Department of Chemistry

Jacobs Group @ Princeton

Theory and simulation of biomolecular self-assembly and soft materials

Publications

  • D. Aierken, S. Aland, S. Bo, S. Boeynaems, D. Cai, S. Carra, L.B. Case, H.S. Chan, J.R. Espinosa, T.K. GrandPre, A.Y. Grosberg, I.S. Haugerud, W.M. Jacobs, J.A. Joseph, F. Jülicher, K. Kremer, G. Kusters, L. Laan, K. Lasker, K.S. Laxhuber, H.O. Lee, K.F. Liu, D. Notani, Y. Qiang, P. Robustelli, L. Saiz, O.A. Saleh, H. Schiessel, J. Schmit, M. Shen, K. Shrinivas, A. Statt, A.R. Tejedor, T. Trcek, C.A. Weber, S.C. Weber, N.S. Wingreen, H. Zhang, Y. Zhang, H.X. Zhou, D. Zwicker, “Roadmap for condensates in cell biology,” PRX Life 4, 032501 (2026).
  • P. de Souza, W.M. Jacobs and H.A. Stone, “Polydisperse polymer fractionation between phases,” Phys. Rev. E 114, 015421 (2026).
  • G.R. Abraham, T. Li, A. Nguyen, W.M. Jacobs*, and O.A. Saleh*, “Cooperation and competition of basepairing and electrostatic interactions in mixtures of DNA nanostars and polylysine,” J. Am. Chem. Soc. 147, 42452–42461 (2025). [*Co‑corresponding authors]
  • W.W. Oliver, W.M. Jacobs and M.A. Webb, “When B2 is not enough: Evaluating simple metrics for predicting phase separation of intrinsically disordered proteins,” J. Phys. Chem. B 129, 9551–9565 (2025).
  • Y. Cho and W.M. Jacobs, “Interfacial effects determine nonequilibrium phase behaviors in chemically driven fluids,” Proc. Natl. Acad. Sci. U.S.A. 122, e2501145122 (2025).
  • J. Jin, W. Oliver, M.A. Webb, and W.M. Jacobs, “Predicting heteropolymer phase separation using two-chain contact maps,” J. Chem. Phys. 163, 014102 (2025).
  • F. Chen and W.M. Jacobs, “Dynamical phase transition in the growth of programmable polymorphic materials,” Phys. Rev. Mater. 9, 053403 (2025).
  • H. Seyforth, T.E. Videbæk, M. Mondal, S. Chatterjee, W.M. Jacobs* and W.B. Rogers*, “The underappreciated role of nonspecific interactions in the crystallization of DNA-coated colloids,” Soft Matter 21, 2654 (2025). [*Co‑corresponding authors]
  • W.M. Jacobs* and W.B. Rogers*, “Assembly of Complex Colloidal Systems Using DNA,” Ann. Rev. Cond. Mat. Phys. 16, 443–463 (2025). [*Co‑corresponding authors]
  • S. Chatterjee and W.M. Jacobs, “Multi-objective optimization for targeted self-assembly among competing polymorphs,” Phys. Rev. X 15, 011075 (2025).
  • T. Li and W.M. Jacobs, “Predicting the morphology of multiphase biomolecular condensates from protein interaction networks,” PRX Life 2, 023013 (2024).
  • F. Chen and W.M. Jacobs, “Emergence of multiphase condensates from a limited set of chemical building blocks,” J. Chem. Theory Comput. 20, 6881–6889 (2024).
  • A.R. Strom, J.M. Eeftens, Y. Polyachenko, C. Weaver, H. Watanabe, D. Bracha, N. Orlovsky, C. Jumper, W.M. Jacobs, and C.P. Brangwynne, “Interplay of condensation and chromatin binding underlies BRD4 targeting,” Mol. Biol. Cell 35, ar88 (2024).
  • O. Hegde, T. Li, A. Sharma, M. Borja, W.M. Jacobs*, and W.B. Rogers*, “Competition between self-assembly and phase separation governs high-temperature condensation of a DNA liquid,” Phys. Rev. Lett. 132, 208401 (2024). [*Co‑corresponding authors]
  • Y. An, M.A. Webb*, and W.M. Jacobs*, “Active learning of the thermodynamics–dynamics tradeoff in protein condensates,” Sci. Adv. 10, adj2448 (2024). [*Co‑corresponding authors]
  • A. Bitran, W.M. Jacobs, and E.I. Shakhnovich,“The critical role of co-translational folding: An evolutionary and biophysical perspective,” Curr. Opin. Systems Biol. 37, 100485 (2024).
  • T. Li, W.B. Rogers, and W.M. Jacobs, “Interplay between self-assembly and phase separation in a polymer-complex model,” Phys. Rev. E 108, 064501 (2023).
  • Y. Cho and W.M. Jacobs, “Nonequilibrium interfacial properties in chemically driven fluids,” J. Chem. Phys. 159, 154101 (2023).
  • A. Hensley, T.E. Videbæk, H. Seyforth, W.M. Jacobs*, and W.B. Rogers*, “Macroscopic photonic single crystals via seeded growth of DNA-coated colloids,” Nat. Commun. 14, 4237 (2023). [*Co‑corresponding authors]
  • W.M. Jacobs, “Theory and simulation of multiphase coexistence in biomolecular mixtures,” J. Chem. Theory Comput. 19, 3429–3445 (2023).
  • F. Chen and W.M. Jacobs, “Programmable phase behavior in fluids with designable interactions,” J. Chem. Phys. 158, 214118 (2023).
  • Y. Cho and W.M. Jacobs, “Tuning nucleation kinetics via nonequilibrium chemical reactions,” Phys. Rev. Lett. 130, 128203 (2023).
  • A. Hensley, W.M. Jacobs*, and W.B. Rogers*, “Self-assembly of photonic crystals by controlling the nucleation and growth of DNA-coated colloids,” Proc. Natl. Acad. Sci. U.S.A. 119, e2114050118 (2022). [*Co‑corresponding authors]
  • W.M. Jacobs, “Self-assembly of biomolecular condensates with shared components,” Phys. Rev. Lett. 126, 258101 (2021).
    [See also commentary in APS Physics.]
  • D.W. Sanders, N. Kedersha, D.S.W. Lee, A.R. Strom, V. Drake, J.A. Riback, D. Bracha, J.M. Eeftens, A. Iwanicki, A. Wang, M.-T. Wei, G. Whitney, S.M. Lyons, P. Anderson, W.M. Jacobs, P. Ivanov, and C.P. Brangwynne, “Competing protein–RNA interaction networks control multiphase intracellular organization,” Cell 181, 306–324 (2020).
    [See also commentary.]

