Van Lehn Group
Molecular Simulations of Synthetic and Biological Soft Materials

Publications

Publications are listed below below; please also see the profile on Google Scholar. * indicates equal contributions.

Preprints

  1. A. D. Smith, S. Runde, A. K. Chew, A. S. Kelkar, U. Maheshwari, R. C. Van Lehn, and V. M. Zavala. “Topological analysis of molecular dynamics simulations using the Euler Characteristic.” ChemRxiv, preprint. [Link]

2023

  1. B. C. Dallin, A. S. Kelkar, and R. C. Van Lehn. “Structural features of interfacial water predict the hydrophobicity of chemically heterogeneous surfaces.” Chemical Science, accepted. [Link][Data]

2022

  1. Z. Sumer and R. C. Van Lehn. “Heuristic computational model for predicting lignin solubility in tailored organic solvents.” ACS Sustainable Chemistry & Engineering, accepted. [Link][Scripts]
  2. C. Gahan, R. C Van Lehn, H. E. Blackwell, and D. M. Lynn. “Interactions of bacterial quorum sensing signals with model lipid membranes: Influence of membrane composition on membrane remodeling.” Langmuir, accepted. [Link]
  3. S. Qin, S. Jiang, J. Li, P. Balaprakash, R. C. Van Lehn, and V. M. Zavala. “Capturing molecular interactions in graph neural networks: A case study in multi-component phase equilibrium.” Digital Discovery, accepted. [Link]
  4. R. G. Dastidar, M. S. Kim, P. Zhou, Z. Luo, C. Shi, K. J. Barnett, D. J. McClelland, E. Y.-X. Chen, R. C. Van Lehn, and G. W. Huber. “Catalytic production of Tetrahydropyran (THP): A biomass-derived, economically competitive solvent with demonstrated use in plastic dissolution.” Green Chemistry, 2022, 24, 9101-9113. [Link]
  5. J. Morstein*, A. Capecchi, K. Hinnah, B. Park, J. Petit-Jacques, R. C. Van Lehn, J-L Reymond, and D. Trauner. “Medium-chain lipid conjugation facilitates cell-permeability and bioactivity.” Journal of the American Chemical Society, 2022, 144 (40), 18532-18544. [Link]
  6. H. Li, H. Aguirre-Villegas, R. D. Allen, X. Bai, C. H. Benson, G. T. Beckham, S. L. Bradshaw, J. L. Brown, M. A. Sanchez Castillo, V. S. Cecon, J. B. Curley, G. W. Curtzwiler, S. Dong, S. Gaddameedi, J. E. Garcia, I. Hermans, M. S. Kim, J. Ma, L. O. Mark, M. Mavrikakis, O. O. Olafasakin, T. A. Osswald, K. G. Papanikolaou, H. Radhakrishnan, K. L. Sanchez-Rivera, K. N. Tuma, R. C. Van Lehn, K. L. Vorst, M. M. Wright, J. Wu, V. M. Zavala, P. Zhou, and G. W. Huber. “Expanding plastics recycling technologies: Chemical aspects, technology status and challenges.” Green Chemistry, 2022, 24, 8899-9002. [Link]. 
  7. N. Bao, S. Jiang, A.D. Smith, J. J. Schauer, M. Mavrikakis, R. C. Van Lehn, V. M. Zavala, and N. L. Abbott. “Sensing gas mixtures by analyzing the spatiotemporal optical responses of liquid crystals using 3D convolutional neural networks.” ACS Sensors, 2022, 7 (9), 2545-2555. [Link]
  8. Z. Sumer and R. C. Van Lehn. “Data-centric development of lignin structure – solubility relationships in deep eutectic solvents using molecular simulations.” ACS Sustainable Chemistry & Engineering, 2022, 10 (31), 10144-10156. [Link]
  9. N. Bao, J. I. Gold, J. K. Sheavly, J. J. Schauer, V. M. Zavala, R. C. Van Lehn, M. Mavrikakis, and N. L. Abbott. “Ordering transitions of liquid crystals triggered by metal oxide-catalyzed reactions of sulfur oxide species.” Journal of the American Chemical Society, 2022, 144 (36), 16378-16388. [Link]
  10. Z. Shen, J. H. Dwyer, J. Sun, K. R. Jinkins, M. S. Arnold, P. Gopalan, and R. C. Van Lehn. “A simple simulation-derived descriptor for the deposition of polymer-wrapped carbon nanotubes on functionalized substrates.” Soft Matter, 2022, 18, 4653-4659. [Link]
  11. J. Li, C. T. Maravelias, and R. C. Van Lehn. “Adaptive conformer sampling for property prediction using the COnductor-Like Screening Model for Real Solvents.” Industrial & Engineering Chemistry Research, 2022, 61 (25), 9025-9036. [Link]
  12. A. K. Chew, J. A. Pedersen, and R. C. Van Lehn. “Predicting the physicochemical properties and biological activities of monolayer-protected gold nanoparticles using simulation-derived descriptors.” ACS Nano, 2022, 16 (4), 6282-6292. [Link]
  13. L. Je, G. W. Huber, R. C. Van Lehn, and V. M. Zavala. “On the integration of molecular dynamics, data science, and experiments for studying solvent effects on catalysis.” Current Opinion in Chemical Engineering, 2022, 36, 100796. [Link]
  14. A. S. Kelkar, B. C. Dallin, and R. C. Van Lehn. “Identifying nonadditive contributions to the hydrophobicity of chemically heterogeneous surfaces via dual-loop active learning.” Journal of Chemical Physics, 2022, 156, 024701. [Link][Data][Scripts]

