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Energy landscapes reviews

Energy Landscapes by D.J. Wales
Cambridge University Press (Cambridge) 2003
Hardback edition: ISBN 0521814154

D.J. Wales, Ann. Rev. Phys. Chem., 69, 401-425, (2018). Exploring Energy Landscapes
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).  Decoding the Energy Landscape: Extracting Structure, Dynamics and Thermodynamics
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)
acking 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
J.P.K. Doye and D.J. Wales, J. Chem. Phys., 116, 3777-3788 (2002)
Saddle points and dynamics of Lennard-Jones clusters, solids, and supercooled liquids https://doi.org/10.1063/1.1436470  

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 and intrinsically multifunctional systems

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 (self-consistent recursive free energy regrouping)

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 group bib entry CarrW05
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 group bib entry StrodelWW07

 

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 group bib entry StrodelWW07

 

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 group bib entry StrodelWW07

 

CONNECTUNC

K. Röder and D.J. Wales, J. Am. Chem. Soc., 140, 4018-4027 (2018). 
Energy Landscapes for the Aggregation of Aβ17–42  group bib entry doi:10.1021/jacs.7b12896

 

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). bib entry MillsJ94
Quantum and thermal effects in  H2 dissociative adsorption: Evaluation of free energy barriers in multidimensional quantum systems
G. Mills, H. Jonsson and G. K. Schenter, Surf. Sci., 324, 305 (1995). Recommended NEB reference. bib entry Millsjs95
Reversible work transition state theory: application to dissociative adsorption of hydrogen,
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. Recommended citation for sliding down and corner cutting.​​​​​​ issues. bib entry JonssonMJ98
G. Henkelman, B. P. Uberuaga and H. Jonsson, J. Chem. Phys., 113, 9901 (2000).Climbing image extension of the NEB method as well as energy weighted spring constants. bib entry HenkelmanUJ00A climbing image nudged elastic band method for finding saddle points and minimum energy paths,
G. Henkelman and H. Jonsson, J. Chem. Phys., 113 , 9978 (2000). bib entry HenkelmanJ00
Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points
Maras, E., Pizzagalli, L., Ala-Nissila, T. and H. Jonsson,  Sci Rep 7, 11966 (2017).  Stabilised NEB method. bib entry MarasPAJ17
Atomic Scale Formation Mechanism of Edge Dislocation Relieving Lattice Strain in a GeSi overlayer on Si(001),

 

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.

Gradient difference formulation of the Rayleigh-Ritz ratio:
R. G. Mantell, C. E. Pitt and D. J. Wales, J. Chem. Theory Comput., 12, 6182−6191, 2016
GPU-Accelerated Exploration of Biomolecular Energy Landscapes
Wales, D. J.; Carr, J. M.; Khalili, M.; de Souza, V. K.; Strodel, B.; Whittleston, C. S. In Proteins: Energy, Heat and Signal Flow; Leitner, D. M., Straub, J. E., Eds.; Computation in Chemistry; CRC Press: Boca Raton, FL, 2010; Vol. 1; pp 318−319. 
Pathways and Rates for Structural Transformations of Peptides and Proteins

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 mean first passage times and corresponding rate constants

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

Analysis of Kinetic Transition Networks and the GT (graph transformation) algorithm

DJ Wales, J. Phys. Chem. Lett., 13, 6349-6358, 2022.
Perspective: Dynamical Signatures of Multifunnel Energy Landscapes
DJ Sharpe, DJ Wales, Phys Rev E (2021) 104, 015301.
Numerical analysis of first-passage processes in finite Markov chains exhibiting metastability. (468 Committor probablities for LJ38, reactive visitation probabilities, productive paths, 468, SharpeW21b)
DJ Sharpe, DJ Wales, J. Chem. Phys. 155, 140901 (2021).
Perspective: Nearly reducible finite Markov chains: Theory and algorithms (469 SharpeW21c)
DJ Sharpe, DJ Wales Physical Review E (2021) 103, 063306.
Graph transformation and shortest paths algorithms for finite Markov chains. (467 edgeGT SharpeW21a)
D Kannan, DJ Sharpe, TD Swinburne, DJ Wales, The Journal of Chemical Physics (2020) 153, 244108.
Optimal dimensionality reduction of Markov chains using graph transformation. (460 discretetimegt optimal coarse-graining Kemeney constant doi:10.1063/5.0025174)
TD Swinburne, D Kannan, DJ Sharpe, DJ Wales, Journal of Chemical Physics (2020) 153, 134115
Rare events and first passage time statistics from the energy landscape. (458 waitpdf LJ38 rates and FPT compared kPS, GT and eigendecomposition, 8 states doi:10.1063/5.0016244)
DJ Sharpe, DJ Wales. The Journal of Chemical Physics (2020) 153, 024121. 
Efficient and exact sampling of transition path ensembles on Markovian networks. (453 kPS for TZ1 peptide, bimodal doi:10.1063/5.0012128)
TD Swinburne, DJ Wales. J Chem Theory Comput (2020) 16, 2661.
Defining, Calculating, and Converging Observables of a Kinetic Transition Network. (451 SwinburneW20)
DJ Sharpe, DJ Wales, Journal of Chemical Physics (2019) 151, 124101.
Identifying mechanistically distinct pathways in kinetic transition networks. (436 SharpeW19)
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 and the new scheme using fourier transforms

