Research Topics
| David ChandlerSummaryAffiliation: University of California Country: USA Publications
Research Grants
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Detail Information
Publications
Dynamics on the way to forming glass: bubbles in space-timeDavid 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...- Interfaces and the driving force of hydrophobic assemblyDavid 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... - Fluctuation-dissipation ratios in the dynamics of self-assemblyRobert 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... 
An improved coarse-grained model of solvation and the hydrophobic effectPatrick 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...- Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chainThomas 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... - Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNAMichael 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... - Coarse-grained modeling of the interface between water and heterogeneous surfacesAdam 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... - The conformational states of Mg.ATP in waterJung-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... - Dynamic pathways for viral capsid assemblyMichael 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... - Elastic energy storage in beta-sheets with application to F1-ATPaseSean 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... - Fluctuations of water near extended hydrophobic and hydrophilic surfacesAmish 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... - The unbinding of ATP from F1-ATPaseIris 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... - Hydrophobicity: two faces of waterDavid Chandler
Department of Chemistry, University of California, Berkeley, California 94720, USA
Nature 417:491. 2002 
The role of solvent fluctuations in hydrophobic assemblyAdam 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...- Corresponding states of structural glass formers. IIYael 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... - Instantaneous liquid interfacesAdam 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... - Drying-induced hydrophobic polymer collapsePieter 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... - Corresponding States of structural glass formersYael 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... - Physical chemistry: oil on troubled watersDavid Chandler
Nature 445:831-2. 2007
Research Grants
- Hydrophobic Effects in Biophysical Systems and Protein-Protein InteractionsDavid 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. ..
- Hydrophobic Effects in Biophysical Systems and Protein-Protein InteractionsDavid 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. ..