Molecular communications in complex systems of dynamic supramolecular polymers

Abstract

Supramolecular polymers are composed of monomers that self-assemble non-covalently, generating distributions of monodimensional fibres in continuous communication with each other and with the surrounding solution. Fibres, exchanging molecular species, and external environment constitute a sole complex system, which intrinsic dynamics is hard to elucidate. Here we report coarse-grained molecular simulations that allow studying supramolecular polymers at the thermodynamic equilibrium, explicitly showing the complex nature of these systems, which are composed of exquisitely dynamic molecular entities. Detailed studies of molecular exchange provide insights into key factors controlling how assemblies communicate with each other, defining the equilibrium dynamics of the system. Using minimalistic and finer chemically relevant molecular models, we observe that a rich concerted complexity is intrinsic in such self-assembling systems. This offers a new dynamic and probabilistic (rather than structural) picture of supramolecular polymer systems, where the travelling molecular species continuously shape the assemblies that statistically emerge at the equilibrium.

Classifying soft self-assembled materials via unsupervised machine learning of defects

“…Among many interesting features, the highest potential of soft supramolecular materials lies in their intrinsically dynamic character at room temperature 5 . The self-assembled monomers continuously exchange within and in-and-out these materials 6 , 7 , controlling how they communicate with each other at the equilibrium 8 , 9 , how they respond to external stimuli 10 , and how they behave out-of-equilibrium 11 . Such dynamical features determine a set of intriguing properties that, on the one hand are crucial for the functioning of biological tissues (e.g., self-healing, chemotacticity, molecular transport, etc.)…”

Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle Superlattices

“…This approach provides a demonstration of the importance of studying such complex molecular systems at sufficiently high resolution to track the individual motion of the ions, while at the same time treating sufficiently large scales to observe collective behaviors. 85 Figure 5 shows the results of the SOAP+PAMM analysis for the same systems at T = 333 K. We note an overall similar behavior to that observed at T = 300 K, with slight differences, coherent with the conductivity results of Figure 2 related to increased thermal agitation. The qualitative insight provided by simulation snapshots (Figure 5b,c) indicates that the localization of the citrates for the two limiting cases of field amplitude (E = 0 and E = 0.11) is substantially the same as in the T = 300 K case.…”

“…However, this is an emergent behavior that originates from the concerted motions of the ions in response to the stimulus ( E ). This approach provides a demonstration of the importance of studying such complex molecular systems at sufficiently high resolution to track the individual motion of the ions, while at the same time treating sufficiently large scales to observe collective behaviors …”

“…This approach provides a demonstration of the importance of studying such complex molecular systems at sufficiently high resolution to track the individual motion of the ions, while at the same time treating sufficiently large scales to observe collective behaviors. 85 …”

Peptide Sequence Determines Structural Sensitivity to Supramolecular Polymerization Pathways and Bioactivity

“…Some progress has been made in predicting the shape and size of supramolecular polymers formed by a particular monomer. However, these predictions may not consider the subtle differences in intermolecular interactions that arise from monomeric structure and polymerization pathway, which ultimately affect the architecture and energy landscape of the resulting nanostructures. − The internal structure can have further implications for the biological and mechanical functions of supramolecular polymers. Thus, selecting polymerization pathways that result in specific internal structures is essential when designing functional supramolecular systems.…”