This paper includes a description of the local permutational alignment scheme, keyword LPERMDIST in OPTIM
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
M Griffiths, SP Niblett, DJ Wales, Journal of chemical theory and computation (2017) 13, 4914 Optimal Alignment of Structures for Finite and Periodic Systems. (DOI: 10.1021/acs.jctc.7b00543)

k-shortest paths analysis (recursive enumeration algorithm) and k distinct paths

DJ Sharpe, DJ Wales, Journal of Chemical Physics (2019) 151, 124101.
Identifying mechanistically distinct pathways in kinetic transition networks. (436 SharpeW19)

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).

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

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

 

Glassy landscapes

 

SP Niblett, VK de Souza, RL Jack, DJ Wales, J. Chem. Phys. (2018) 149, 114503 (DOI: 10.1063/1.5042140)
Effects of random pinning on the potential energy landscape of a supercooled liquid
SP Niblett, M Biedermann, DJ Wales, VK de Souza, J. Chem. Phys. (2017) 147, 152726 (DOI: 10.1063/1.5005924)
Pathways for diffusion in the potential energy landscape of the network glass former SiO2
VK de Souza, JD Stevenson, SP Niblett, JD Farrell, DJ Wales , J. Chem. Phys. (2017) 146, 124103 (DOI: 10.1063/1.4977794)
Defining and quantifying frustration in the energy landscape: Applications to atomic and molecular clusters, biomolecules, jammed and glassy systems
SP Niblett, VK de Souza, JD Stevenson, DJ Wales, J. Chem. Phys. (2016) 145, 024505 (DOI: 10.1063/1.4954324)
Dynamics of a molecular glass former: Energy landscapes for diffusion in ortho-terphenyl
VK De Souza, DJ Wales, Journal of Statistical Mechanics Theory and Experiment (2016) 2016, 074001 (DOI: 10.1088/1742-5468/2016/07/074001)
The potential energy landscape for crystallisation of a Lennard-Jones fluid
VK de Souza, DJ Wales, J. Chem. Phys. (2009) 130, 194508 (DOI: 10.1063/1.3131690)
Connectivity in the potential energy landscape for binary Lennard-Jones systems
VK de Souza, DJ Wales, J. Chem. Phys. (2008) 129, 164507 (DOI: 10.1063/1.2992128)
Energy landscapes for diffusion: Analysis of cage-breaking processes

 

Machine learning landscapes

T Desautels, R Das, J Calvert, M Trivedi, C Summers, DJ Wales, A Ercole,   BMJ open (2017) 7, e017199  (DOI: 10.1136/bmjopen-2017-017199)
Prediction of early unplanned intensive care unit readmission in a UK tertiary care hospital: a cross-sectional machine learning approach
R Das, DJ Wales,  R Soc Open Sci (2017) 4, 170175 (DOI: 10.1098/rsos.170175)
Machine learning landscapes and predictions for patient outcomes.
AJ Ballard, R Das, S Martiniani, D Mehta, L Sagun, JD Stevenson, DJ Wales, Physical chemistry chemical physics : PCCP (2017) 19, 12585 (DOI: 10.1039/c7cp01108c)
Energy landscapes for machine learning.
R Das, DJ Wales,  Chemical Physics Letters (2017) 667, 158 (DOI: 10.1016/j.cplett.2016.11.031)
Machine learning prediction for classification of outcomes in local minimisation
T Desautels, J Calvert, J Hoffman, M Jay, Y Kerem, L Shieh, D Shimabukuro, U Chettipally, MD Feldman, C Barton, DJ Wales, R Das,  JMIR Medical Informatics (2016) 4, e28 (DOI: 10.2196/medinform.5909)
Prediction of Sepsis in the Intensive Care Unit With Minimal Electronic Health Record Data: A Machine Learning Approach
AJ Ballard, JD Stevenson, R Das, DJ Wales,   J Chem Phys (2016) 144, 124119 (DOI: 10.1063/1.4944672)
Energy landscapes for a machine learning application to series data.

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