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1

Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms

Wales, David J., Doye, Jonathan P. K.

Journal:

Journal of Physical Chemistry A

Year:

1997

Language:

english

File:

PDF, 197 KB

english, 1997

2

A self-consistent approach to measure preferential attachment in networks and its application to an inherent structure network

Claire P. Massen, Jonathan P.K. Doye

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

2007

Language:

english

File:

PDF, 311 KB

english, 2007

3

What can calculations employing empirical potentials teach us about bare transition-metal clusters?

Wales, David J., Munro, Lindsey J., Doye, Jonathan P. K.

Journal:

Journal of the Chemical Society Dalton Transactions

Year:

1996

Language:

english

File:

PDF, 25.56 MB

english, 1996

4

The mechanism of thickness selection in the Sadler-Gilmer model of polymer crystallization

Doye, Jonathan P. K., Frenkel, Daan

Journal:

The Journal of Chemical Physics

Year:

1999

Language:

english

File:

PDF, 641 KB

english, 1999

5

Evolution of the potential energy surface with size for Lennard-Jones clusters

Doye, Jonathan P. K., Miller, Mark A., Wales, David J.

Journal:

The Journal of Chemical Physics

Year:

1999

Language:

english

File:

PDF, 1.71 MB

english, 1999

6

The effect of the range of the potential on the structure and stability of simple liquids: from clusters to bulk, from sodium to

Doye, Jonathan P K, Wales, David J

Journal:

Journal of Physics B Atomic Molecular and Optical Physics

Year:

1996

Language:

english

File:

PDF, 2.97 MB

english, 1996

7

Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA

Matek, Christian, Ouldridge, Thomas E., Doye, Jonathan P. K., Louis, Ard A.

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 868 KB

english, 2015

8

Force-Induced Unravelling of DNA Origami

Engel, Megan C., Smith, David M., Jobst, Markus A., Sajfutdinow, Martin, Liedl, Tim, Romano, Flavio, Rovigatti, Lorenzo, Louis, Ard A., Doye, Jonathan P.K.

Journal:

Year:

2018

Language:

english

File:

PDF, 38.81 MB

english, 2018

9

Coarse-grained modelling of the structural properties of DNA origami

Snodin, Benedict E K, Schreck, John S, Romano, Flavio, Louis, Ard A, Doye, Jonathan P K

Journal:

Nucleic Acids Research

Year:

2019

Language:

english

File:

PDF, 17.24 MB

english, 2019

10

Designer protein assemblies with tunable phase diagrams in living cells

Heidenreich, Meta, Georgeson, Joseph M., Locatelli, Emanuele, Rovigatti, Lorenzo, Nandi, Saroj Kumar, Steinberg, Avital, Nadav, Yotam, Shimoni, Eyal, Safran, Samuel A., Doye, Jonathan P. K., Levy, Emm

Journal:

Nature Chemical Biology

Year:

2020

File:

PDF, 6.19 MB

2020

11

Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures

Chhabra, Hemani, Mishra, Garima, Cao, Yijing, PreÅ¡ern, Domen, Skoruppa, Enrico, Tortora, Maxime M. C., Doye, Jonathan P. K.

Journal:

Journal of Chemical Theory and Computation

Year:

2020

File:

PDF, 1.72 MB

2020

12

Exploring the origins of the power-law properties of energy landscapes: An egg-box model

Claire P. Massen, Jonathan P.K. Doye, Rupert W. Nash

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

2007

Language:

english

File:

PDF, 440 KB

english, 2007

13

Magic numbers and growth sequences of small face-centered-cubic and decahedral clusters

Jonathan P.K. Doye, David J. Wales

Journal:

Chemical Physics Letters

Year:

1995

Language:

english

File:

PDF, 785 KB

english, 1995

14

Structural predictions for (C60)N clusters with an all-atom potential

Jonathan P.K. Doye, Andreas Dullweber, David J. Wales

Journal:

Chemical Physics Letters

Year:

1997

Language:

english

File:

PDF, 366 KB

english, 1997

15

The structure of (C60)N clusters

Jonathan P.K. Doye, David J. Wales

Journal:

Chemical Physics Letters

Year:

1996

Language:

english

File:

PDF, 690 KB

english, 1996

16

Protein crystallization in vivo

Jonathan P.K. Doye, Wilson C.K. Poon

Journal:

