David Chandler

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Dynamics on the way to forming glass: bubbles in space-time
    David Chandler
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Annu Rev Phys Chem 61:191-217. 2010
  2. ncbi request reprint Interfaces and the driving force of hydrophobic assembly
    David Chandler
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 437:640-7. 2005
  3. ncbi request reprint Fluctuation-dissipation ratios in the dynamics of self-assembly
    Robert L Jack
    Department of Chemistry, University of California at Berkeley, Berkeley, California 94709, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 76:021119. 2007
  4. doi request reprint Water evaporation: a transition path sampling study
    Patrick Varilly
    Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
    J Phys Chem B 117:1419-28. 2013
  5. pmc Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain
    Thomas F Miller
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:14559-64. 2007
  6. pmc An improved coarse-grained model of solvation and the hydrophobic effect
    Patrick Varilly
    Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
    J Chem Phys 134:074109. 2011
  7. pmc Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA
    Michael F Hagan
    Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 100:13922-7. 2003
  8. ncbi request reprint Elastic energy storage in beta-sheets with application to F1-ATPase
    Sean Sun
    Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
    Eur Biophys J 32:676-83. 2003
  9. ncbi request reprint The conformational states of Mg.ATP in water
    Jung Chi Liao
    Departments of Molecular and Cellular Biology and ESPM, University of California, 201 Wellman Hall, Berkeley, CA 94720 3112, USA
    Eur Biophys J 33:29-37. 2004
  10. ncbi request reprint Coarse-grained modeling of the interface between water and heterogeneous surfaces
    Adam P Willard
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Faraday Discuss 141:209-20; discussion 309-46. 2009

