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\n  \n 2020\n \n \n (15)\n \n \n
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\n \n\n \n \n \n \n \n Designing exceptional gas-separation polymer membranes using machine learning.\n \n \n \n\n\n \n Barnett, J., W.; Bilchak, C., R.; Wang, Y.; Benicewicz, B., C.; Murdock, L., A.; Bereau, T.; and Kumar, S., K.\n\n\n \n\n\n\n Science Advances, 6(20): 1-8. 2020.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Designing exceptional gas-separation polymer membranes using machine learning},\n type = {article},\n year = {2020},\n pages = {1-8},\n volume = {6},\n id = {aad101a7-1da0-311d-925f-bf9b804f0cc3},\n created = {2020-07-23T15:33:54.142Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-07-23T15:33:54.142Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Barnett2020},\n private_publication = {false},\n abstract = {The field of polymer membrane design is primarily based on empirical observation, which limits discovery of new materials optimized for separating a given gas pair. Instead of relying on exhaustive experimental investigations, we trained a machine learning (ML) algorithm, using a topological, path-based hash of the polymer repeating unit. We used a limited set of experimental gas permeability data for six different gases in ~700 polymeric constructs that have been measured to date to predict the gas-separation behavior of over 11,000 homopolymers not previously tested for these properties. To test the algorithm’s accuracy, we synthesized two of the most promising polymer membranes predicted by this approach and found that they exceeded the upper bound for CO2/CH4 separation performance. This ML technique, which is trained using a relatively small body of experimental data (and no simulation data), evidently represents an innovative means of exploring the vast phase space available for polymer membrane design.},\n bibtype = {article},\n author = {Barnett, J. Wesley and Bilchak, Connor R. and Wang, Yiwen and Benicewicz, Brian C. and Murdock, Laura A. and Bereau, Tristan and Kumar, Sanat K.},\n doi = {10.1126/sciadv.aaz4301},\n journal = {Science Advances},\n number = {20}\n}
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\n The field of polymer membrane design is primarily based on empirical observation, which limits discovery of new materials optimized for separating a given gas pair. Instead of relying on exhaustive experimental investigations, we trained a machine learning (ML) algorithm, using a topological, path-based hash of the polymer repeating unit. We used a limited set of experimental gas permeability data for six different gases in ~700 polymeric constructs that have been measured to date to predict the gas-separation behavior of over 11,000 homopolymers not previously tested for these properties. To test the algorithm’s accuracy, we synthesized two of the most promising polymer membranes predicted by this approach and found that they exceeded the upper bound for CO2/CH4 separation performance. This ML technique, which is trained using a relatively small body of experimental data (and no simulation data), evidently represents an innovative means of exploring the vast phase space available for polymer membrane design.\n
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\n \n\n \n \n \n \n \n \n Hydration free energies from kernel-based machine learning: Compound-database bias.\n \n \n \n \n\n\n \n Rauer, C.; and Bereau, T.\n\n\n \n\n\n\n , 014101(1). 2020.\n \n\n\n\n
\n\n\n\n \n \n \"HydrationWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Hydration free energies from kernel-based machine learning: Compound-database bias},\n type = {article},\n year = {2020},\n volume = {014101},\n websites = {http://arxiv.org/abs/2007.00407%0Ahttp://dx.doi.org/10.1063/5.0012230},\n publisher = {AIP Publishing, LLC},\n id = {3e886615-189d-32f9-989f-dbde7aa55065},\n created = {2020-07-23T15:33:54.143Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-07-23T15:33:54.143Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Rauer2020},\n private_publication = {false},\n abstract = {We consider the prediction of a basic thermodynamic property---hydration free energies---across a large subset of the chemical space of small organic molecules. Our in silico study is based on computer simulations at the atomistic level with implicit solvent. We report on a kernel-based machine learning approach that is inspired by recent work in learning electronic properties, but differs in key aspects: The representation is averaged over several conformers to account for the statistical ensemble. We also include an atomic-decomposition ansatz, which we show offers significant added transferability compared to molecular learning. Finally, we explore the existence of severe biases from databases of experimental compounds. By performing a combination of dimensionality reduction and cross-learning models, we show that the rate of learning depends significantly on the breadth and variety of the training dataset. Our study highlights the dangers of fitting machine-learning models to databases of narrow chemical range.},\n bibtype = {article},\n author = {Rauer, Clemens and Bereau, Tristan},\n doi = {10.1063/5.0012230},\n number = {1}\n}
\n
\n\n\n
\n We consider the prediction of a basic thermodynamic property---hydration free energies---across a large subset of the chemical space of small organic molecules. Our in silico study is based on computer simulations at the atomistic level with implicit solvent. We report on a kernel-based machine learning approach that is inspired by recent work in learning electronic properties, but differs in key aspects: The representation is averaged over several conformers to account for the statistical ensemble. We also include an atomic-decomposition ansatz, which we show offers significant added transferability compared to molecular learning. Finally, we explore the existence of severe biases from databases of experimental compounds. By performing a combination of dimensionality reduction and cross-learning models, we show that the rate of learning depends significantly on the breadth and variety of the training dataset. Our study highlights the dangers of fitting machine-learning models to databases of narrow chemical range.\n
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\n \n\n \n \n \n \n \n Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders.\n \n \n \n\n\n \n Bozkurt Varolgüneş, Y.; Bereau, T.; and Rudzinski, J., F.\n\n\n \n\n\n\n Machine Learning: Science and Technology, 1(1): 015012. 2020.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n 