2021

  1. CG Gahan, RC Van Lehn, HE Blackwell, and DM Lynn. “Interactions of bacterial quorum sensing signals with model lipid membranes: Influence of acyl tail structure on multi-scale response.” Langmuir, 2021, 37 (41), 12049-12058. [Link]
  2. S. Qin, T. Jin, R. C. Van Lehn, and V. M. Zavala. “Predicting critical micelle concentrations for surfactants using graph convolutional neural networks.” Journal of Physical Chemistry B, 2021, 125, 10610-10620. [Link]
  3. P. Zhou, K. L. Sánchez-Rivera, G. W. Huber, and R. C. Van Lehn. “Computational approach for rapidly predicting temperature-dependent polymer solubilities using molecular-scale models.” ChemSusChem, 2021, 14 (9), 4307-4316.  [Link]
  4. K. L. Sánchez-Rivera, P. Zhou, M. S. Kim, L. D. González Chávez, S. Grey, K. Nelson, S-C. Wang, I. Hermans, V. M. Zavala, R.C. Van Lehn, and G. W. Huber. “Reducing antisolvent use in the STRAP process by enabling temperature-controlled polymer dissolution and precipitation for the recycling of multilayer plastic films.” ChemSusChem, 2021, 14 (9), 4317-4329. [Link]
  5. C. G. Gahan, S. J. Patel, L. M. Chen, D. E. Manson, Z. J. Ehmer, H. E. Blackwell, R. C. Van Lehn, and D. M. Lynn. “Bacterial quorum sensing signals promote large-scale remodeling of lipid membranes.” Langmuir, 2021, 35 (30), 9120-9136. [Link]
  6. S. J. Patel and R. C. Van Lehn. “Analysis of charged peptide loop-flipping across a lipid bilayer using the string method with swarms-of-trajectories.” Journal of Physical Chemistry B, 2021, 125 (22), 5862-5873. [Link][Data]
  7. C. A. Lochbaum, A. K. Chew, X. Zhang, V. M. Rotello, R. C. Van Lehn, and J. A. Pedersen. “The lipophilicity of cationic ligands promotes irreversible adsorption of nanoparticles to lipid bilayers.” ACS Nano, 2021, 15, 6562-6572. [Link]
  8. A. K. Chew, B. C. Dallin, and R. C. Van Lehn. “The interplay of ligand properties and core size dictates the hydrophobicity of monolayer-protected gold nanoparticles.” ACS Nano, 2021, 15 (3), 4534-4545. [Link]
  9. B. M. Hoover, Z. Shen, C. G. Gahan, D. M. Lynn, R. C. Van Lehn, and R. M. Murphy. “Membrane remodeling and simulation of aggregation following alpha-synuclein adsorption to phosphatidylserine vesicles.” Journal of Physical Chemistry B, 2021, 125 (6), 1582-1594. [Link]
  10. T. Jin, S. J. Patel, and R. C. Van Lehn. “Molecular simulations of lipid membrane partitioning and translocation by bacterial quorum sensing modulators.” PLoS ONE, 2021, 16:2, e0246187. [Link][Data]

