Theory Facility, Molecular Foundry
Lawrence Berkeley National Lab
2004 Ph.D. in Theoretical Physics, Linacre College, University of Oxford. Supervised by Juan P. Garrahan and David Sherrington
2001 MPhys, Trinity College, University of Oxford
1991-1997 Dunblane High School, Dunblane, Scotland
Theory and simulation of nanoscale pattern formation, self-assembly, and phase transformations.
- Dr. Ranjan Mannige (May 2012-). Ranjan is working to understand the structure, dynamics and uses of peptoid nanomaterials, in collaboration with Ron Zuckermann. Ranjan is funded by DTRA.
- Dr. Joyjit Kundu (Jul 2015-). Joyjit is working with our group and with David Prendergast to study fundamental aspects of the dynamics of carbon capture within solid frameworks. Joyjit is funded by UC Berkeley's Center for Gas Separations Relevant to Clean Energy Technologies.
- Dr. John Edison (Nov 2015-). John is working to understand the structure, dynamics and uses of peptoid nanomaterials, in collaboration with Ron Zuckermann. John is funded by DTRA.
- Katie Klymko (Oct 2012-). Katie works with our group and with Phill Geissler, at UC Berkeley, to understand pattern formation in driven and growing systems.
- Katie Deeg (Oct 2013-). Katie is working on metal-organic framework formation with our group and with Berend Smit at UC Berkeley.
Former group members
- Dr. Dina Mirijanian (Jun 2009-Jul 2012). Dina developed this atomistic forcefield for peptoid polymers. Dina is now a postdoc with Mike Hagan at Brandeis.
- Dr. Lester Hedges (Jan 2010-Jul 2014). Lester studied fundamental aspects of crystallization, supported by LBNL's Center for Nanoscale Control of Geologic CO2. Lester is now a postdoc with Rob Jack at Bath University.
- Dr. Tom Haxton (Aug 2010-2015). Tom worked on fundamental aspects of protein crystallization, self-assembly at surfaces, and peptoid assembly. Tom is now a senior data scientist at Chegg Inc.
- Tom Haxton's MF-CG-TOID-MC is software to initialize, simulate, and analyze Monte Carlo simulations of the Molecular Foundry Coarse-grained Model for Peptoids
- Lester Hedges' http://vmmc.xyz is a simple C++ library for doing dynamic (virtual-move Monte Carlo) simulations of interacting particles
- Similarity of ensembles of trajectories of reversible and irreversible growth processes, K. Klymko, J.P. Garrahan, S. Whitelam*, preprint here
- Minimal positive design for self-assembly of the Archimedean tilings, S. Whitelam*, Phys. Rev. Lett. 117, 228003 (2016); phys.org article here
- On the microscopic origin and macroscopic implications of lane formation in mixtures of oppositely-driven particles, K. Klymko, P.L. Geissler*, S. Whitelam*, Phys. Rev. E 94, 022608 (2016)
- Nucleation in Atomic, Molecular, and Colloidal Systems, J.J. DeYoreo*, S. Whitelam*, editorial on nucleation-themed issue of MRS Bulletin, Volume 41 , Issue 05 (2106)
- Selective gas capture via kinetic trapping, J. Kundu*, T. Pascal, D.G. Prendergast, S. Whitelam*, preprint Phys. Chem. Chem. Phys., 18, 21760 (2016)
- The Ramachandran number: an order parameter for protein geometry, R.V. Mannige*, J. Kundu, S. Whitelam*, PLoS ONE 11(8) (2016)
- Predicting the outcome of the growth of binary solids far from equilibrium, R.V. Mannige*, S. Whitelam*, Phys. Rev. E 93, 042136 (2016)
- Minimal physical requirements for crystal growth self-poisoning, S. Whitelam*, Y. R. Dahal, J.D. Schmit*, J. Chem. Phys. 144, 064903 (2016)
- Implicit-Solvent Coarse-Grained Simulation with a Fluctuating Interface Reveals a Molecular Mechanism for Peptoid Monolayer Buckling, T.K. Haxton*, R.N. Zuckermann, S. Whitelam*, J. Chem. Theory Comput, 12, 1, 345 (2016)
- Design, Synthesis, Assembly, and Engineering of Peptoid Nanosheets, E.J. Robertson, A. Battigelli, C. Proulx, R.V. Mannige, T.K. Haxton, L. Yun, S. Whitelam, R.N. Zuckermann*, Accounts of Chemical Research (2016)
- Peptoid nanosheets exhibit a new secondary-structure motif, R.V. Mannige*, T.K. Haxton, C. Proulx, E.J. Robertson, A. Battigelli, G.L. Butterfoss, R.N. Zuckermann, S. Whitelam*, Nature (2015)