@article{\n title = {Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders},\n type = {article},\n year = {2020},\n keywords = {article is available online,clustering,dimensionality reduction,markov state models,molecular dynamics simulations,supplementary material for this,variational autoencoders},\n pages = {015012},\n volume = {1},\n id = {a230cc1d-722f-3967-9ab2-20233e447009},\n created = {2020-07-23T15:33:54.226Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-07-23T15:33:54.226Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {BozkurtVarolgunes2020},\n private_publication = {false},\n abstract = {Extracting insight from the enormous quantity of data generated from molecular simulations requires the identification of a small number of collective variables whose corresponding low-dimensional free-energy landscape retains the essential features of the underlying system. Data-driven techniques provide a systematic route to constructing this landscape, without the need for extensive a priori intuition into the relevant driving forces. In particular, autoencoders are powerful tools for dimensionality reduction, as they naturally force an information bottleneck and, thereby, a low-dimensional embedding of the essential features. While variational autoencoders ensure continuity of the embedding by assuming a unimodal Gaussian prior, this is at odds with the multi-basin free-energy landscapes that typically arise from the identification of meaningful collective variables. In this work, we incorporate this physical intuition into the prior by employing a Gaussian mixture variational autoencoder (GMVAE), which encourages the separation of metastable states within the embedding. The GMVAE performs dimensionality reduction and clustering within a single unified framework, and is capable of identifying the inherent dimensionality of the input data, in terms of the number of Gaussians required to categorize the data. We illustrate our approach on two toy models, alanine dipeptide, and a challenging disordered peptide ensemble, demonstrating the enhanced clustering effect of the GMVAE prior compared to standard VAEs. The resulting embeddings appear to be promising representations for constructing Markov state models, highlighting the transferability of the dimensionality reduction from static equilibrium properties to dynamics.},\n bibtype = {article},\n author = {Bozkurt Varolgüneş, Yasemin and Bereau, Tristan and Rudzinski, Joseph F},\n doi = {10.1088/2632-2153/ab80b7},\n journal = {Machine Learning: Science and Technology},\n number = {1}\n}
\n
\n\n\n
\n Extracting insight from the enormous quantity of data generated from molecular simulations requires the identification of a small number of collective variables whose corresponding low-dimensional free-energy landscape retains the essential features of the underlying system. Data-driven techniques provide a systematic route to constructing this landscape, without the need for extensive a priori intuition into the relevant driving forces. In particular, autoencoders are powerful tools for dimensionality reduction, as they naturally force an information bottleneck and, thereby, a low-dimensional embedding of the essential features. While variational autoencoders ensure continuity of the embedding by assuming a unimodal Gaussian prior, this is at odds with the multi-basin free-energy landscapes that typically arise from the identification of meaningful collective variables. In this work, we incorporate this physical intuition into the prior by employing a Gaussian mixture variational autoencoder (GMVAE), which encourages the separation of metastable states within the embedding. The GMVAE performs dimensionality reduction and clustering within a single unified framework, and is capable of identifying the inherent dimensionality of the input data, in terms of the number of Gaussians required to categorize the data. We illustrate our approach on two toy models, alanine dipeptide, and a challenging disordered peptide ensemble, demonstrating the enhanced clustering effect of the GMVAE prior compared to standard VAEs. The resulting embeddings appear to be promising representations for constructing Markov state models, highlighting the transferability of the dimensionality reduction from static equilibrium properties to dynamics.\n
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\n \n\n \n \n \n \n \n Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids.\n \n \n \n\n\n \n Scherer, C.; Scheid, R.; Andrienko, D.; and Bereau, T.\n\n\n \n\n\n\n Journal of Chemical Theory and Computation, 16(5): 3194-3204. 2020.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n  \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids},\n type = {article},\n year = {2020},\n pages = {3194-3204},\n volume = {16},\n id = {64a8f26b-f9ae-390c-a1b9-265e4e712e52},\n created = {2020-07-23T15:33:54.245Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-07-23T15:33:54.245Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Scherer2020},\n private_publication = {false},\n abstract = {Current machine learning (ML) models aimed at learning force fields are plagued by their high computational cost at every integration time step. We describe a number of practical and computationally efficient strategies to parametrize traditional force fields for molecular liquids from ML: the particle decomposition ansatz to two- and three-body force fields, the use of kernel-based ML models that incorporate physical symmetries, the incorporation of switching functions close to the cutoff, and the use of covariant meshing to boost the training set size. Results are presented for model molecular liquids: pairwise Lennard-Jones, three-body Stillinger-Weber, and bottom-up coarse-graining of water. Here, covariant meshing proves to be an efficient strategy to learn canonically averaged instantaneous forces. We show that molecular dynamics simulations with tabulated two- and three-body ML potentials are computationally efficient and recover two- and three-body distribution functions. Many-body representations, decomposition, and kernel regression schemes are all implemented in the open-source software package VOTCA.},\n bibtype = {article},\n author = {Scherer, Christoph and Scheid, René and Andrienko, Denis and Bereau, Tristan},\n doi = {10.1021/acs.jctc.9b01256},\n journal = {Journal of Chemical Theory and Computation},\n number = {5}\n}
\n
\n\n\n
\n Current machine learning (ML) models aimed at learning force fields are plagued by their high computational cost at every integration time step. We describe a number of practical and computationally efficient strategies to parametrize traditional force fields for molecular liquids from ML: the particle decomposition ansatz to two- and three-body force fields, the use of kernel-based ML models that incorporate physical symmetries, the incorporation of switching functions close to the cutoff, and the use of covariant meshing to boost the training set size. Results are presented for model molecular liquids: pairwise Lennard-Jones, three-body Stillinger-Weber, and bottom-up coarse-graining of water. Here, covariant meshing proves to be an efficient strategy to learn canonically averaged instantaneous forces. We show that molecular dynamics simulations with tabulated two- and three-body ML potentials are computationally efficient and recover two- and three-body distribution functions. Many-body representations, decomposition, and kernel regression schemes are all implemented in the open-source software package VOTCA.\n
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\n \n\n \n \n \n \n \n \n Inserting Small Molecules across Membrane Mixtures: Insight from the Potential of Mean Force.\n \n \n \n \n\n\n \n Centi, A.; Dutta, A.; Parekh, S., H.; and Bereau, T.\n\n\n \n\n\n\n Biophysical Journal, 118(6): 1321-1332. 2020.\n \n\n\n\n