2020

  1. T. W. Walker, N. Frelka, Z. Shen, A. K. Chew, J. Bannick, S. Grey, J. A. Dumesic, R. C. Van Lehn, and G. W. Huber. “Recycling of multilayer plastic packaging materials by solvent-targeted recovery and precipitation.” Science Advances, 2020, 6 (47), eaba7599. [Link][Data]
  2. A. K. Chew, S. Jiang, W. Zhang, V. M. Zavala, and R. C. Van Lehn. “Fast predictions of liquid-phase acid-catalyzed reaction rates using molecular dynamics and convolutional neural networks.” Chemical Science, 2o20, 11, 12464-12476. [Link] [Data]
  3. A. S. Kelkar, B. C. Dallin, and R. C. Van Lehn. “Predicting Interfacial Hydrophobicity by Learning Spatiotemporal Features of Interfacial Water Structure: Combining Molecular Dynamics Simulations with Convolutional Neural Networks.” Journal of Physical Chemistry B, 2020, 124 (41), 9103-9114. [Link][Data][Scripts]
  4. J. K. Sheavly and R. C. Van Lehn. “Bilayer-mediated Assembly of Cationic Nanoparticles Adsorbed to Lipid Bilayers: Insights from Molecular Simulations.” AIChE Journal, 2020, 66 (12), e16993. [Link]
  5. C. G. Gahan*, S. J. Patel*, M. E. Boursier, K. E. Nyffeler, J. Jennings, N. L. Abbott, H. E. Blackwell, R. C. Van Lehn, D. M. Lynn. “Gram-negative bacterial quorum sensing signals self-assemble in aqueous media to form micelles and vesicles: an integrated experimental and molecular dynamics study.” Journal of Physical Chemistry B 2020, 124 (18), 3616-3628. [Link]
  6. T. W. Walker*, A. K. Chew*, R. C. Van Lehn,  J. A. Dumesic, and G. W. Huber. “Rational design of mixed solvent systems for acid-catalyzed biomass conversion processes using a combined experimental, molecular dynamics and machine learning approach.” Topics in Catalysis 2020, 63, 649-663. [Link]
  7. Z. Shen and R. C. Van Lehn. “Solvent selection for the separation of lignin-derived monomers using the Conductor-like Screening Model for Real Solvents.” Industrial & Engineering Chemistry Research 2020, 59 (16), 7755-7764 . [Link]
  8. A. K. Chew*, T. W. Walker*, Z. Shen, B. Demir, L. Witteman, J. Euclide, G. W. Huber, J. A. Dumesic, and R. C. Van Lehn. “Effect of mixed-solvent environments on the selectivity of acid-catalyzed dehydration reactions.” ACS Catalysis 2020, 10, 1679-1691. [Link]
  9. J. K. Sheavly, J. I. Gold, M. Mavrikakis, and R. C. Van Lehn. “Molecular Simulations of Analyte Partitioning and Diffusion in Liquid Crystal Sensors.” Molecular Systems Design & Engineering 2020, 5, 304-316. [Link]

2019

  1. J. H. Dwyer, Z. Shen, K. R. Jinkins, W. Wei, M. S. Arnold, R. C. Van Lehn, and P. Gopalan. “Solvent-Mediated Affinity of Polymer-Wrapped Single-Walled Carbon Nanotubes for Chemically Modified Surfaces.” Langmuir 2019, 35, 12492-12500. [Link]
  2. B. C. Dallin and R. C. Van Lehn. “Spatially Heterogenous Water Properties at Disordered Surfaces Decrease the Hydrophobicity of Nonpolar Self-Assembled Monolayers.” Journal of Physical Chemical Letters 2019, 10, 3991-3997. [Link]
  3. A. K. Chew and R. C. Van Lehn. “Quantifying the Stability of the Hydronium Ion in Organic Solvents With Molecular Dynamics Simulations.” Frontiers in Chemistry 2019, 7(439). [Link]
  4. B. C. Dallin, H. Yeon, A. R. Ostwalt, N. L. Abbott, and R. C. Van Lehn. “Molecular Order Affects Interfacial Water Structure and Temperature-Dependent Hydrophobic Interactions between Nonpolar Self-Assembled Monolayers.” Langmuir 2019, 35(6), 2078-2088. [Link][Data]
  5. J. K. Sheavly, J. A. Pedersen, and R. C. Van Lehn. “Curvature-Driven Adsorption of Cationic Nanoparticles to Phase Boundaries in Multicomponent Lipid Bilayers.” Nanoscale 2019, 11, 2767. [Link]
  6. R. C. Van Lehn and A. Alexander-Katz. “Energy Landscape for the Insertion of Amphiphilic Nanoparticles into Lipid Membranes: A Computational Study.” PLoS ONE 2019, 14(1), e0209492. [Link][Data]

2018

  1. S. J. Patel and R. C. Van Lehn. “Characterizing the Molecular Mechanisms for Flipping Charged Peptide Flanking Loops across a Lipid Bilayer.” The Journal of Physical Chemistry B 2018, 122(45), 10337-10348. [Link][Data]
  2. A. K. Chew and R. C. Van Lehn. “Effect of Core Morphology on the Structural Asymmetry of Alkanethiol Monolayer-Protected Gold Nanoparticles.” The Journal of Physical Chemistry C 2018, 122(45), 26288-26297. [Link][Data]
  3. M. Werner, T. Auth, P. A. Beales, J. B. Fleury, F. Hook, H. Kress, R. C. Van Lehn, M. Muller, E. P. Petrov, L. Sarkisov, J-U. Sommer, V. A. Baulin. “Nanomaterial interactions with biomembranes: Bridging the gap between soft matter models and biological context.” Biointerphases 2018, 028501. [Link]
  4. A. Alexander-Katz and R. C. Van Lehn. “Perspective: Random copolymers that protect proteins.” Science 2018, 359. [Link]
  5. P. U. Atukorale, D. S. Yun, R. C. Van Lehn, R. P. Carney, A. Bekdemir, P. H. Silva, A. Alexander-Katz, F. Stellacci, and D. J. Irvine. “Structure-property relationships of amphiphilic nanoparticles that penetrate or fuse lipid membranes.” Bioconjugate Chemistry 2018, 29, 1131-1140.  [Link]
  6. T. W. Walker*, A. K. Chew*, H, Li, B. Demir, Z. C. Zhang, G. Huber, R. C. Van Lehn, and J. Dumesic. “Universal kinetic solvent effects in acid-catalyzed reactions of biomass-derived oxygenates.” Energy & Environmental Science 2018, 11, 617-628. [Link][Data]

