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1

Understanding Molecular Simulation: From Algorithms to Applications

Frenkel, Daan, Smit, Berend, Ratner, Mark A.

Journal:

Year:

1997

Language:

english

File:

PDF, 572 KB

english, 1997

2

Gibbs, Boltzmann, and negative temperatures

Frenkel, Daan, Warren, Patrick B.

Journal:

American Journal of Physics

Year:

2015

Language:

english

File:

PDF, 467 KB

english, 2015

3

Order through disorder: entropy strikes back

Journal:

Year:

1993

Language:

english

File:

PDF, 2.72 MB

english, 1993

4

Homogeneous nucleation and the Ostwald step rule

Rein ten Wolde, Pieter, Frenkel, Daan

Journal:

Physical Chemistry Chemical Physics

Year:

1999

Language:

english

File:

PDF, 205 KB

english, 1999

5

Why colloidal systems can be described by statistical mechanics: some not very original comments on the Gibbs paradox

Journal:

Molecular Physics

Year:

2014

Language:

english

File:

PDF, 157 KB

english, 2014

6

New Monte Carlo method to compute the free energy of arbitrary solids. Application to the fcc and hcp phases of hard spheres

Frenkel, Daan, Ladd, Anthony J. C.

Journal:

The Journal of Chemical Physics

Year:

1984

Language:

english

File:

PDF, 708 KB

english, 1984

7

Order through entropy

Journal:

Nature Materials

Year:

2014

Language:

english

File:

PDF, 703 KB

english, 2014

8

Breakdown of the law of rectilinear diameter and related surprises in the liquid-vapor coexistence in systems of patchy particles

Espinosa, Jorge R., Garaizar, Adiran, Vega, Carlos, Frenkel, Daan, Collepardo-Guevara, Rosana

Journal:

The Journal of Chemical Physics

Year:

2019

Language:

english

File:

PDF, 2.13 MB

english, 2019

9

Entropy-driven phase transitions

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

1999

Language:

english

File:

PDF, 878 KB

english, 1999

10

Perspective on “The effect of shape on the interaction of colloidal particles”

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2000

Language:

english

File:

PDF, 49 KB

english, 2000

11

Numerical prediction of the melting curve of n-octane

Polson, James M., Frenkel, Daan

Journal:

The Journal of Chemical Physics

Year:

1999

Language:

english

File:

PDF, 817 KB

english, 1999

12

Relation between Molecular Shape and the Morphology of Self-Assembling Aggregates: A Simulation Study

Vácha, Robert, Frenkel, Daan

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 519 KB

english, 2011

13

Visualizing Basins of Attraction for Different Minimization Algorithms

Asenjo, Daniel, Stevenson, Jacob D., Wales, David J., Frenkel, Daan

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 2.02 MB

english, 2013

14

Re-entrant melting as a design principle for DNA-coated colloids

Angioletti-Uberti, Stefano, Mognetti, Bortolo M., Frenkel, Daan

Journal:

Nature Materials

Year:

2012

Language:

english

File:

PDF, 535 KB

english, 2012

15

Simulations Suggest Possible Novel Membrane Pore Structure

Vácha, Robert, Frenkel, Daan

Journal:

Year:

2014

Language:

english

File:

PDF, 1.40 MB

english, 2014

16

The other entropy

Frenkel, Daan, Asenjo, Daniel, Paillusson, Fabien

Journal:

Molecular Physics

Year:

2013

Language:

english

File:

PDF, 550 KB

english, 2013

17

Personal Tribute

Journal:

Molecular Physics

Year:

2013

Language:

english

File:

PDF, 52 KB

english, 2013

18

Stability of Bicelles: A Simulation Study

Vácha, Robert, Frenkel, Daan

Journal:

Year:

2014

Language:

english

File:

PDF, 2.51 MB

english, 2014

19

Competition of Percolation and Phase Separation in a Fluid of Adhesive Hard Spheres

Miller, Mark A., Frenkel, Daan

Journal:

Physical Review Letters

Year:

2003

Language:

english

File:

PDF, 124 KB

english, 2003

20

Fluid–fluid coexistence in colloidal systems with short-ranged strongly directional attraction

Kern, Norbert, Frenkel, Daan

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 446 KB

english, 2003

21

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

22

Velocity fluctuations and dispersion in a simple porous medium

Capuani, Fabrizio, Frenkel, Daan, Lowe, Christopher P.

Journal:

Physical Review E

Year:

2003

Language:

english

File:

PDF, 93 KB

english, 2003

23

Crucial role of nonspecific interactions in amyloid nucleation

Šarić, Anđela, Chebaro, Yassmine C., Knowles, Tuomas P. J., Frenkel, Daan

Journal:

Proceedings of the National Academy of Sciences

Year:

2014

Language:

english

File:

PDF, 1.10 MB

english, 2014

24

Calculation of solid-fluid phase equilibria for systems of chain molecules

Polson, James M., Frenkel, Daan

Journal:

The Journal of Chemical Physics

Year:

1998

Language:

english

File:

PDF, 791 KB

english, 1998

25

Cubatic phase for tetrapods

Blaak, Ronald, Mulder, Bela M., Frenkel, Daan

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 367 KB

english, 2004

26

Connecting Macroscopic Observables and Microscopic Assembly Events in Amyloid Formation Using Coarse Grained Simulations

Bieler, Noah S., Knowles, Tuomas P. J., Frenkel, Daan, Vácha, Robert, Tajkhorshid, Emad