\n\n\n\n \n \n \"InsertingWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Inserting Small Molecules across Membrane Mixtures: Insight from the Potential of Mean Force},\n type = {article},\n year = {2020},\n pages = {1321-1332},\n volume = {118},\n websites = {https://doi.org/10.1016/j.bpj.2020.01.039},\n publisher = {Biophysical Society},\n id = {2c158b26-7b5c-3ad2-a879-249ca35da793},\n created = {2020-08-13T11:42:05.699Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-13T11:42:05.699Z},\n read = {true},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Centi2020},\n private_publication = {false},\n abstract = {Small solutes have been shown to alter the lateral organization of cell membranes and reconstituted phospholipid bilayers; however, the mechanisms by which these changes happen are still largely unknown. Traditionally, both experiment and simulation studies have been restricted to testing only a few compounds at a time, failing to identify general molecular descriptors or chemical properties that would allow extrapolating beyond the subset of considered solutes. In this work, we probe the competing energetics of inserting a solute in different membrane environments by means of the potential of mean force. We show that these calculations can be used as a computationally efficient proxy to establish whether a solute will stabilize or destabilize domain phase separation. Combined with umbrella-sampling simulations and coarse-grained molecular dynamics simulations, we are able to screen solutes across a wide range of chemistries and polarities. Our results indicate that for the system under consideration, preferential partitioning and therefore effectiveness in altering membrane phase separation are strictly linked to the location of insertion in the bilayer (i.e., midplane or interface). Our approach represents a fast and simple tool for obtaining structural and thermodynamic insight into the partitioning of small molecules between lipid domains and its relation to phase separation, ultimately providing a platform for identifying the key determinants of this process.},\n bibtype = {article},\n author = {Centi, Alessia and Dutta, Arghya and Parekh, Sapun H. and Bereau, Tristan},\n doi = {10.1016/j.bpj.2020.01.039},\n journal = {Biophysical Journal},\n number = {6}\n}
\n
\n\n\n
\n Small solutes have been shown to alter the lateral organization of cell membranes and reconstituted phospholipid bilayers; however, the mechanisms by which these changes happen are still largely unknown. Traditionally, both experiment and simulation studies have been restricted to testing only a few compounds at a time, failing to identify general molecular descriptors or chemical properties that would allow extrapolating beyond the subset of considered solutes. In this work, we probe the competing energetics of inserting a solute in different membrane environments by means of the potential of mean force. We show that these calculations can be used as a computationally efficient proxy to establish whether a solute will stabilize or destabilize domain phase separation. Combined with umbrella-sampling simulations and coarse-grained molecular dynamics simulations, we are able to screen solutes across a wide range of chemistries and polarities. Our results indicate that for the system under consideration, preferential partitioning and therefore effectiveness in altering membrane phase separation are strictly linked to the location of insertion in the bilayer (i.e., midplane or interface). Our approach represents a fast and simple tool for obtaining structural and thermodynamic insight into the partitioning of small molecules between lipid domains and its relation to phase separation, ultimately providing a platform for identifying the key determinants of this process.\n
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\n \n\n \n \n \n \n \n Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations.\n \n \n \n\n\n \n Hoffmann, C.; Centi, A.; Menichetti, R.; and Bereau, T.\n\n\n \n\n\n\n Scientific Data, 7(1): 1-7. 2020.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n  \n \n 1 download\n \n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations},\n type = {article},\n year = {2020},\n pages = {1-7},\n volume = {7},\n id = {2c12c684-cf32-346e-b0c7-a29174d76859},\n created = {2020-08-13T11:42:05.782Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-13T11:42:05.782Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Hoffmann2020},\n private_publication = {false},\n abstract = {The permeation of small-molecule drugs across a phospholipid membrane bears much interest both in the pharmaceutical sciences and in physical chemistry. Connecting the chemistry of the drug and the lipids to the resulting thermodynamic properties remains of immediate importance. Here we report molecular dynamics (MD) simulation trajectories using the coarse-grained (CG) Martini force field. A wide, representative coverage of chemistry is provided: across solutes—exhaustively enumerating all 105 CG dimers—and across six phospholipids. For each combination, umbrella-sampling simulations provide detailed structural information of the solute at all depths from the bilayer midplane to bulk water, allowing a precise reconstruction of the potential of mean force. Overall, the present database contains trajectories from 15,120 MD simulations. This database may serve the further identification of structure-property relationships between compound chemistry and drug permeability.},\n bibtype = {article},\n author = {Hoffmann, Christian and Centi, Alessia and Menichetti, Roberto and Bereau, Tristan},\n doi = {10.1038/s41597-020-0391-0},\n journal = {Scientific Data},\n number = {1}\n}
\n
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\n The permeation of small-molecule drugs across a phospholipid membrane bears much interest both in the pharmaceutical sciences and in physical chemistry. Connecting the chemistry of the drug and the lipids to the resulting thermodynamic properties remains of immediate importance. Here we report molecular dynamics (MD) simulation trajectories using the coarse-grained (CG) Martini force field. A wide, representative coverage of chemistry is provided: across solutes—exhaustively enumerating all 105 CG dimers—and across six phospholipids. For each combination, umbrella-sampling simulations provide detailed structural information of the solute at all depths from the bilayer midplane to bulk water, allowing a precise reconstruction of the potential of mean force. Overall, the present database contains trajectories from 15,120 MD simulations. This database may serve the further identification of structure-property relationships between compound chemistry and drug permeability.\n
