3rd International Workshop, WAE'99, London, UK, July 1999., edited by J.S. Vitter and C.D. Zaroliagis, vol. 1668, pp. 15--29. Springer Berlin, Heidelberg (1999).

 

L-BFGS minimization

J.Nocedal, Math. Comput., 35, 773 (1980)
Updating quasi-Newton matrices with limited storage
D.Liu and J.Nocedal, Mathematical Programming B, 45, 503 (1989)
On the Limited Memory Method for Large Scale Optimization

 

Local rigidification

V. Rühle, H. Kusumaatmaja, D. Chakrabarti and D.J. Wales, J. Chem. Theory Comput., 9, 4026-4034 (2013).
Exploring energy landscapes: metrics, pathways, and normal mode analysis for rigid-body molecules
H. Kusumaatmaja, C.S. Whittleston and D.J. Wales, J. Chem. Theory Comput., 8, 5159-5165 (2012).
A Local Rigid Body Framework for Global Optimization of Biomolecules

 

NGT (new graph transformation) algorithm for calculation of phenomenological rate constants

D.J. Wales, J. Chem. Phys., 130, 204111 (2009).
Calculating Rate Constants and Committor Probabilities for Transition Networks by Graph Transformation

 

GT (graph transformation) algorithm for calculation of phenomenological rate constants

D.J. Wales, J. Chem. Phys., 130, 204111 (2009).
Calculating Rate Constants and Committor Probabilities for Transition Networks by Graph Transformation
S.A. Trygubenko and D.J. Wales, J. Chem. Phys., 124, 234110 (2006)
Graph Transformation Method for Calculating Waiting Times in Markov Chains
S.A. Trygubenko and D.J. Wales, Mol. Phys., 104, 1497-1507 (2006)
Kinetic Analysis of Discrete Path Sampling Stationary Point Databases

 

Optimal alignment of two structures with respect to overall translation, rotation and permutational isomerisation via the shortest augmenting path algorithm: PERMDIST

D.J. Wales and J.M. Carr, J. Chem. Theory Comput., 8, 5020-5034 (2012).
A Quasi-Continuous Interpolation Scheme for Pathways Between Distant Configurations

 

Quasi-continuous interpolation scheme

K. Röder and D.J. Wales, J. Chem. Theory Comput., 14, 4271-4278 (2018).
Predicting Pathways between Distant Configurations for Biomolecules
D.J. Wales and J.M. Carr, J. Chem. Theory Comput., 8, 5020-5034 (2012).
A Quasi-Continuous Interpolation Scheme for Pathways Between Distant Configurations

 

Self-consistent (re)grouping of stationary points on the PES into free energy minima and transition states

J.M. Carr and D.J. Wales, J. Phys. Chem. B, 112, 8760-8769 (2008).
Folding Pathways and Rates for the Three-Stranded beta-sheet Peptide Beta3s Using Discrete Path Sampling

 

Stone-Wales rearrangement

Y. Kumeda, D.J. Wales and L.J. Munro, Chem. Phys. Lett., 341, 185-194 (2001)
Transition States and Rearrangement Mechanisms from Hybrid Eigenvector-Following and Density Functional Theory. Application to C10H10 and Defect Migration in Crystalline Silicon
A.J. Stone and D.J. Wales, Chem. Phys. Lett., 128, 501-503 (1986)
Theoretical Studies of Icosahedral C60 and Some Related Structures

 

Catastrophe theory

T.V. Bogdan and D.J. Wales, J. Chem. Phys., 120, 11090-11099, (2004)
New Results for Phase Transitions From Catastrophe Theory
D.J. Wales, Science, 293, 2067-2070 (2001)
A Microscopic Basis for the Global Appearance of Energy Landscapes Abstract Full text
Perspectives article: R.H. Leary, Science 293, 2013-2014 (2001)
Flirting with Catastrophe
NCSA press: http://www.npaci.edu/online/v5.19/leary.html

 

Range of the potential

F. Calvo, J.P.K. Doye and D.J. Wales, Nanoscale, 4, 1085-1100 (2012).
Energy Landscapes of Colloidal Clusters: Thermodynamics and Rearrangement Mechanisms
D.J. Wales, ChemPhysChem, 11, 2491-2494 (2010)
Highlights: Energy Landscapes of Clusters Bound by Short-Ranged Potentials
J.P.K. Doye and D.J. Wales, J. Chem. Soc., Faraday Trans., 93, 4233-4243 (1997)
Structural Consequences of the Range of the Interatomic Potential. A Menagerie of Clusters
J.P.K. Doye and D.J. Wales, Science, 271, 484-487 (1996)
The structure and stability of atomic liquids: from clusters to bulk
J.P.K. Doye and D.J. Wales, J. Phys. B, 29, 4859-4894 (1996)
The effect of the range of the potential on the structure and stability of simple liquids: from clusters to bulk, from sodium to C60
J.P.K. Doye, D.J. Wales and R.S. Berry, J. Chem. Phys., 103, 4234-4249 (1995)
The effect of the range of the potential on the structures of clusters
P.A. Braier, R.S. Berry and D.J. Wales, J. Chem. Phys., 93, 8745-8756 (1990)
How the Range of Pair Interactions Governs Features of Multidimensional Potentials