Proofreading mechanism for colloidal self-assembly DOI Creative Commons

Qian-Ze Zhu,

Chrisy Xiyu Du, Ella M. King

et al.

Physical Review Research, Journal Year: 2024, Volume and Issue: 6(4)

Published: Dec. 9, 2024

Designing components that can robustly self-assemble into structures with biological complexity is a grand challenge for material science. Proofreading and error correction required to improve assembly yield beyond equilibrium limits, using energy avoid kinetic traps in the landscape. Here, we introduce an explicit two-staged proofreading scheme patchy particle colloidal assemblies substantially improves robustness. The first stage implements local rules whereby particles increase their binding strengths when they detect environment corresponding desired target. second corrects remaining errors, adding reverse pathway inspired by proofreading. shows significant improvements, eliminating traps, giving much broader temperature range high yield. Additionally, robust against quenched disorder components. Our findings illuminate advancing programmable design of synthetic living materials, potentially fostering synthesis novel materials functional behaviors. Published American Physical Society 2024

Language: Английский

Machine learning meets physics: A two-way street DOI Creative Commons
Herbert Levine, Yuhai Tu

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(27)

Published: June 24, 2024

Emotions coordinate our behavior and physiological states during survival-salient events pleasurable interactions. Even though we are often consciously aware of current emotional state, such as anger or happiness, the mechanisms giving ...Emotions felt in body, somatosensory feedback has been proposed to trigger conscious experiences. Here reveal maps bodily sensations associated with different emotions using a unique topographical self-report method. In ...

Language: Английский

Citations

9
Programming patchy particles for materials assembly design DOI
Ella M. King, Chrisy Xiyu Du,

Qian-Ze Zhu

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(27)

Published: June 24, 2024

Direct design of complex functional materials would revolutionize technologies ranging from printable organs to novel clean energy devices. However, even incremental steps toward designing have proven challenging. If the material is constructed highly components, space properties rapidly becomes too computationally expensive search. On other hand, very simple components such as uniform spherical particles are not powerful enough capture rich behavior. Here, we introduce a differentiable model with that yet properties: rigid bodies composed directional interactions (patchy particles). We showcase method self-assembly designs open lattices self-limiting clusters, all which notoriously challenging goals achieve using purely isotropic particles. By directly optimizing over location and interaction patches on patchy gradient descent, dramatically reduce computation time for finding optimal building blocks.

Language: Английский

Citations

8
Flexible interaction patches lead to building blocks with fluctuating valency DOI

Trevor C. Stevens,

Pepijn G. Moerman

Nature Chemistry, Journal Year: 2025, Volume and Issue: 17(3), P. 305 - 306

Published: Feb. 27, 2025

Language: Английский

Citations

0
Nonequilibrium Self-Assembly Control by the Stochastic Landscape Method DOI Creative Commons
Michael Faran, Gili Bisker

Journal of Chemical Information and Modeling, Journal Year: 2025, Volume and Issue: unknown

Published: April 8, 2025

Self-assembly of building blocks is a fundamental process in nanotechnology, materials science, and biological systems, offering pathways to the formation complex functional structures through local interactions. However, lack effective error correction mechanisms often limits efficiency precision assembly, particularly systems with strong binding energies. Inspired by cellular processes stochastic resetting, we present closed-loop feedback control method that employs transient modulations interaction energies, mimicking, for instance, global effect pH changes as nonequilibrium drives optimize assembly outcomes real time. By leveraging landscape method, framework using energy trend-based segmentation predict self-assembly behavior, our approach dynamically analyzes system's state trends guide actions. We show modulation during kinetic trapping conditions substantially enhances yields reduces times across diverse scenarios. This strategy provides broadly applicable, data-driven optimizing processes, potential implications manufacturing responsive design, while also advancing understanding controlled molecular synthetic contexts.

Language: Английский

Citations

0
Tuning Colloidal Reactions DOI
Ryan Krueger, Ella M. King, Michael P. Brenner

et al.

Physical Review Letters, Journal Year: 2024, Volume and Issue: 133(22)

Published: Nov. 27, 2024

The precise control of complex reactions is critical for biological processes, yet our inability to design specific outcomes limits the development synthetic analogs. Here, we leverage differentiable simulators nontrivial reaction pathways in colloidal assemblies. By optimizing over external structures, achieve controlled disassembly and particle release from shells. Lastly, characterize role configurational entropy structure via both forward calculations optimization, inspiring new parameterizations designed reactions. locked icon Physics Subject Headings (PhySH)Applications soft matterOptimization problemsColloidsMolecular dynamics

Language: Английский

Citations

1
Automating Blueprints for the Assembly of Colloidal Quasicrystal Clusters DOI
Diogo E. P. Pinto, Petr Šulc, Francesco Sciortino

et al.

ACS Nano, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 20, 2024

One of the frontiers nanotechnology is advancing beyond periodic self-assembly materials. Icosahedral quasicrystals, aperiodic in all directions, represent one most challenging targets that has yet to be experimentally realized at colloidal scale. Previous attempts have required meticulous human-designed building blocks and often resulted interactions current experimental capabilities. In this work, we introduce a framework for generating accessible designs self-assemble into quasicrystalline arrangements. We present design icosahedral deoxyribonucleic acid (DNA) origami demonstrate, through molecular simulations, their successful assembly target structure. Our results highlight feasibility using automated protocols achieve complex patterns, with applications material science nanotechnology.

Language: Английский

Citations

1
Coarse-grained modeling of DNA-protein interactions helps elucidate DNA compaction DOI
Petr Šulc

Biophysical Journal, Journal Year: 2024, Volume and Issue: 123(18), P. 2961 - 2963

Published: Aug. 5, 2024

Language: Английский

Citations

0
Proofreading mechanism for colloidal self-assembly DOI Creative Commons

Qian-Ze Zhu,

Chrisy Xiyu Du, Ella M. King

et al.

Physical Review Research, Journal Year: 2024, Volume and Issue: 6(4)

Published: Dec. 9, 2024

Designing components that can robustly self-assemble into structures with biological complexity is a grand challenge for material science. Proofreading and error correction required to improve assembly yield beyond equilibrium limits, using energy avoid kinetic traps in the landscape. Here, we introduce an explicit two-staged proofreading scheme patchy particle colloidal assemblies substantially improves robustness. The first stage implements local rules whereby particles increase their binding strengths when they detect environment corresponding desired target. second corrects remaining errors, adding reverse pathway inspired by proofreading. shows significant improvements, eliminating traps, giving much broader temperature range high yield. Additionally, robust against quenched disorder components. Our findings illuminate advancing programmable design of synthetic living materials, potentially fostering synthesis novel materials functional behaviors. Published American Physical Society 2024

Language: Английский

Citations

0