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\n \n\n \n \n \n \n \n Probing Nanoparticle/Membrane Interactions by Combining Amphiphilic Diblock Copolymer Assembly and Plasmonics.\n \n \n \n\n\n \n Koch, A., H.; Morsbach, S.; Bereau, T.; Lévêque, G.; Butt, H., J.; Deserno, M.; Landfester, K.; and Fytas, G.\n\n\n \n\n\n\n Journal of Physical Chemistry B, 124(5): 742-750. 2020.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Probing Nanoparticle/Membrane Interactions by Combining Amphiphilic Diblock Copolymer Assembly and Plasmonics},\n type = {article},\n year = {2020},\n pages = {742-750},\n volume = {124},\n id = {184b28e5-f960-302f-82a5-5fb48dfe6fdd},\n created = {2020-08-13T11:42:05.827Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-13T11:42:05.827Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Koch2020},\n private_publication = {false},\n abstract = {Understanding the interactions between nanoparticles (NPs) and boundaries of cells is crucial both for their toxicity and therapeutic applications. Besides specific receptor-mediated endocytosis of surface-functionalized NPs, passive internalization is prompted by relatively unspecific parameters, such as particle size and charge. Based on theoretical treatments, adhesion to and bending of the cell membrane can induce NP wrapping. Experimentally, powerful tools are needed to selectively probe possible membrane-NP motifs at very dilute conditions and avoid dye labeling. In this work, we employ surface resonance-enhanced dynamic light scattering, surface plasmon resonance, electron microscopy, and simulations for sensing interactions between plasmonic AuNPs and polymersomes. We distinguish three different interaction scenarios at nanomolar concentrations by tuning the surface charge of AuNPs and rationalize these events by balancing vesicle bending and electrostatic/van der Waals AuNP and vesicle adhesion. The clarification of the physical conditions under which nanoparticles passively translocate across membranes can aid in the rational design of drugs that cannot exploit specific modes of cellular uptake and also elucidates physical properties that render nanoparticles in the environment particularly toxic.},\n bibtype = {article},\n author = {Koch, Amelie H.R. and Morsbach, Svenja and Bereau, Tristan and Lévêque, Gaëtan and Butt, Hans Jürgen and Deserno, Markus and Landfester, Katharina and Fytas, George},\n doi = {10.1021/acs.jpcb.9b10469},\n journal = {Journal of Physical Chemistry B},\n number = {5}\n}
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\n\n\n
\n Understanding the interactions between nanoparticles (NPs) and boundaries of cells is crucial both for their toxicity and therapeutic applications. Besides specific receptor-mediated endocytosis of surface-functionalized NPs, passive internalization is prompted by relatively unspecific parameters, such as particle size and charge. Based on theoretical treatments, adhesion to and bending of the cell membrane can induce NP wrapping. Experimentally, powerful tools are needed to selectively probe possible membrane-NP motifs at very dilute conditions and avoid dye labeling. In this work, we employ surface resonance-enhanced dynamic light scattering, surface plasmon resonance, electron microscopy, and simulations for sensing interactions between plasmonic AuNPs and polymersomes. We distinguish three different interaction scenarios at nanomolar concentrations by tuning the surface charge of AuNPs and rationalize these events by balancing vesicle bending and electrostatic/van der Waals AuNP and vesicle adhesion. The clarification of the physical conditions under which nanoparticles passively translocate across membranes can aid in the rational design of drugs that cannot exploit specific modes of cellular uptake and also elucidates physical properties that render nanoparticles in the environment particularly toxic.\n
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\n \n\n \n \n \n \n \n \n Statistical mechanics of local force dipole responses in computer glasses.\n \n \n \n \n\n\n \n Rainone, C.; Bouchbinder, E.; and Lerner, E.\n\n\n \n\n\n\n J. Chem. Phys., 152(19): 194503. 2020.\n \n\n\n\n
\n\n\n\n \n \n \"StatisticalWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Statistical mechanics of local force dipole responses in computer glasses},\n type = {article},\n year = {2020},\n pages = {194503},\n volume = {152},\n websites = {https://doi.org/10.1063/5.0005655},\n id = {20816abe-ad49-3d26-ad51-89e7af0ac82a},\n created = {2020-08-27T16:46:28.862Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:28.862Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {kappa_statistics_jcp_2020},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Rainone, Corrado and Bouchbinder, Eran and Lerner, Edan},\n doi = {10.1063/5.0005655},\n journal = {J. Chem. Phys.},\n number = {19}\n}
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\n \n\n \n \n \n \n \n \n Finite-size effects in the nonphononic density of states in computer glasses.\n \n \n \n \n\n\n \n Lerner, E.\n\n\n \n\n\n\n Phys. Rev. E, 101(3): 32120. 3 2020.\n \n\n\n\n
\n\n\n\n \n \n \"Finite-sizeWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{\n title = {Finite-size effects in the nonphononic density of states in computer glasses},\n type = {article},\n year = {2020},\n pages = {32120},\n volume = {101},\n websites = {https://link.aps.org/doi/10.1103/PhysRevE.101.032120},\n month = {3},\n publisher = {American Physical Society},\n id = {bc217df2-0bca-32ec-a48b-90881bff442e},\n created = {2020-08-27T16:46:29.088Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.088Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {PhysRevE.101.032120},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Lerner, Edan},\n doi = {10.1103/PhysRevE.101.032120},\n journal = {Phys. Rev. E},\n number = {3}\n}
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\n \n\n \n \n \n \n \n \n Nonlinear quasilocalized excitations in glasses: True representatives of soft spots.\n \n \n \n \n\n\n \n Kapteijns, G.; Richard, D.; and Lerner, E.\n\n\n \n\n\n\n Phys. Rev. E, 101(3): 32130. 3 2020.\n \n\n\n\n
\n\n\n\n \n \n \"NonlinearWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Nonlinear quasilocalized excitations in glasses: True representatives of soft spots},\n type = {article},\n year = {2020},\n pages = {32130},\n volume = {101},\n websites = {https://link.aps.org/doi/10.1103/PhysRevE.101.032130},\n month = {3},\n publisher = {American Physical Society},\n id = {cac35235-7b03-37e3-b2e5-c5c2dd218a37},\n created = {2020-08-27T16:46:29.095Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.095Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {episode_1_2020},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Kapteijns, Geert and Richard, David and Lerner, Edan},\n doi = {10.1103/PhysRevE.101.032130},\n journal = {Phys. Rev. E},\n number = {3}\n}
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\n \n\n \n \n \n \n \n \n Robustness of density of low-frequency states in amorphous solids.\n \n \n \n \n\n\n \n Das, P.; Hentschel, H., G., E.; Lerner, E.; and Procaccia, I.\n\n\n \n\n\n\n Phys. Rev. B, 102(1): 14202. 7 2020.\n \n\n\n\n
\n\n\n\n \n \n \"RobustnessWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Robustness of density of low-frequency states in amorphous solids},\n type = {article},\n year = {2020},\n pages = {14202},\n volume = {102},\n websites = {https://link.aps.org/doi/10.1103/PhysRevB.102.014202},\n month = {7},\n publisher = {American Physical Society},\n id = {c06b48d9-9943-368c-8415-19a3c921ab69},\n created = {2020-08-27T16:46:29.215Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.215Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {IP_schober_modes_prn_2020},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Das, Prasenjit and Hentschel, H George E and Lerner, Edan and Procaccia, Itamar},\n doi = {10.1103/PhysRevB.102.014202},\n journal = {Phys. Rev. B},\n number = {1}\n}