Current Opinion in Colloid & Interface Science

Year:

2006

Language:

english

File:

PDF, 278 KB

english, 2006

17

The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks

Sam F. Greenbury, Iain G. Johnston, Matthew A. Smith, Jonathan P.K. Doye, Ard A. Louis

Journal:

Journal of Theoretical Biology

Year:

2010

Language:

english

File:

PDF, 675 KB

english, 2010

18

Polytetrahedral Clusters

Doye, Jonathan, Wales, David

Journal:

Physical Review Letters

Year:

2001

Language:

english

File:

PDF, 187 KB

english, 2001

19

Energy landscapes of colloidal clusters: thermodynamics and rearrangement mechanisms

Calvo, Florent, Doye, Jonathan P. K., Wales, David J.

Journal:

Year:

2012

Language:

english

File:

PDF, 3.23 MB

english, 2012

20

Free energy landscapes for homogeneous nucleation of ice for a monatomic water model

Reinhardt, Aleks, Doye, Jonathan P. K.

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 1.17 MB

english, 2012

21

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

Ouldridge, Thomas E., Louis, Ard A., Doye, Jonathan P. K.

Journal:

Physical Review Letters

Year:

2010

Language:

english

File:

PDF, 470 KB

english, 2010

22

Lead clusters: Different potentials, different structures

Jonathan P.K. Doye

Journal:

Computational Materials Science

Year:

2006

Language:

english

File:

PDF, 400 KB

english, 2006

23

Contract duration and the division of labor in agricultural land leases

Jonathan Yoder, Ishrat Hossain, Francis Epplin, Damona Doye

Journal:

Journal of Economic Behavior & Organization

Year:

2008

Language:

english

File:

PDF, 202 KB

english, 2008

24

The effect of the range of the potential on the structures of clusters

Doye, Jonathan P. K., Wales, David J., Berry, R. Stephen

Journal:

The Journal of Chemical Physics

Year:

1995

Language:

english

File:

PDF, 1.42 MB

english, 1995

25

Global Optimization of Morse Clusters by Potential Energy Transformations

Doye, Jonathan P. K., Leary, Robert H., Locatelli, Marco, Schoen, Fabio

Journal:

INFORMS Journal on Computing

Year:

2004

Language:

english

File:

PDF, 169 KB

english, 2004

26

Global optimization and the energy landscapes of Dzugutov clusters

Doye, Jonathan P. K., Wales, David J., Simdyankin, Sergei I.

Journal:

Faraday Discussions

Year:

2001

Language:

english

File:

PDF, 242 KB

english, 2001

27

Structural consequences of the range of the interatomic potential A menagerie of clusters

Doye, Jonathan P. K., Wales, David J.

Journal:

Journal of the Chemical Society Faraday Transactions

Year:

1997

Language:

english

File:

PDF, 2.52 MB

english, 1997

28

Crystallization of a polymer on a surface

Doye, Jonathan P. K., Frenkel, Daan

Journal:

The Journal of Chemical Physics

Year:

1998

Language:

english

File:

PDF, 702 KB

english, 1998

29

Global minima for transition metal clusters described by Sutton–Chen potentials

Doye, Jonathan P. K., Wales, David J.

Journal:

New Journal of Chemistry

Year:

1998

Language:

english

File:

PDF, 1.06 MB

english, 1998

30

The double-funnel energy landscape of the 38-atom Lennard-Jones cluster

Doye, Jonathan P. K., Miller, Mark A., Wales, David J.

Journal:

The Journal of Chemical Physics

Year:

1999

Language:

english

File:

PDF, 607 KB

english, 1999

31

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

Ouldridge, Thomas E., Louis, Ard A., Doye, Jonathan P. K.

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.21 MB

english, 2011

32

Modelling the self-assembly of virus capsids

Johnston, Iain G, Louis, Ard A, Doye, Jonathan P K

Journal:

Journal of Physics Condensed Matter

Year:

2010

Language:

english

File:

PDF, 1.06 MB

english, 2010

33

DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism

Matek, Christian, Ouldridge, Thomas E., Levy, Adam, Doye, Jonathan P. K., Louis, Ard A.

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 1.59 MB

english, 2012

34

Computing Phase Diagrams for a Quasicrystal-Forming Patchy-Particle System

Reinhardt, Aleks, Romano, Flavio, Doye, Jonathan P. K.