- Crystallization and arrest mechanisms of model colloids, T.K. Haxton*, L.O. Hedges, S. Whitelam*, Soft Matter 11, 9307 (2015)
- Hierarchical assembly may be a way to make large information-rich structures, S. Whitelam*, Soft Matter 11, 8225 (2015)
- Crystallization by particle attachment in synthetic, biogenic, and geologic environments, J.J. De Yoreo, P.U.P.A. Gilbert, N.A.J.M. Sommerdijk, R.L. Penn, S. Whitelam, D. Joester, H. Zhang, J.D. Rimer, A. Navrotsky, J.F. Banfield, A.F. Wallace, F.M. Michel, F.C. Meldrum, H. Cölfen, P. M. Dove*, Science 349, 6247 (2015)
- Heterogenity of functional groups in a metal-organic framework displays magic number ratios, A.C.-H. Sue, R.V. Mannige, H. Deng, G. Cao, C. Wang, F. Gandara, J.F. Stoddart*, S. Whitelam,* O.M. Yaghi*, PNAS (2015)
- Examples of molecular self-assembly at surfaces, S. Whitelam*, Advanced Materials (2015)
- Emergent rhombus tilings from molecular interactions with M-fold rotational symmetry, S. Whitelam*, I. Tamblyn, J.P. Garrahan, P.H. Beton, Phys. Rev. Lett. 114, 115702 (2015)
- The statistical mechanics of dynamic pathways to self-assembly, S. Whitelam* and R.L. Jack*, Annual Review of Physical Chemistry 66, 143 (2015)
- Ion-Specific Control of the Self-Assembly Dynamics of a Nanostructured Protein Lattice, B. Rad, T. K. Haxton, A. Shon, S.-H. Shin, S. Whitelam, C.M. Ajo-Franklin*, ACS Nano, 9, 1, 180 (2015)
- Modeling Sequence-Specific Polymers Using Anisotropic Coarse-Grained Sites Allows Quantitative Comparison with Experiment, T.K. Haxton*, R.V. Mannige , R.N. Zuckermann, S.Whitelam*, J. Chem. Theory Comput., 11, 1, 303 (2015)
- Structure-determining step in the hierarchical assembly of peptoid nanosheets, B. Sanii, T.K. Haxton, G.K. Olivier, A. Cho, B. Barton, C. Proulx, S. Whitelam, R.N. Zuckermann*, ACS Nano, 8, 11, 11674 (2014)
- Growth of equilibrium structures built from a large number of distinct component types, L.O. Hedge, R.V. Mannige and S. Whitelam* Soft Matter 10, 6404 (2014)
- Viewpoint: A Recipe for Error-Free Self-Assembly, S. Whitelam, Physics 7, 62 (2014)
- Self-assembly at a nonequilibrium critical point, S. Whitelam*, L.O. Hedges and J.D. Schmit, Phys. Rev. Lett. 112, 155504 (2014)
- Common physical framework explains phase behavior and dynamics of atomic, molecular and polymeric network-formers , S. Whitelam*, I. Tamblyn*, T.K. Haxton, M.B. Wieland, N.R. Champness, J.P. Garrahan and P.H. Beton*, Phys. Rev. X 4, 011044 (2014)
- Development and use of an atomistic CHARMM-based forcefield for peptoid simulation, D.T. Mirijanian, R.V. Mannige, R.Z. Zuckermann, S. Whitelam*, J. Computational Chemistry, 35, 5, 360 (2014)
- Competing thermodynamic and dynamic factors select molecular assemblies on a gold surface, T. K. Haxton, H. Zhou, I. Tamblyn, D. Eom, Z. Hu, J.B. Neaton, T. Heinz*, S. Whitelam*, Phys. Rev. Lett. 111, 265701 (2013)
- Selective nucleation in porous media, L.O. Hedges and S. Whitelam*, Soft Matter, 9, 41, 9763 (2013)
- Microscopic Evidence for Liquid-Liquid Separation in Supersaturated CaCO3 Solutions, A. F. Wallace*, L. O. Hedges, A. Fernandez-Martinez, P. Raiteri, J. D. Gale, G. A. Waychunas, S. Whitelam, J. F. Banfield, J.J. De Yoreo*, Science 341, 648, 885 (2013)
- Uncovering the intrinsic size dependence of hydriding phase transformations in nanocrystals, R. Bardhan, L.O. Hedges, C.L. Pint, A. Javey, S. Whitelam*, J.J. Urban*, Nature Materials (2013)
- Do hierarchical structures assemble best via hierarchical pathways?, T. K. Haxton, S. Whitelam*, Soft Matter 9, 6851-6861 (2013)
- Self-assembly of multicomponent structures in and out of equilibrium, S. Whitelam*, R. Schulman*, L.O. Hedges, Phys. Rev. Lett. 109, 265506 (2012)
- Patterning a surface so as to speed nucleation from solution, L.O. Hedges and S. Whitelam*, Soft Matter 8, 8624 (2012)
- Real-time Imaging of Pt3Fe Nanorod Growth in Solution, H.-G. Liao, L. Cui, S. Whitelam, H. Zheng*, Science 336, 6084, 1011 (2012)