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\n \n\n \n \n \n \n \n \n Pinching a glass reveals key properties of its soft spots.\n \n \n \n \n\n\n \n Rainone, C.; Bouchbinder, E.; and Lerner, E.\n\n\n \n\n\n\n Proc. Natl. Acad. Sci. U.S.A., 117(10): 5228-5234. 2020.\n \n\n\n\n
\n\n\n\n \n \n \"PinchingWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Pinching a glass reveals key properties of its soft spots},\n type = {article},\n year = {2020},\n pages = {5228-5234},\n volume = {117},\n websites = {https://www.pnas.org/content/117/10/5228},\n publisher = {National Academy of Sciences},\n id = {8fa0a8a4-7843-376d-8fc5-7535e0441235},\n created = {2020-08-27T16:46:29.219Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.219Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {pinching_pnas},\n source_type = {article},\n private_publication = {false},\n abstract = {Glasses form when liquids are quickly cooled. Many of the properties of glasses are universal\\textemdashi.e., independent of their composition and the liquid-phase temperature Tp from which they were cooled. One such property is the existence of noncrystalline soft vibrational excitations, which are highly localized in space and follow a universal vibrational frequency distribution, with a nonuniversal coefficient. We show that pinching glasses\\textemdashi.e., applying local force perturbations to them\\textemdashreveals dramatic variability in the physics of this coefficient with Tp. In particular, it reveals how the number of noncrystalline soft vibrational excitations, their size, and typical degree of softness vary with Tp, having major implications for the behavior of glasses in a wide variety of situations.It is now well established that glasses feature quasilocalized nonphononic excitations\\textemdashcoined \\textquotedblleftsoft spots\\textquotedblright\\textemdash, which follow a universal ω4 density of states in the limit of low frequencies ω. All glass-specific properties, such as the dependence on the preparation protocol or composition, are encapsulated in the nonuniversal prefactor of the universal ω4 law. The prefactor, however, is a composite quantity that incorporates information both about the number of quasilocalized nonphononic excitations and their characteristic stiffness, in an apparently inseparable manner. We show that by pinching a glass\\textemdashi.e., by probing its response to force dipoles\\textemdashone can disentangle and independently extract these two fundamental pieces of physical information. This analysis reveals that the number of quasilocalized nonphononic excitations follows a Boltzmann-like law in terms of the parent temperature from which the glass is quenched. The latter, sometimes termed the fictive (or effective) temperature, plays important roles in nonequilibrium thermodynamic approaches to the relaxation, flow, and deformation of glasses. The analysis also shows that the characteristic stiffness of quasilocalized nonphononic excitations can be related to their characteristic size, a long sought-for length scale. These results show that important physical information, which is relevant for various key questions in glass physics, can be obtained through pinching a glass.},\n bibtype = {article},\n author = {Rainone, Corrado and Bouchbinder, Eran and Lerner, Edan},\n doi = {10.1073/pnas.1919958117},\n journal = {Proc. Natl. Acad. Sci. U.S.A.},\n number = {10}\n}
\n
\n\n\n
\n Glasses form when liquids are quickly cooled. Many of the properties of glasses are universal\\textemdashi.e., independent of their composition and the liquid-phase temperature Tp from which they were cooled. One such property is the existence of noncrystalline soft vibrational excitations, which are highly localized in space and follow a universal vibrational frequency distribution, with a nonuniversal coefficient. We show that pinching glasses\\textemdashi.e., applying local force perturbations to them\\textemdashreveals dramatic variability in the physics of this coefficient with Tp. In particular, it reveals how the number of noncrystalline soft vibrational excitations, their size, and typical degree of softness vary with Tp, having major implications for the behavior of glasses in a wide variety of situations.It is now well established that glasses feature quasilocalized nonphononic excitations\\textemdashcoined \\textquotedblleftsoft spots\\textquotedblright\\textemdash, which follow a universal ω4 density of states in the limit of low frequencies ω. All glass-specific properties, such as the dependence on the preparation protocol or composition, are encapsulated in the nonuniversal prefactor of the universal ω4 law. The prefactor, however, is a composite quantity that incorporates information both about the number of quasilocalized nonphononic excitations and their characteristic stiffness, in an apparently inseparable manner. We show that by pinching a glass\\textemdashi.e., by probing its response to force dipoles\\textemdashone can disentangle and independently extract these two fundamental pieces of physical information. This analysis reveals that the number of quasilocalized nonphononic excitations follows a Boltzmann-like law in terms of the parent temperature from which the glass is quenched. The latter, sometimes termed the fictive (or effective) temperature, plays important roles in nonequilibrium thermodynamic approaches to the relaxation, flow, and deformation of glasses. The analysis also shows that the characteristic stiffness of quasilocalized nonphononic excitations can be related to their characteristic size, a long sought-for length scale. These results show that important physical information, which is relevant for various key questions in glass physics, can be obtained through pinching a glass.\n
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\n \n\n \n \n \n \n \n \n Universality of the Nonphononic Vibrational Spectrum across Different Classes of Computer Glasses.\n \n \n \n \n\n\n \n Richard, D.; González-López, K.; Kapteijns, G.; Pater, R.; Vaknin, T.; Bouchbinder, E.; and Lerner, E.\n\n\n \n\n\n\n Phys. Rev. Lett., 125(8): 85502. 8 2020.\n \n\n\n\n
\n\n\n\n \n \n \"UniversalityWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Universality of the Nonphononic Vibrational Spectrum across Different Classes of Computer Glasses},\n type = {article},\n year = {2020},\n pages = {85502},\n volume = {125},\n websites = {https://link.aps.org/doi/10.1103/PhysRevLett.125.085502},\n month = {8},\n publisher = {American Physical Society},\n id = {19fcc706-9fea-32db-ad85-10116704683b},\n created = {2020-08-27T16:46:29.219Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.219Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {modes_prl_2020},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Richard, David and González-López, Karina and Kapteijns, Geert and Pater, Robert and Vaknin, Talya and Bouchbinder, Eran and Lerner, Edan},\n doi = {10.1103/PhysRevLett.125.085502},\n journal = {Phys. Rev. Lett.},\n number = {8}\n}
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\n \n\n \n \n \n \n \n Compression-induced anti-nematic order in glassy and semicrystalline polymers.\n \n \n \n\n\n \n Jabbari-Farouji, S.; and and Damien Vandembroucq\n\n\n \n\n\n\n Soft Matter, 16: 102-106. 2020.\n \n\n\n\n
