David J Wales

发表

Exploring the potential energy landscape of the Thomson problem via Newton homotopies.

Dhagash Mehta, Tianran Chen, John W R Morgan, 2015, The Journal of chemical physics.

Archetypal landscapes for deep neural networks

David J Wales, Philipp C Verpoort, Alpha A Lee, 2020, Proceedings of the National Academy of Sciences.

Benchmarks for Characterization of Minima, Transition States, and Pathways in Atomic, Molecular, and Condensed Matter Systems.

David J Wales, Graeme Henkelman, Cheng Shang, 2014, Journal of chemical theory and computation.

Decoding heat capacity features from the energy landscape.

David J Wales, D. Wales, 2017, Physical review. E.

Evolved Minimal Frustration in Multifunctional Biomolecules.

David J Wales, Konstantin Röder, D. Wales, 2018, The journal of physical chemistry. B.

Efficient and exact sampling of transition path ensembles on Markovian networks.

David J Wales, Daniel J Sharpe, D. Wales, 2020, The Journal of chemical physics.

Exploring Energy Landscapes.

David J Wales, D. Wales, 2018, Annual review of physical chemistry.

Identifying mechanistically distinct pathways in kinetic transition networks.

David J Wales, Daniel J Sharpe, D. Wales, 2019, The Journal of chemical physics.

Dynamics of an adenine-adenine RNA conformational switch from discrete path sampling.

David J Wales, Debayan Chakraborty, D. Wales, 2019, The Journal of chemical physics.

Communication: Analysing kinetic transition networks for rare events.

David J Wales, Jacob D Stevenson, D. Wales, 2014, The Journal of chemical physics.

GPU-Accelerated Exploration of Biomolecular Energy Landscapes.

David J Wales, Rosemary G. Mantell, Rosemary G Mantell, 2016, Journal of chemical theory and computation.

Exploring Energy Landscapes: Metrics, Pathways, and Normal-Mode Analysis for Rigid-Body Molecules.

Halim Kusumaatmaja, David J Wales, Dwaipayan Chakrabarti, 2013, Journal of chemical theory and computation.

Go-Kit: A Tool To Enable Energy Landscape Exploration of Proteins

David J Wales, Sridhar Neelamraju, Shachi Gosavi, 2019, J. Chem. Inf. Model..

Protein energy landscape exploration with structure-based models.

David J Wales, Sridhar Neelamraju, Shachi Gosavi, 2020, Current opinion in structural biology.

Symmetrisation schemes for global optimisation of atomic clusters.

David J Wales, Mark T. Oakley, Roy L Johnston, 2013, Physical chemistry chemical physics : PCCP.

Machine learning landscapes and predictions for patient outcomes

David J Wales, Ritankar Das, D. Wales, 2017, Royal Society Open Science.

Energy landscapes for a machine learning application to series data.

David J Wales, Andrew J Ballard, Ritankar Das, 2016, The Journal of chemical physics.

Predicting Pathways between Distant Configurations for Biomolecules.

David J Wales, Konstantin Röder, D. Wales, 2018, Journal of chemical theory and computation.

Perspective: new insights from loss function landscapes of neural networks

Alpha Lee, David J Wales, Sathya R. Chitturi, 2020, Mach. Learn. Sci. Technol..

Decoding the energy landscape: extracting structure, dynamics and thermodynamics

David J Wales, D. Wales, 2012, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

Potential energy landscapes for the 2D XY model: minima, transition states, and pathways.

Dhagash Mehta, David J Wales, Mario Schröck, 2013, The Journal of chemical physics.

Kinetic Transition Networks for the Thomson Problem and Smale's Seventh Problem.

Dhagash Mehta, Jianxu Chen, Halim Kusumaatmaja, 2016, Physical review letters.

Refined kinetic transition networks for the GB1 hairpin peptide.

David J Wales, D. Wales, Joanne M Carr, 2009, Physical chemistry chemical physics : PCCP.

Prediction of early unplanned intensive care unit readmission in a UK tertiary care hospital: a cross-sectional machine learning approach

Ari Ercole, David J Wales, Ritankar Das, 2017, BMJ Open.

Effect of salt bridges on the energy landscape of a model protein.

David J Wales, D. Wales, Peter E J Dewsbury, 2004, The Journal of chemical physics.

Interpolation schemes for peptide rearrangements.

David J Wales, Birgit Strodel, Elena F Koslover, 2010, The Journal of chemical physics.

Analysis of cooperativity and localization for atomic rearrangements.

David J Wales, Semen A Trygubenko, 2004, The Journal of chemical physics.

Turning intractable counting into sampling: Computing the configurational entropy of three-dimensional jammed packings.

Daan Frenkel, David J Wales, K. J. Schrenk, 2015, Physical review. E.

Structure, Thermodynamics, and Folding Pathways for a Tryptophan Zipper as a Function of Local Rigidification.

David J Wales, Jerelle A. Joseph, D. Wales, 2016, Journal of chemical theory and computation.

Folding of the GB1 hairpin peptide from discrete path sampling.

David J Wales, D. Wales, David A. Evans, 2004, The Journal of chemical physics.

Connectivity in the potential energy landscape for binary Lennard-Jones systems.

David J Wales, D. Wales, V. K. de Souza, 2009, The Journal of chemical physics.

Energy landscapes for water clusters in a uniform electric field.

David J Wales, D. Wales, Tim James, 2007, The Journal of chemical physics.

Protein structure prediction using basin-hopping.

Peter G Wolynes, David J Wales, Michael C Prentiss, 2008, The Journal of chemical physics.