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.12 MB

english, 2012

27

Onsager's spherocylinders revisited

Journal:

Journal of Physical Chemistry

Year:

1987

Language:

english

File:

PDF, 643 KB

english, 1987

28

[WORLD SCIENTIFIC Proceedings of the International School of Physics - LERICI, Villa Marigola (7 – 18 July 1997)] Classical and Quantum Dynamics in Condensed Phase Simulations - Monte Carlo simulations

Language:

english

File:

PDF, 1.94 MB

english

29

Physical determinants of the self-replication of protein fibrils

Šarić, Anđela, Buell, Alexander K., Meisl, Georg, Michaels, Thomas C. T., Dobson, Christopher M., Linse, Sara, Knowles, Tuomas P. J., Frenkel, Daan

Journal:

Year:

2016

Language:

english

File:

PDF, 1.08 MB

english, 2016

30

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

Martiniani, Stefano, Schrenk, K. Julian, Stevenson, Jacob D., Wales, David J., Frenkel, Daan

Journal:

Physical Review E

Year:

2016

Language:

english

File:

PDF, 1011 KB

english, 2016

31

Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation

Šarić, Anđela, Michaels, Thomas C. T., Zaccone, Alessio, Knowles, Tuomas P. J., Frenkel, Daan

Journal:

The Journal of Chemical Physics

Year:

2016

Language:

english

File:

PDF, 1.21 MB

english, 2016

32

Special Issue on Liquid Matter 2017

Journal:

Journal of Physics Condensed Matter

Year:

2018

Language:

english

File:

PDF, 168 KB

english, 2018

33

Breakdown of the law of rectilinear diameter and related surprises in the liquid-vapor coexistence in systems of patchy particles

Espinosa, Jorge R., Garaizar, Adiran, Vega, Carlos, Frenkel, Daan, Collepardo-Guevara, Rosana

Journal:

The Journal of Chemical Physics

Year:

2019

File:

PDF, 2.13 MB

2019

34

Virtual-Move Parallel Tempering

Ivan Coluzza, Daan Frenkel

Journal:

Year:

2005

Language:

english

File:

PDF, 129 KB

english, 2005

35

Multiple Histogram Method and Static Monte Carlo Sampling

Márcia A. Inda, Daan Frenkel

Journal:

Macromolecular Theory and Simulations

Year:

2004

Language:

english

File:

PDF, 143 KB

english, 2004

36

Cover Picture: Macromol. Theory Simul. 1/2004

Márcia A. Inda, Daan Frenkel

Journal:

Macromolecular Theory and Simulations

Year:

2004

File:

PDF, 67 KB

2004

37

Computation challenges in complex liquids: Entropy-driven phase transitions

Journal:

Future Generation Computer Systems

Year:

1994

Language:

english

File:

PDF, 480 KB

english, 1994

38

Preface

Daan Frenkel, Henk Lekkerkerker, Theo Odijk

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

1991

Language:

english

File:

PDF, 59 KB

english, 1991

39

Confinement free energy of semiflexible polymers

Marjolein Dijkstra, Daan Frenkel, Henk N.W. Lekkerkerker

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

1993

Language:

english

File:

PDF, 1019 KB

english, 1993

40

Computer simulation of colloid-polymer mixtures

Evert Jan Meijer, Daan Frenkel

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

1995

Language:

english

File:

PDF, 405 KB

english, 1995

41

Nucleation in suspensions of anisotropic colloids

Tanja Schilling, Daan Frenkel

Journal:

Computer Physics Communications

Year:

2005

Language:

english

File:

PDF, 129 KB

english, 2005

42

Mesoscopic lattice modeling of electrokinetic phenomena

Ignacio Pagonabarraga, Fabrizio Capuani, Daan Frenkel

Journal:

Computer Physics Communications

Year:

2005

Language:

english

File:

PDF, 211 KB

english, 2005

43

Length, protein–protein interactions, and complexity

Taison Tan, Daan Frenkel, Vishal Gupta, Michael W. Deem

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

2005

Language:

english

File:

PDF, 408 KB

english, 2005

44

Soft condensed matter

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

2002

Language:

english

File:

PDF, 425 KB

english, 2002

45

Liquid-like behavior in colloidal crystals

Daan Frenkel, Peter Bladon, Peter Bolhuis, Maarten Hagen

Journal:

Physica B: Condensed Matter

Year:

1996

Language:

english

File:

PDF, 563 KB

english, 1996

46

Enhanced protein crystallization around the metastable critical point

Pieter Rein ten Wolde, Daan Frenkel

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

1999

Language:

english

File:

PDF, 188 KB

english, 1999

47

Perspective on “Statistical mechanical theory of irreversible processes. I. General theory and simple applications to magnetic and conduction problems.”

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2000

Language:

english

File:

PDF, 46 KB

english, 2000

48

Microscopic and mesoscopic simulation of entropic micelles

Peter G. Bolhuis, Daan Frenkel

Journal:

Physica A: Statistical Mechanics and its Applications

Year:

1997

Language:

english

File:

PDF, 693 KB

english, 1997

49

Prediction of absolute crystal-nucleation rate in hard-sphere colloids

Auer, Stefan, Frenkel, Daan

Journal:

Year:

2001

Language:

english

File:

PDF, 212 KB

english, 2001

50

10.1038/35099513

Auer, Stefan, Frenkel, Daan

Journal:

Year:

2001

Language:

english

File:

PDF, 140 KB

english, 2001