- Design rules for the self-assembly of a protein crystal, T.K. Haxton and S. Whitelam*, Soft Matter 8, 3558 (2012)
- Random and ordered phases of off-lattice rhombus tiles, S. Whitelam*, I. Tamblyn, P.H. Beton, J.P. Garrahan, Phys. Rev. Lett. 108, 035702 (2012)
- Analyzing mechanisms and microscopic reversibility of self-assembly, J. Grant, R.L. Jack*, S.Whitelam*, J. Chem. Phys. 135, 214505 (2011)
- Limit of validity of Ostwald's rule of stages in a statistical mechanical model of crystallization, L.O. Hedges and S. Whitelam*, J. Chem. Phys. 135, 164902 (2011)
- Electrostatics and aggregation: how charge can turn a crystal into a gel, J. Schmit*, S. Whitelam and K. Dill, J. Chem. Phys. 135, 085103 (2011)
- Approximating the dynamical evolution of systems of strongly-interacting overdamped particles, S. Whitelam*, Molecular Simulation, 37, 7 (2011); preprint here
- Folding of a Single-Chain, Information-Rich Polypeptoid Sequence into a Highly-Ordered Nanosheet, R. Kudirka, H. Tran, B. Sanii, K.-T. Nam, P. H. Choi, N. Venkateswaran, R. Chen, S. Whitelam, and R. N. Zuckermann* Biopolymers: Peptide Science (2011)
- Control of pathways and yields of protein crystallization through the interplay of nonspecific and specific attractions, S. Whitelam*, Phys. Rev. Lett. 105, 088102 (2010) (version with high-resolution images here)
- Microscopic implications of S-DNA, S. Whitelam*, P.L. Geissler, and S. Pronk Phys. Rev. E 82, 021907 (2010)
- Nonclassical assembly pathways of anisotropic particles, S. Whitelam*, J. Chem. Phys. 132, 194901 (2010)
- Self-assembly of amphiphilic peanut-shaped nanoparticles, S. Whitelam* and S.A.F. Bon, J. Chem. Phys. 132, 074901 (2010)
- Transformation from spots to waves in a model of actin pattern formation, S. Whitelam*, T. Bretschneider and N.J. Burroughs, Phys. Rev. Lett. 102, 198103 (2009)
- The impact of conformational fuctuations on self-assembly: Cooperative aggregation of archaeal chaperonin proteins, S. Whitelam, C. Rogers, A. Pasqua, C. Paavola, J. Trent and P. L. Geissler, Nano Letters, 9, p. 292-297 (2009)
- Stretching chimeric DNA: a test for the putative S-form, S. Whitelam, S. Pronk and P.L. Geissler, J. Chem. Phys. 129, 205101 (2008)
- The role of collective motion in examples of coarsening and self-assembly, S. Whitelam, E. H. Feng, M. F. Hagan, P. L. Geissler, Soft Matter 5, 6, p1251 (2009)
- There and (slowly) back again: Entropy-driven hysteresis in a model of DNA overstretching, S. Whitelam, S. Pronk and P.L. Geissler, Biophys. J. 94, 2452 (2008)
- Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles, S. Whitelam and P.L. Geissler, J. Chem. Phys. 127, 1 (2007)
- Two-stage coarsening mechanism in a kinetically constrained model of an attractive colloid, S. Whitelam and P. L. Geissler, Phys. Rev. E 73, 016115 (2006)
- Renormalization group study of a kinetically constrained model for strong glasses, S. Whitelam, L. Berthier and J.P. Garrahan, Phys. Rev. E 71, 026128 (2005)
- Facilitated spin models in one dimension: a real-space renormalization group study, S. Whitelam and J.P. Garrahan, Phys. Rev. E 70, 046129 (2004)
- Geometrical picture of dynamical facilitation, S. Whitelam and J. P. Garrahan, J. Phys. Chem. B 108, 6611 (2004) (issue in honor of H.C. Andersen)
- Dynamic criticality in glass-forming liquids, S. Whitelam, L. Berthier and J. P. Garrahan, Phys. Rev. Lett. 92, 185705 (2004)
- Microscopic implications of competing pictures of DNA overstretching, S. Whitelam Physics of Life Reviews, Elsevier 2010 (invited comment on "Biophysical characterization of DNA binding from single molecule force measurements", by Kathy R. Chaurasiya et al.)
2007-2008 Postdoctoral Fellow, Systems Biology Centre, University of Warwick. Supervised by Nigel Burroughs
2004-2007 Postdoctoral Fellow, Department of Chemistry, University of California at Berkeley. Supervised by Phillip L. Geissler
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