Preprints

  • Y. Polyachenko, H. Watanabe, A. Korolev, and W.M. Jacobs, “Co-condensation and multivalency enable acetylation-sensitive, concentration-robust assembly of BRD4 condensates,” arXiv 2606.02275.
  • Z. Liu, B. Yuan, M. Rao, G. Reddy, and W.M. Jacobs, “A thermodynamic metric quantitatively predicts disordered protein partitioning and multicomponent phase behavior,” arXiv 2603.08300.

Publications from Undergraduate, Graduate, and Postdoctoral Training

  • A. Bitran, W.M. Jacobs, and E.I. Shakhnovich, “Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins,” PLoS Comp. Biol. 16, e1008323 (2020).
  • V. Zhao, W.M. Jacobs, and E.I. Shakhnovich, “Effect of protein structure on evolution of cotranslational folding,” Biophys. J. 119, 1123–1134 (2020).
    [See also commentary.]
  • A. Bitran, W.M. Jacobs, X. Zhai, and E.I. Shakhnovich, “Co-translational folding allows misfolding-prone proteins to circumvent deep kinetic traps,” Proc. Natl. Acad. Sci. U.S.A. 117, 1485–1495 (2020).
  • W.M. Jacobs and E.I. Shakhnovich, “Accurate protein-folding transition-path statistics from a simple free-energy landscape,” J. Phys. Chem. B 122, 11126–11136 (2018).
  • M. Sajfutdinow, W.M. Jacobs, A. Reinhardt, C. Schneider, and David M. Smith, “Direct observation and rational design of nucleation behavior in addressable self-assembly,” Proc. Natl. Acad. Sci. U.S.A. 115, E5877–E5886 (2018).
  • S. Bhattacharyya*, W.M. Jacobs*, B.V. Adkar, J. Yan, W. Zhang and E.I. Shakhnovich, “Accessibility of the Shine–Dalgarno sequence dictates N-terminal codon bias in E. coli,” Mol. Cell 114, 894–905 (2018). [*Equal contribution]
  • W.M. Jacobs and E.I. Shakhnovich, “Evidence of evolutionary selection for co-translational folding,” Proc. Natl. Acad. Sci. U.S.A. 114, 11434–11439 (2017).
  • W.M. Jacobs and D. Frenkel, “Phase transitions in biological systems with many components,” Biophys. J. 112, 683–691 (2017).
    [See also commentary.]
  • W.M. Jacobs and E.I. Shakhnovich, “Structure-based prediction of protein-folding transition paths,” Biophys. J. 111, 925–936 (2016).
    [See also commentary.]
  • W.M. Jacobs and D. Frenkel, “Self-assembly of structures with addressable complexity,” J. Am. Chem. Soc. 138, 2457–2467 (2016).
  • W.M. Jacobs, T.P.J. Knowles, and D. Frenkel, “Oligomers of heat-shock proteins: Structures that don't imply function,” PLoS Comp. Biol. 12, e1004756 (2016).
  • W.M. Jacobs and D. Frenkel, “Self-assembly protocol design for periodic multicomponent structures,” Soft Matter 11, 8930–8938 (2015).
  • W.M. Jacobs, A. Reinhardt, and D. Frenkel, “Rational design of self-assembly pathways for complex multicomponent structures,” Proc. Natl. Acad. Sci. U.S.A. 112, 6313–6318 (2015).
  • W.M. Jacobs, A. Reinhardt, and D. Frenkel, “Theoretical prediction of free-energy landscapes for complex self-assembly,” J. Chem. Phys. 142, 021101 (2015).
  • W.M. Jacobs, D.W. Oxtoby, and D. Frenkel, “Phase separation in solutions with specific and nonspecific interactions,” J. Chem. Phys. 140, 024108 (2014).
  • W.M. Jacobs and D. Frenkel, “Predicting phase behavior in multicomponent mixtures,” J. Chem. Phys. 139, 024108 (2013).
  • W.M. Jacobs, D.A. Nicholson, H. Zemmer, A.N. Volkov, and L.V. Zhigilei, “Acoustic energy dissipation and thermalization in carbon nanotubes: Atomistic modeling and mesoscopic description,” Phys. Rev. B 86, 165414 (2012).

The Jacobs Group
Frick Chemistry Laboratory
Princeton, NJ 08544