\n\n\n\n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{\n title = {Compression-induced anti-nematic order in glassy and semicrystalline polymers},\n type = {article},\n year = {2020},\n pages = {102-106},\n volume = {16},\n publisher = {Royal Society of Chemistry},\n id = {0bf1fe42-bbbc-3781-8c45-c95408efefc7},\n created = {2020-08-28T15:46:26.246Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-28T15:46:26.246Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Jabbari_2020},\n source_type = {article},\n user_context = {Communication},\n private_publication = {false},\n abstract = {We provide new insights into the molecular origin of the asymmetry between uniaxial tensile and compressive deformation of glassy and semicrystalline polymers using molecular dynamics simulations. The difference between the two responses strongly depends on the chain length and is the largest at intermediate chain lengths. Irrespective of chain length, the intra- and interchain organization of polymers under extension and compression are remarkably distinct. The chains align along the tensile axis leading to a global nematic order of the bonds and end-to-end vectors, whereas compression reorganizes polymers to lie in planes perpendicular to the compressive axis resulting in the emergence of an anti-nematic order and destruction of crystallinity. Regardless of the initial glassy or semicrystalline structure, the deformed state of polymers at large strains converge towards the same kind of structure that only depends on the deformation mode.},\n bibtype = {article},\n author = {Jabbari-Farouji, Sara and and Damien Vandembroucq, undefined},\n doi = {10.1039/C9SM01848D},\n journal = {Soft Matter}\n}
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\n We provide new insights into the molecular origin of the asymmetry between uniaxial tensile and compressive deformation of glassy and semicrystalline polymers using molecular dynamics simulations. The difference between the two responses strongly depends on the chain length and is the largest at intermediate chain lengths. Irrespective of chain length, the intra- and interchain organization of polymers under extension and compression are remarkably distinct. The chains align along the tensile axis leading to a global nematic order of the bonds and end-to-end vectors, whereas compression reorganizes polymers to lie in planes perpendicular to the compressive axis resulting in the emergence of an anti-nematic order and destruction of crystallinity. Regardless of the initial glassy or semicrystalline structure, the deformed state of polymers at large strains converge towards the same kind of structure that only depends on the deformation mode.\n
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\n \n\n \n \n \n \n \n \n Emergent pattern formation of active magnetic suspensions in an external field.\n \n \n \n \n\n\n \n Koessel, F., R.; and Jabbari-Farouji, S.\n\n\n \n\n\n\n . 2020.\n \n\n\n\n
\n\n\n\n \n \n \"EmergentWebsite\n  \n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Emergent pattern formation of active magnetic suspensions in an external field},\n type = {article},\n year = {2020},\n websites = {https://arxiv.org/abs/2006.03352},\n id = {7b27a92f-7deb-3b69-8e78-614644395278},\n created = {2020-08-28T15:46:26.332Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-28T15:46:26.332Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Koessel_2020},\n source_type = {article},\n private_publication = {false},\n abstract = {We study collective self-organization of weakly magnetic active suspensions in a uniform external field byanalyzing a mesoscopic continuum model that we have recently developed. Our model is based on a Smoluchowskiequation for a particle probability density function in an alignment field coupled to a mean-field descriptionof the flow arising from the activity and the alignment torque. Performing linear stability analysisof the Smoluchowski equation and the resulting orientational moment equations combined with non-linear 3Dsimulations, we provide a comprehensive picture of instability patterns as a function of strengths of activity andmagnetic field. For sufficiently high activity and moderate magnetic field strengths, the competition betweenthe activity-induced flow and external magnetic torque renders a homogeneous polar steady state unstable. As aresult, four distinct dynamical patterns of collective motion emerge. The instability patterns for pushers includetraveling sheets governed by bend-twist instabilities and dynamical aggregates. For pullers, finite-sized andsystem spanning pillar-like concentrated regions predominated by splay deformations emerge which migrate inthe field direction. Notably, at very strong magnetic fields, we observe a reentrant hydrodynamic stability of thepolar steady state.},\n bibtype = {article},\n author = {Koessel, Fabian R and Jabbari-Farouji, Sara}\n}
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\n We study collective self-organization of weakly magnetic active suspensions in a uniform external field byanalyzing a mesoscopic continuum model that we have recently developed. Our model is based on a Smoluchowskiequation for a particle probability density function in an alignment field coupled to a mean-field descriptionof the flow arising from the activity and the alignment torque. Performing linear stability analysisof the Smoluchowski equation and the resulting orientational moment equations combined with non-linear 3Dsimulations, we provide a comprehensive picture of instability patterns as a function of strengths of activity andmagnetic field. For sufficiently high activity and moderate magnetic field strengths, the competition betweenthe activity-induced flow and external magnetic torque renders a homogeneous polar steady state unstable. As aresult, four distinct dynamical patterns of collective motion emerge. The instability patterns for pushers includetraveling sheets governed by bend-twist instabilities and dynamical aggregates. For pullers, finite-sized andsystem spanning pillar-like concentrated regions predominated by splay deformations emerge which migrate inthe field direction. Notably, at very strong magnetic fields, we observe a reentrant hydrodynamic stability of thepolar steady state.\n
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\n  \n 2019\n \n \n (10)\n \n \n
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\n \n\n \n \n \n \n \n \n Non-reciprocal robotic metamaterials.\n \n \n \n \n\n\n \n Brandenbourger, M.; Locsin, X.; Lerner, E.; and Coulais, C.\n\n\n \n\n\n\n Nat. Commun., 10(1): 4608. 10 2019.\n \n\n\n\n
