Escaping Kinetic Traps Using Nonreciprocal Interactions

Physical Review Letters, Journal Year: 2024, Volume and Issue: 133(2)

Published: July 12, 2024

Kinetic traps are a notorious problem in equilibrium statistical mechanics, where temperature quenches ultimately fail to bring the system low energy configurations. Using multifarious self-assembly as model system, we introduce mechanism escape kinetic by utilizing nonreciprocal interactions between components. Introducing nonequilibrium effects offered broken action-reaction symmetry pushes trajectory of out arrested dynamics. The dynamics is studied using tools from physics interfaces and defects. Our proposal can find applications self-assembly, glassy systems, systems with facilitate local minima rough landscapes.

Language: Английский

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Selectively advantageous instability in biotic and pre-biotic systems and implications for evolution and aging

Frontiers in Aging, Journal Year: 2024, Volume and Issue: 5

Published: May 16, 2024

Rules of biology typically involve conservation resources. For example, common patterns such as hexagons and logarithmic spirals require minimal materials, scaling laws energy. Here a relationship with the opposite theme is discussed, which selectively advantageous instability (SAI) one or more components replicating system, cell. By increasing complexity SAI can have benefits in addition to generation energy mobilization building blocks. involves potential cost system for materials and/or required create unstable component, some cases, its active degradation. well-studied cells. Short-lived transcription signaling factors enable rapid response changing environment, turnover critical replacement damaged macromolecules. The gene set viable cell includes proteases nuclease, suggesting essential life. promotes genetic diversity several ways. Toxin/antitoxin systems promote maintenance genes, mitochondria facilitates uniparental transmission. creating two distinct states, subject different selective pressures, maintain diversity. synthetic replicators favors replicator cycling, promoting emergence increased complexity. Both classical recent computer modeling reveals SAI. may be involved at additional levels biological organization. In summary, reproductive fitness, aging through loss resources deleterious alleles.

Language: Английский

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Confinement Induces Morphological and Topological Transitions in Multivesicles

ACS Nano, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 21, 2025

The study of self-assembly in confined spaces has gained significant attention among amphiphilic superstructures and colloidal design. additional complexity introduced by interactions between contents their containers, along with the effects shape lipid mixing, makes multivesicular bodies an interesting subject study. Despite its promising applications biomedicine, such as drug delivery biomimetic materials, much remains unexplored. Here we investigate confinement on vesicles varying tail lengths. We first analyze morphological changes single spherical undergoing dehydration, which leads to a prolate-to-oblate transition. Our findings reveal that reductions water content induce while minimally affecting surface area needed maintain hydration layer phosphate groups. Additionally, using extensive coarse-grained molecular dynamics simulations, explore how within other evolve through topological into unexpected structures, mainly influenced hydrocarbon results highlight interplay confinement, curvature-induced sorting, lipid-mixing entropy, leading exquisitely self-assembled superstructures.

Language: Английский

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Accessing Semiaddressable Self-Assembly with Efficient Structure Enumeration

Physical Review Letters, Journal Year: 2025, Volume and Issue: 134(5)

Published: Feb. 7, 2025

Modern experimental methods enable the creation of self-assembly building blocks with tunable interactions, but optimally exploiting this tunability for desired structures remains an important challenge. Many studies inverse problem start so-called fully addressable limit, where every particle in a target structure is different. This leads to clear design principles that often result high assembly yield, it not scalable approach-at some point, one must grapple "reusing" blocks, which lowers degree addressability and may cause multitude off-target form, complicating process. Here, we solve key obstacle preventing robust "semiaddressable regime" by developing highly efficient algorithm enumerates all can be formed from given set blocks. By combining established partition-function-based yield calculations, show almost always possible find economical semiaddressable designs entropic gain reusing outweighs presence even increases target. Thus, only does our enumeration regime, results demonstrate operate regime while maintaining level control associated full addressability.

Language: Английский

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Nonequilibrium Self-Assembly Control by the Stochastic Landscape Method

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

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Driven Self-Assembly of Patchy Particles Overcoming Equilibrium Limitations

Journal of Chemical Theory and Computation, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 10, 2024

Bridging biological complexity and synthetic material design, we investigate dissipative self-assembly in patchy particle systems. Utilizing Monte Carlo Molecular Dynamics simulations, demonstrate how external driving forces mitigate equilibrium trade-offs between assembly time structural stability, traditionally encountered processes. Our findings also extend to biological-mimicking environments, where explore the dynamics of particles under crowded conditions. This comprehensive analysis offers insights into advanced opening avenues for innovations nanotechnology applications.

Language: Английский

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A Bagworm-Inspired Robot That Acquires Its Exterior from External Environments

Biomimetics, Journal Year: 2025, Volume and Issue: 10(4), P. 252 - 252

Published: April 20, 2025

In this research, we propose a bagworm-inspired robot that can acquire its exterior by incorporating various objects from the surrounding environment into skin. This study was inspired bagworm, larva of giant bagworm moth, which wraps itself around straw and other materials to use as nest. When is active outdoors, it surrounded natural such sand, fallen leaves, pieces wood, change skin attaching or detaching these needed. previous study, authors developed camouflage assimilates with outside world environmental sand. using water-soluble adhesive material, possible take in larger number external substances than before. We also conducted experiments materials, including leaves pebbles, confirmed could pick them up. expect developing functions, robots will not only have capabilities but ability reinforce their own like bagworms.

Language: Английский

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Dissipative Self-Assembly of Patchy Particles under Nonequilibrium Drive: A Computational Study

Journal of Chemical Theory and Computation, Journal Year: 2024, Volume and Issue: 20(20), P. 8844 - 8861

Published: Oct. 4, 2024

Inspired by biology and implemented using nanotechnology, the self-assembly of patchy particles has emerged as a pivotal mechanism for constructing complex structures that mimic natural systems with diverse functionalities. Here, we explore dissipative under nonequilibrium conditions, aim overcoming constraints imposed equilibrium assembly. Utilizing extensive Monte Carlo (MC) Molecular Dynamics (MD) simulations, provide insight into effects external forces mirror chemical processes on assembly rates stability resulting assemblies comprising 8, 10, 13 particles. Implemented favorable bond-promoting drive in MC or pulsed square wave potential MD, our simulations reveal role these drives play accelerating kinetics enhancing structural stability, evidenced decrease time to first an increase duration system remains assembled state. Through analysis order parameter, entropy production, bond dynamics, interparticle forces, unravel underlying mechanisms driving advancements. We also validated key findings simulating larger 100 Our comprehensive results not only shed light impact stimuli but open promising pathway expanding application leveraging novel nanostructures.

Language: Английский

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Shape Matters in Self-Assembly

Physics, Journal Year: 2024, Volume and Issue: 17

Published: April 3, 2024

Language: Английский

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Escaping kinetic traps using non-reciprocal interactions

arXiv (Cornell University), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 1, 2023

Kinetic traps are a notorious problem in equilibrium statistical mechanics, where temperature quenches ultimately fail to bring the system low energy configurations. Using multifarious self-assembly as model system, we introduce mechanism escape kinetic by utilizing non-reciprocal interactions between components. Introducing non-equilibrium effects offered broken action-reaction symmetry can push trajectory of out arrested dynamics. The dynamics is studied using tools from physics interfaces and defects. Our proposal find applications self-assembly, glassy systems with

Language: Английский

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