Thermodynamics and kinetics of aggregation for the GNNQQNY peptide.

David J Wales, Birgit Strodel, D. Wales, 2007, Journal of the American Chemical Society.

Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch.

Samuela Pasquali, David J Wales, Philippe Derreumaux, 2017, The Journal of chemical physics.

Simulations of rigid bodies in an angle-axis framework.

David J Wales, Dwaipayan Chakrabarti, D. Wales, 2009, Physical chemistry chemical physics : PCCP.

Improving Computational Predictions of Single-Stranded RNA Tetramers with Revised α/γ Torsional Parameters for the Amber Force Field.

David J Wales, D. Wales, Ilyas Yildirim, 2017, The journal of physical chemistry. B.

Comparison of double-ended transition state search methods.

David J Wales, Elena F Koslover, Elena F. Koslover, 2007, The Journal of chemical physics.

Helix self-assembly from anisotropic molecules.

David J Wales, Szilard N Fejer, D. Wales, 2007, Physical review letters.

A Local Rigid Body Framework for Global Optimization of Biomolecules.

Halim Kusumaatmaja, David J Wales, D. Wales, 2012, Journal of chemical theory and computation.

How many dimensions are required to approximate the potential energy landscape of a model protein?

Tamiki Komatsuzaki, Yasuhiro Matsunaga, David J Wales, 2005, The Journal of chemical physics.

Protonated water clusters described by an empirical valence bond potential.

David J Wales, D. Wales, Tim James, 2005, The Journal of chemical physics.

Archetypal energy landscapes: dynamical diagnosis.

David J Wales, R Stephen Berry, D. Wales, 2005, The Journal of chemical physics.

Tilted and helical columnar phases for an axially symmetric discoidal system.

David J Wales, Dwaipayan Chakrabarti, 2008, Physical review letters.

New results for phase transitions from catastrophe theory.

David J Wales, D. Wales, T. V. Bogdan, 2004, The Journal of chemical physics.

Virulence-Associated Substitution D222G in the Hemagglutinin of 2009 Pandemic Influenza A(H1N1) Virus Affects Receptor Binding

John Steel, Jianqiang Ye, Marion Koopmans, 2010, Journal of Virology.

Evolution of the potential energy landscape with static pulling force for two model proteins.

David J Wales, Teresa Head-Gordon, D. Wales, 2012, The journal of physical chemistry. B.

Certification and the potential energy landscape.

Dhagash Mehta, David J Wales, D. Mehta, 2014, The Journal of chemical physics.

Structural analysis of high-dimensional basins of attraction.

Daan Frenkel, David J Wales, Stefano Martiniani, 2016, Physical review. E.

Visualizing basins of attraction for different minimization algorithms.

Daan Frenkel, David J Wales, Jacob D Stevenson, 2013, The journal of physical chemistry. B.

Equilibrium thermodynamics from basin-sampling.

David J Wales, Florent Calvo, D. Wales, 2006, The Journal of chemical physics.

Global optimization and folding pathways of selected alpha-helical proteins.

David J Wales, Joanne M Carr, 2005, The Journal of chemical physics.

Communication: Certifying the potential energy landscape.

Dhagash Mehta, David J Wales, D. Mehta, 2013, The Journal of chemical physics.

Implicit Solvent Models and the Energy Landscape for Aggregation of the Amyloidogenic KFFE Peptide.

David J Wales, Birgit Strodel, D. Wales, 2008, Journal of chemical theory and computation.

Transforming the Energy Landscape of a Coiled-Coil Peptide via Point Mutations.

David J Wales, Konstantin Röder, D. Wales, 2017, Journal of chemical theory and computation.

Energy Landscapes of Mini-Dumbbell DNA Octanucleotides.

David J Wales, Konstantin Röder, D. Wales, 2018, Journal of chemical theory and computation.

Energy landscapes: some new horizons.

David J Wales, D. Wales, 2010, Current opinion in structural biology.

Finding pathways between distant local minima.

David J Wales, Joanne M Carr, Semen A Trygubenko, 2005, The Journal of chemical physics.

Potential energy and free energy landscapes.

David J Wales, D. Wales, T. V. Bogdan, 2006, The journal of physical chemistry. B.

Geometry optimization for peptides and proteins: comparison of Cartesian and internal coordinates.

David J Wales, Elena F Koslover, Elena F. Koslover, 2007, The Journal of chemical physics.

Folding pathways and rates for the three-stranded beta-sheet peptide Beta3s using discrete path sampling.

David J Wales, D. Wales, Joanne M Carr, 2008, The journal of physical chemistry. B.

An inversion-relaxation approach for sampling stationary points of spin model Hamiltonians.

Dhagash Mehta, David J Wales, D. Mehta, 2014, The Journal of chemical physics.

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

Peter Salamon, David J Wales, D. Wales, 2013, Proceedings of the National Academy of Sciences.

Energy landscapes for diffusion: analysis of cage-breaking processes.

David J Wales, D. Wales, V. K. de Souza, 2008, The Journal of chemical physics.

Calculating rate constants and committor probabilities for transition networks by graph transformation.

David J Wales, D. Wales, 2009, The Journal of chemical physics.

Graph transformation method for calculating waiting times in Markov chains.

David J Wales, D. Wales, S. Trygubenko, 2006, The Journal of chemical physics.

Novel structural motifs in clusters of dipolar spheres: knots, links, and coils.

Mark A Miller, David J Wales, 2005, The journal of physical chemistry. B.

Energy landscapes for a machine-learning prediction of patient discharge.

David J Wales, Ritankar Das, D. Wales, 2016, Physical review. E.