Journal:

Physical Review Letters

Year:

2013

Language:

english

File:

PDF, 1.49 MB

english, 2013

35

Controlling crystallization and its absence: proteins, colloids and patchy models

Doye, Jonathan P. K., Louis, Ard A., Lin, I-Chun, Allen, Lucy R., Noya, Eva G., Wilber, Alex W., Kok, Hoong Chwan, Lyus, Rosie

Journal:

Physical Chemistry Chemical Physics

Year:

2007

Language:

english

File:

PDF, 1.05 MB

english, 2007

36

Entropic effects on the structure of Lennard-Jones clusters

Doye, Jonathan P. K., Calvo, Florent

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 712 KB

english, 2002

37

Reversible self-assembly of patchy particles into monodisperse icosahedral clusters

Wilber, Alex W., Doye, Jonathan P. K., Louis, Ard A., Noya, Eva G., Miller, Mark A., Wong, Pauline

Journal:

The Journal of Chemical Physics

Year:

2007

Language:

english

File:

PDF, 2.57 MB

english, 2007

38

Note: Homogeneous TIP4P/2005 ice nucleation at low supercooling

Reinhardt, Aleks, Doye, Jonathan P. K.

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 472 KB

english, 2013

39

Formation of dodecagonal quasicrystals in two-dimensional systems of patchy particles

van der Linden, Marjolein N., Doye, Jonathan P. K., Louis, Ard A.

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 6.80 MB

english, 2012

40

Evolutionary dynamics in a simple model of self-assembly

Johnston, Iain G., Ahnert, Sebastian E., Doye, Jonathan P. K., Louis, Ard A.

Journal:

Physical Review E

Year:

2011

Language:

english

File:

PDF, 751 KB

english, 2011

41

A model metal potential exhibiting polytetrahedral clusters

Doye, Jonathan P. K.

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 1.24 MB

english, 2003

42

Tetrahedral global minimum for the 98-atom Lennard-Jones cluster

Leary, Robert H., Doye, Jonathan P. K.

Journal:

Physical Review E

Year:

1999

Language:

english

File:

PDF, 161 KB

english, 1999

43

Coarse-Grained Modelling of Extreme DNA Bending

Harrison, Ryan M., Louis, A.A., Doye, Jonathan P.K.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 63 KB

english, 2014

44

Self-Assembly and Evolution of Homomeric Protein Complexes

Villar, Gabriel, Wilber, Alex W., Williamson, Alex J., Thiara, Parvinder, Doye, Jonathan P. K., Louis, Ard A., Jochum, Mara N., Lewis, Anna C. F., Levy, Emmanuel D.

Journal:

Physical Review Letters

Year:

2009

Language:

english

File:

PDF, 1.10 MB

english, 2009

45

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model

Šulc, Petr, Ouldridge, Thomas E., Romano, Flavio, Doye, Jonathan P. K., Louis, Ard A.

Journal:

Natural Computing

Year:

2014

Language:

english

File:

PDF, 748 KB

english, 2014

46

Entropic Effects on the Size Dependence of Cluster Structure

Doye, Jonathan P. K., Calvo, Florent

Journal:

Physical Review Letters

Year:

2001

Language:

english

File:

PDF, 150 KB

english, 2001

47

Identifying structural patterns in disordered metal clusters

Doye, Jonathan P. K.

Journal:

Physical Review B

Year:

2003

Language:

english

File:

PDF, 1.10 MB

english, 2003

48

Coarse-graining DNA for simulations of DNA nanotechnology

Doye, Jonathan P. K., Ouldridge, Thomas E., Louis, Ard A., Romano, Flavio, Šulc, Petr, Matek, Christian, Snodin, Benedict E. K., Rovigatti, Lorenzo, Schreck, John S., Harrison, Ryan M., Smith, William

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 9.28 MB

english, 2013

49

Re-entrant phase behavior for systems with competition between phase separation and self-assembly

Reinhardt, Aleks, Williamson, Alexander J., Doye, Jonathan P. K., Carrete, Jesús, Varela, Luis M., Louis, Ard A.

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 744 KB

english, 2011

50

The dynamics of structural transitions in sodium chloride clusters

Doye, Jonathan P. K., Wales, David J.

Journal:

The Journal of Chemical Physics

Year:

1999

Language:

english

File:

PDF, 493 KB

english, 1999

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