2017

  1. H. Yeon, C. Wang, R. C. Van Lehn, and N. L. Abbott. “Influence of order within nonpolar monolayers on hydrophobic interactions.” Langmuir 2017, 33, 4628. [Link]
  2. M. J. M. Niesen, C. Y. Wang, R. C. Van Lehn, and T. F. Miller III. “Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration.” PLoS Computational Biology 2017, 13, e1005427. [Link]
  3. R. C. Van Lehn and A. Alexander-Katz. “Grafting charged species to membrane-embedded scaffolds dramatically increases the rate of bilayer flipping.” ACS Central Science 2017, 3, 186. [Link]

2016

  1. M. Tahir*, R. C. Van Lehn*, S. H. Choi, and A. Alexander-Katz. “Solvent-exposed lipid tail protrusions depend on lipid membrane composition and curvature.” BBA Biomembranes 2016, 1858, 1207. [Link]

2010-2015

  1. R. C. Van Lehn, B. Zhang, and T. F. Miller III. “Regulation of multispanning membrane protein topology by post-translational annealing.” eLife 2015, 4, e08697. [Link]
  2. R. C. Van Lehn and A. Alexander-Katz. “Pathway for insertion of amphiphilic nanoparticles into defect-free lipid bilayers from atomistic molecular dynamics simulations.” Soft Matter 2015, 11, 3165. [Link]
  3. R. C. Van Lehn and A. Alexander-Katz. “Membrane-embedded nanoparticles induce lipid rearrangements similar to those exhibited by biological membrane proteins.” The Journal of Physical Chemistry B 2014, 118, 12586. [Link]
  4. R. C. Van Lehn*, M. Ricci*, P. H. J. Silva, P. Andreozzi, J. Reguera, K. Voïtchovsky, F. Stellacci, and A. Alexander-Katz. “Lipid tail protrusions mediate the insertion of nanoparticles into model cell membranes.” Nature Communications 2014, 5, 4482. [Link]
  5. R. C. Van Lehn and A. Alexander-Katz, “Fusion of ligand-coated nanoparticles with lipid bilayers: Effect of ligand flexibility.”  Journal of Physical Chemistry A 2014, 118, 5848. [Link]
  6. R. C. Van Lehn and A. Alexander-Katz, “Free energy change for insertion of charged, monolayer-protected nanoparticles into lipid bilayers.”  Soft Matter 2014, 10, 648. [Link]
  7. R. C. Van Lehn and A. Alexander-Katz, “Structure of mixed-monolayer-protected gold nanoparticles in aqueous salt solution from atomistic molecular dynamics simulations.” Journal of Physical Chemistry C 2013, 117, 20104. [Link]
  8. R. C. Van Lehn, P. U. Atukorale, R. P. Carney, Y-S Yang, F. Stellacci, D. J. Irvine, and A. Alexander-Katz, “Effect of particle diameter and surface composition on the spontaneous fusion of monolayer-protected gold nanoparticles with lipid bilayers.” Nano Letters 2013, 13, 4060. [Link]
  9. R. C. Van Lehn and A. Alexander-Katz, “Ligand-mediated short-range attraction drives aggregation of charged monolayer-protected gold nanoparticles.” Langmuir 2013, 29, 8788. [Link]
  10. R. C. Van Lehn and A. Alexander-Katz, “Penetration of lipid bilayers by nanoparticles with environmentally-responsive surfaces: simulations and theory.” Soft Matter 2011, 7, 11392. [Link]
  11. R. C. Van Lehn and A. Alexander-Katz, “Lateral phase separation of mixed polymer brushes physisorbed on planar substrates.” Journal of Chemical Physics 2011, 135, 141106. [Link]
  12. R. C. Van Lehn, C. E. Sing, H. Chen, and A. Alexander-Katz. “Multidimensional targeting: using physical and chemical forces in unison.” Current Pharmaceutical Biotechnology 2010, 11, 320. [Link]