\n\n\n\n \n \n \"Non-reciprocalWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{\n title = {Non-reciprocal robotic metamaterials},\n type = {article},\n year = {2019},\n pages = {4608},\n volume = {10},\n websites = {https://doi.org/10.1038/s41467-019-12599-3},\n month = {10},\n id = {6aae0ec9-29ff-36cd-9fee-0480ad66a1b6},\n created = {2020-08-27T16:46:28.796Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:28.796Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Brandenbourger2019},\n source_type = {article},\n private_publication = {false},\n abstract = {Non-reciprocal transmission of motion is potentially highly beneficial to a wide range of applications, ranging from wave guiding to shock and vibration damping and energy harvesting. To date, large levels of non-reciprocity have been realized using broken spatial or temporal symmetries, yet mostly in the vicinity of resonances, bandgaps or using nonlinearities, thereby non-reciprocal transmission remains limited to narrow ranges of frequencies or input magnitudes and sensitive to attenuation. Here, we create a robotic mechanical metamaterials wherein we use local control loops to break reciprocity at the level of the interactions between the unit cells. We show theoretically and experimentally that first-of-their-kind spatially asymmetric standing waves at all frequencies and unidirectionally amplified propagating waves emerge. These findings realize the mechanical analogue of the non-Hermitian skin effect. They significantly advance the field of active metamaterials for non hermitian physics and open avenues to channel mechanical energy in unprecedented ways.},\n bibtype = {article},\n author = {Brandenbourger, Martin and Locsin, Xander and Lerner, Edan and Coulais, Corentin},\n doi = {10.1038/s41467-019-12599-3},\n journal = {Nat. Commun.},\n number = {1}\n}
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\n Non-reciprocal transmission of motion is potentially highly beneficial to a wide range of applications, ranging from wave guiding to shock and vibration damping and energy harvesting. To date, large levels of non-reciprocity have been realized using broken spatial or temporal symmetries, yet mostly in the vicinity of resonances, bandgaps or using nonlinearities, thereby non-reciprocal transmission remains limited to narrow ranges of frequencies or input magnitudes and sensitive to attenuation. Here, we create a robotic mechanical metamaterials wherein we use local control loops to break reciprocity at the level of the interactions between the unit cells. We show theoretically and experimentally that first-of-their-kind spatially asymmetric standing waves at all frequencies and unidirectionally amplified propagating waves emerge. These findings realize the mechanical analogue of the non-Hermitian skin effect. They significantly advance the field of active metamaterials for non hermitian physics and open avenues to channel mechanical energy in unprecedented ways.\n
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\n \n\n \n \n \n \n \n \n Anisotropic structural predictor in glassy materials.\n \n \n \n \n\n\n \n Schwartzman-Nowik, Z.; Lerner, E.; and Bouchbinder, E.\n\n\n \n\n\n\n Phys. Rev. E, 99(6): 60601. 6 2019.\n \n\n\n\n
\n\n\n\n \n \n \"AnisotropicWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{\n title = {Anisotropic structural predictor in glassy materials},\n type = {article},\n year = {2019},\n pages = {60601},\n volume = {99},\n websites = {https://link.aps.org/doi/10.1103/PhysRevE.99.060601},\n month = {6},\n publisher = {American Physical Society},\n id = {8102402c-4e84-3323-aa36-b662f3757a52},\n created = {2020-08-27T16:46:29.004Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.004Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {PhysRevE.99.060601},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Schwartzman-Nowik, Zohar and Lerner, Edan and Bouchbinder, Eran},\n doi = {10.1103/PhysRevE.99.060601},\n journal = {Phys. Rev. E},\n number = {6}\n}
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\n \n\n \n \n \n \n \n \n Characterizing nonaffinity upon decompression of soft-sphere packings.\n \n \n \n \n\n\n \n Kooij, S.; and Lerner, E.\n\n\n \n\n\n\n Phys. Rev. E, 100(4): 42609. 10 2019.\n \n\n\n\n
\n\n\n\n \n \n \"CharacterizingWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Characterizing nonaffinity upon decompression of soft-sphere packings},\n type = {article},\n year = {2019},\n pages = {42609},\n volume = {100},\n websites = {https://link.aps.org/doi/10.1103/PhysRevE.100.042609},\n month = {10},\n publisher = {American Physical Society},\n id = {c080ba99-f7e7-3343-9bb7-7b613f1a8e2a},\n created = {2020-08-27T16:46:29.083Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.083Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {PhysRevE.100.042609},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Kooij, Stefan and Lerner, Edan},\n doi = {10.1103/PhysRevE.100.042609},\n journal = {Phys. Rev. E},\n number = {4}\n}
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\n \n\n \n \n \n \n \n \n Mechanical properties of simple computer glasses.\n \n \n \n \n\n\n \n Lerner, E.\n\n\n \n\n\n\n J. Non-Cryst. Solids, 522: 119570. 2019.\n \n\n\n\n
\n\n\n\n \n \n \"MechanicalWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n \n \n \n \n \n \n \n \n \n \n\n\n\n
\n 
@article{\n title = {Mechanical properties of simple computer glasses},\n type = {article},\n year = {2019},\n keywords = {Elastic moduli,Elasticity,Mechanical properties,Poisson's ratio,Structural glasses},\n pages = {119570},\n volume = {522},\n websites = {http://www.sciencedirect.com/science/article/pii/S0022309319304417},\n id = {01551898-1e21-3096-aada-59c215f25c02},\n created = {2020-08-27T16:46:29.087Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.087Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {LERNER2019119570},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Lerner, Edan},\n doi = {https://doi.org/10.1016/j.jnoncrysol.2019.119570},\n journal = {J. Non-Cryst. Solids}\n}
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\n \n\n \n \n \n \n \n \n Theory for the density of interacting quasilocalized modes in amorphous solids.\n \n \n \n \n\n\n \n Ji, W.; Popovi\\ifmmode \\acutec\\else ć\\fi, M.; de Geus, T., W., J.; Lerner, E.; and Wyart, M.\n\n\n \n\n\n\n Phys. Rev. E, 99(2): 23003. 2 2019.\n \n\n\n\n
\n\n\n\n \n \n \"TheoryWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Theory for the density of interacting quasilocalized modes in amorphous solids},\n type = {article},\n year = {2019},\n pages = {23003},\n volume = {99},\n websites = {https://link.aps.org/doi/10.1103/PhysRevE.99.023003},\n month = {2},\n publisher = {American Physical Society},\n id = {ce2d1081-dfc0-3fde-a6e6-9d579bda1d9f},\n created = {2020-08-27T16:46:29.090Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.090Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {PhysRevE.99.023003},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Ji, Wencheng and Popovi\\ifmmode \\acutec\\else ć\\fi, Marko and de Geus, Tom W J and Lerner, Edan and Wyart, Matthieu},\n doi = {10.1103/PhysRevE.99.023003},\n journal = {Phys. Rev. E},\n number = {2}\n}
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\n \n\n \n \n \n \n \n \n Wave attenuation in glasses: Rayleigh and generalized-Rayleigh scattering scaling.\n \n \n \n \n\n\n \n Moriel, A.; Kapteijns, G.; Rainone, C.; Zylberg, J.; Lerner, E.; and Bouchbinder, E.\n\n\n \n\n\n\n J. Chem. Phys., 151(10): 104503. 2019.\n \n\n\n\n