Collaborators

Detail Information

Publications22

  1. ncbi request reprint Dynamics on the way to forming glass: bubbles in space-time
    David Chandler
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Annu Rev Phys Chem 61:191-217. 2010
    ..Nevertheless, the central ideas are easily illustrated with reference to molecular dynamics of more realistic atomistic models, and we use that illustrative approach here...
  2. ncbi request reprint Interfaces and the driving force of hydrophobic assembly
    David Chandler
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 437:640-7. 2005
    ..Despite the basic principles underlying the hydrophobic effect being qualitatively well understood, only recently have theoretical developments begun to explain and quantify many features of this ubiquitous phenomenon...
  3. ncbi request reprint Fluctuation-dissipation ratios in the dynamics of self-assembly
    Robert L Jack
    Department of Chemistry, University of California at Berkeley, Berkeley, California 94709, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 76:021119. 2007
    ..We use fluctuation-dissipation ratios to extract information about the degree of this frustration. We show that our analysis is a useful indicator of the long-term fate of the system, based on the early stages of assembly...
  4. doi request reprint Water evaporation: a transition path sampling study
    Patrick Varilly
    Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
    J Phys Chem B 117:1419-28. 2013
    ..Equivalently, they are consistent with a near-unity probability for a water molecule impinging upon a liquid droplet to condense. These results agree with previous simulations and with some, but not all, recent experiments...
  5. pmc Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain
    Thomas F Miller
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 104:14559-64. 2007
    ..In particular, we show that length-scale-dependent hydrophobic dewetting is the rate-limiting step in the hydrophobic collapse of the considered chain...
  6. pmc An improved coarse-grained model of solvation and the hydrophobic effect
    Patrick Varilly
    Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
    J Chem Phys 134:074109. 2011
    ..Our model is intermediate in detail and complexity between implicit-solvent models and explicit-water simulations...
  7. pmc Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA
    Michael F Hagan
    Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 100:13922-7. 2003
    ..Both on- and off-pathway intermediates are observed. The relation of the results to coarse-grained models for DNA-based biosensors is discussed...
  8. ncbi request reprint Elastic energy storage in beta-sheets with application to F1-ATPase
    Sean Sun
    Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
    Eur Biophys J 32:676-83. 2003
    ..The technique should be useful for beta-sheets in other proteins and aid in the construction of phenomenological models for molecular motors that are computationally prohibitive for MD alone...
  9. ncbi request reprint The conformational states of Mg.ATP in water
    Jung Chi Liao
    Departments of Molecular and Cellular Biology and ESPM, University of California, 201 Wellman Hall, Berkeley, CA 94720 3112, USA
    Eur Biophys J 33:29-37. 2004
    ..The average water density around Mg.ATP is investigated to show the average number of hydrogen bonds and the hydrophobicity...
  10. ncbi request reprint Coarse-grained modeling of the interface between water and heterogeneous surfaces
    Adam P Willard
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Faraday Discuss 141:209-20; discussion 309-46. 2009
    ..Nevertheless, the interfacial fluctuations are large and spatially heterogeneous in response to the underlying patchy substrate. We discuss the implications of these findings for the assembly of heterogeneous surfaces...
  11. pmc Dynamic pathways for viral capsid assembly
    Michael F Hagan
    Department of Chemistry, University of California, Berkeley, California, USA
    Biophys J 91:42-54. 2006
    ..We discuss the relationship between these mechanisms and experimental evaluations of capsid assembly processes...
  12. pmc Fluctuations of water near extended hydrophobic and hydrophilic surfaces
    Amish J Patel
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    J Phys Chem B 114:1632-7. 2010
    ..In contrast, we find that the statistics of water density fluctuations near a model hydrophilic surface are similar to that in the bulk...
  13. pmc The unbinding of ATP from F1-ATPase
    Iris Antes
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Biophys J 85:695-706. 2003
    ..Our results for the energetics during rotation suggest that the nucleotide's coordination with Mg(2+) during binding and release is necessary to account for the observed high efficiency of the motor...
  14. ncbi request reprint Hydrophobicity: two faces of water
    David Chandler
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 417:491. 2002
  15. pmc Instantaneous liquid interfaces
    Adam P Willard
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    J Phys Chem B 114:1954-8. 2010
    ..In applications to a molecular dynamics simulation of liquid water, it is shown that this procedure provides instructive and useful pictures of liquid-vapor interfaces and of liquid-protein interfaces...
  16. doi request reprint The role of solvent fluctuations in hydrophobic assembly
    Adam P Willard
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    J Phys Chem B 112:6187-92. 2008
    ..This tunnel accelerates assembly. While considering this specific model system, the approach we use illustrates a methodology that is broadly applicable...
  17. ncbi request reprint Corresponding states of structural glass formers. II
    Yael S Elmatad
    Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States, USA
    J Phys Chem B 114:17113-9. 2010
    ..Expressions demonstrated to fail in this way include the Vogel-Fulcher-Tammann formula, a double-exponential formula, and a fractional exponential formula...
  18. pmc Hydration of metal surfaces can be dynamically heterogeneous and hydrophobic
    David T Limmer
    Department of Chemistry, University of California, Berkeley, CA 94609
    Proc Natl Acad Sci U S A 110:4200-5. 2013
    ..Consequences for electrochemistry are discussed in the context of hydronium ions being attracted from the liquid to the metal-adlayer surface...
  19. doi request reprint The putative liquid-liquid transition is a liquid-solid transition in atomistic models of water. II
    David T Limmer
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    J Chem Phys 138:214504. 2013
    ..Recent reports of evidence of a liquid-liquid critical point in computer simulations of supercooled water are considered in this light...
  20. ncbi request reprint Corresponding States of structural glass formers
    Yael S Elmatad
    Department of Chemistry, University of California, Berkeley, California 94720, and School of Physics and Astronomy, University of Nottingham, Nottingham NG7 2RD
    J Phys Chem B 113:5563-7. 2009
    ..This behavior is bounded by an onset temperature T(o) above which liquid transport has a much weaker temperature dependence. A similar collapse is also demonstrated over the smaller available range for existing numerical simulation data...
  21. pmc Drying-induced hydrophobic polymer collapse
    Pieter Rein ten Wolde
    Department of Chemistry, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:6539-43. 2002
    ..The study is made possible through the application of transition path sampling and a coarse-grained treatment of liquid water. Relevance of our findings to understanding the folding and assembly of proteins is discussed...
  22. ncbi request reprint Physical chemistry: oil on troubled waters
    David Chandler
    Nature 445:831-2. 2007

Research Grants4

  1. Hydrophobic Effects in Biophysical Systems and Protein-Protein Interactions
    David Chandler; Fiscal Year: 2010
    ..The hydrophobic effect is arguably the most fundamental of physical forces orchestrating the structure of proteins and protein complexes. It is therefore central to health and life. ..
  2. Hydrophobic Effects in Biophysical Systems and Protein-Protein Interactions
    David Chandler; Fiscal Year: 2007
    ..The hydrophobic effect is arguably the most fundamental of physical forces orchestrating the structure of proteins and protein complexes. It is therefore central to health and life. ..