\n\n\n\n \n \n \"WaveWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Wave attenuation in glasses: Rayleigh and generalized-Rayleigh scattering scaling},\n type = {article},\n year = {2019},\n pages = {104503},\n volume = {151},\n websites = {https://doi.org/10.1063/1.5111192},\n id = {885a3fef-0393-39ac-93fb-49738000b10a},\n created = {2020-08-27T16:46:29.124Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.124Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {scattering_jcp},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Moriel, Avraham and Kapteijns, Geert and Rainone, Corrado and Zylberg, Jacques and Lerner, Edan and Bouchbinder, Eran},\n doi = {10.1063/1.5111192},\n journal = {J. Chem. Phys.},\n number = {10}\n}
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\n \n\n \n \n \n \n \n \n Rigidity and auxeticity transitions in networks with strong bond-bending interactions.\n \n \n \n \n\n\n \n Rens, R.; and Lerner, E.\n\n\n \n\n\n\n Eur. Phys. J. E, 42(9): 114. 9 2019.\n \n\n\n\n
\n\n\n\n \n \n \"RigidityWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Rigidity and auxeticity transitions in networks with strong bond-bending interactions},\n type = {article},\n year = {2019},\n pages = {114},\n volume = {42},\n websites = {https://doi.org/10.1140/epje/i2019-11888-5},\n month = {9},\n id = {e1ffbc14-3623-38a4-9a91-d0a23f9b5bd0},\n created = {2020-08-27T16:46:29.195Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.195Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Rens2019},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Rens, Robbie and Lerner, Edan},\n doi = {10.1140/epje/i2019-11888-5},\n journal = {Eur. Phys. J. E},\n number = {9}\n}
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\n \n\n \n \n \n \n \n \n Fast generation of ultrastable computer glasses by minimization of an augmented potential energy.\n \n \n \n \n\n\n \n Kapteijns, G.; Ji, W.; Brito, C.; Wyart, M.; and Lerner, E.\n\n\n \n\n\n\n Phys. Rev. E, 99(1): 12106. 1 2019.\n \n\n\n\n
\n\n\n\n \n \n \"FastWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Fast generation of ultrastable computer glasses by minimization of an augmented potential energy},\n type = {article},\n year = {2019},\n pages = {12106},\n volume = {99},\n websites = {https://link.aps.org/doi/10.1103/PhysRevE.99.012106},\n month = {1},\n publisher = {American Physical Society},\n id = {e3308f8d-28c1-3c8b-94fc-63126c01c2c9},\n created = {2020-08-27T16:46:29.196Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-27T16:46:29.196Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {fsp},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {Kapteijns, Geert and Ji, Wencheng and Brito, Carolina and Wyart, Matthieu and Lerner, Edan},\n doi = {10.1103/PhysRevE.99.012106},\n journal = {Phys. Rev. E},\n number = {1}\n}
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\n \n\n \n \n \n \n \n \n Controlling stability and transport of magnetic microswimmers by an external field.\n \n \n \n \n\n\n \n Koessel, F., R.; and Jabbari-Farouji, S.\n\n\n \n\n\n\n EPL (Europhysics Letters), 125(2): 28001. 2019.\n \n\n\n\n
\n\n\n\n \n \n \"ControllingWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n  \n \n abstract \n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Controlling stability and transport of magnetic microswimmers by an external field},\n type = {article},\n year = {2019},\n pages = {28001},\n volume = {125},\n websites = {https://doi.org/10.1209%2F0295-5075%2F125%2F28001},\n publisher = {IOP Publishing},\n id = {8840bc96-516c-33c0-be1d-734a8032179b},\n created = {2020-08-28T15:46:26.241Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-28T15:46:26.241Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {Koessel_2019},\n source_type = {article},\n private_publication = {false},\n abstract = {The interplay between external field and fluid-mediated interactions in active suspensions leads to patterns of collective motion that are poorly understood. Here, we study the hydrodynamic stability and transport of microswimmers with weak magnetic dipole moments in an external field using a kinetic theory framework. Combining linear stability analysis and non-linear 3D continuum simulations, we show that for sufficiently high activity and moderate magnetic field strengths, a homogeneous polar steady state is unstable and distinct types of splay and bend instabilities for puller and pusher swimmers emerge. The instabilities arise from the amplification of anisotropic hydrodynamic interactions due to the external alignment and lead to a partial depolarisation and a reduction of the average transport speed of the swimmers in the field direction. Interestingly, at higher field strengths the homogeneous polar state becomes stable and a transport efficiency identical to that of active particles without hydrodynamic interactions is restored.},\n bibtype = {article},\n author = {Koessel, Fabian R and Jabbari-Farouji, Sara},\n doi = {10.1209/0295-5075/125/28001},\n journal = {EPL (Europhysics Letters)},\n number = {2}\n}
\n
\n\n\n
\n The interplay between external field and fluid-mediated interactions in active suspensions leads to patterns of collective motion that are poorly understood. Here, we study the hydrodynamic stability and transport of microswimmers with weak magnetic dipole moments in an external field using a kinetic theory framework. Combining linear stability analysis and non-linear 3D continuum simulations, we show that for sufficiently high activity and moderate magnetic field strengths, a homogeneous polar steady state is unstable and distinct types of splay and bend instabilities for puller and pusher swimmers emerge. The instabilities arise from the amplification of anisotropic hydrodynamic interactions due to the external alignment and lead to a partial depolarisation and a reduction of the average transport speed of the swimmers in the field direction. Interestingly, at higher field strengths the homogeneous polar state becomes stable and a transport efficiency identical to that of active particles without hydrodynamic interactions is restored.\n
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\n \n\n \n \n \n \n \n \n Supramolecular copolymers predominated by alternating order: Theory and application.\n \n \n \n \n\n\n \n van Buel, R.; Spitzer, D.; Berac, C., M.; van der Schoot, P.; Besenius, P.; and Jabbari-Farouji, S.\n\n\n \n\n\n\n The Journal of Chemical Physics, 151(1): 14902. 2019.\n \n\n\n\n
\n\n\n\n \n \n \"SupramolecularWebsite\n  \n \n\n \n \n doi\n  \n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{\n title = {Supramolecular copolymers predominated by alternating order: Theory and application},\n type = {article},\n year = {2019},\n pages = {14902},\n volume = {151},\n websites = {https://doi.org/10.1063/1.5097577},\n id = {55434ec3-88a0-30ea-bae9-e1e059cf3585},\n created = {2020-08-28T15:46:26.246Z},\n file_attached = {false},\n profile_id = {6a122574-9fbc-32f4-b166-53bc4f07b051},\n group_id = {44f966a6-5fc6-3fbf-92d0-5cda043c5bd2},\n last_modified = {2020-08-28T15:46:26.246Z},\n read = {false},\n starred = {false},\n authored = {false},\n confirmed = {true},\n hidden = {false},\n citation_key = {doi:10.1063/1.5097577},\n source_type = {article},\n private_publication = {false},\n bibtype = {article},\n author = {van Buel, Reinier and Spitzer, Daniel and Berac, Christian Marijan and van der Schoot, Paul and Besenius, Pol and Jabbari-Farouji, Sara},\n doi = {10.1063/1.5097577},\n journal = {The Journal of Chemical Physics},\n number = {1}\n}
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