1
|
Cao Z, Chen R, Xu L, Zhou X, Fu X, Zhong W, Grima R. Efficient and scalable prediction of stochastic reaction-diffusion processes using graph neural networks. Math Biosci 2024; 375:109248. [PMID: 38986837 DOI: 10.1016/j.mbs.2024.109248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 05/07/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
The dynamics of locally interacting particles that are distributed in space give rise to a multitude of complex behaviours. However the simulation of reaction-diffusion processes which model such systems is highly computationally expensive, the cost increasing rapidly with the size of space. Here, we devise a graph neural network based approach that uses cheap Monte Carlo simulations of reaction-diffusion processes in a small space to cast predictions of the dynamics of the same processes in a much larger and complex space, including spaces modelled by networks with heterogeneous topology. By applying the method to two biological examples, we show that it leads to accurate results in a small fraction of the computation time of standard stochastic simulation methods. The scalability and accuracy of the method suggest it is a promising approach for studying reaction-diffusion processes in complex spatial domains such as those modelling biochemical reactions, population evolution and epidemic spreading.
Collapse
Affiliation(s)
- Zhixing Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China; Department of Chemical Engineering, Queen's University, Kingston, Canada K7L 3N6.
| | - Rui Chen
- Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Libin Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xinyi Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xiaoming Fu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Weimin Zhong
- Key Laboratory of Smart Manufacturing in Energy Chemical Process, Ministry of Education, East China University of Science and Technology, Shanghai 200237, China
| | - Ramon Grima
- School of Biological Sciences, the University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, Scotland, United Kingdom.
| |
Collapse
|
2
|
Amano S, Hermans TM. Repurposing a Catalytic Cycle for Transient Self-Assembly. J Am Chem Soc 2024; 146:23289-23296. [PMID: 39127918 DOI: 10.1021/jacs.4c05871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
Life operates out of equilibrium to enable various sophisticated behaviors. Synthetic chemists have strived to mimic biological nonequilibrium systems in such fields as autonomous molecular machines and dissipative self-assembly. Central to these efforts has been the development of new chemical reaction cycles, which drive systems out of equilibrium by conversion of chemical fuel into waste species. However, the construction of reaction cycles has been challenging due to the difficulty of finding compatible reactions that constitute a cycle. Here, we realize an alternative approach by repurposing a known catalytic cycle as a chemical reaction cycle for driving dissipative self-assembly. This approach can overcome the compatibility problem because all steps involved in a catalytic cycle are already known to proceed concurrently under the same conditions. Our repurposing approach is applicable to diverse combinations of catalytic cycles and systems to drive out of equilibrium, which will substantially broaden the scope of out-of-equilibrium systems.
Collapse
Affiliation(s)
- Shuntaro Amano
- University of Strasbourg, CNRS, Strasbourg 67083, France
| | | |
Collapse
|
3
|
Guo J, Chen J, Zhao K, Bai X, Wang W. Unveiling Hidden Hyperuniformity: Radial Turing Pattern Formation of Marangoni-Driven SiO 2 Nanoparticles on Liquid Metal Surface. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400163. [PMID: 39075843 DOI: 10.1002/advs.202400163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/29/2024] [Indexed: 07/31/2024]
Abstract
Mastering the self-organization of nanoparticle morphologies is pivotal in soft matter physics and film growth. Silicon dioxide (SiO2) nanoparticles are an archetypical model of nanomotor in soft matter. Here, the emphasis is on the self-organizing behavior of SiO2 nanoparticles under extreme conditions. It is unveiled that manipulating the states of the metal substrate profoundly dictates the motion characteristics of SiO2 nanoparticles. This manipulation triggers the emergence of intricate morphologies and distinctive patterns. Employing a reaction-diffusion model, the fundamental roles played by Brownian motion and Marangoni-driven motion in shaping fractal structures and radial Turing patterns are demonstrated, respectively. Notably, these radial Turing patterns showcase hyperuniform order, challenging conventional notions of film morphology. These discoveries pave the way for crafting non-equilibrium morphological materials, poised with the potential for self-healing, adaptability, and innovative applications.
Collapse
Affiliation(s)
- Jinjian Guo
- State Key Laboratory for Surface Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials of Ministry of Education, Shanxi Normal University, Taiyuan, 030000, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jie Chen
- School of Electronic and Information Engineering, Tiangong University, Tianjin, 300387, China
| | - Kang Zhao
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100190, China
| | - Xuedong Bai
- State Key Laboratory for Surface Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Wenlong Wang
- State Key Laboratory for Surface Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100190, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| |
Collapse
|
4
|
Wu H, Chen QX, Su Y, Chen Z. The Role of Hydrogen Bonds in Thermally Responsive Crystallization-Driven Template Autocatalysis. Angew Chem Int Ed Engl 2024; 63:e202404838. [PMID: 38654551 DOI: 10.1002/anie.202404838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]
Abstract
Autocatalysis has been recognized to be involved in the emergence of life and intrinsic to biomolecular replication. Recently, an efficient template autocatalysis driven by solvent-free crystallization has been reported. Herein, we unveil the role of intermolecular hydrogen bonds formed by amides in crystallization-driven template autocatalysis (CDTA), which involves the autocatalytic activity, template selectivity, and thermal responsiveness. We found that the thermal-induced cis-trans isomerization of amides possibly affects the H-bonding-mediated template ability of products for autocatalytic transformation. As a result, CDTA can be reversibly inhibited and activated by tuning the reaction temperatures. Our work sheds light on the significance of noncovalent H-bonding interactions in artificial self-replicators.
Collapse
Affiliation(s)
- Huimin Wu
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
- School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Qing-Xuan Chen
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
- School of Materials Science and Engineering, Tsinghua University, Beijing, 100084, P. R. China
| | - Yang Su
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
| | - Zhen Chen
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
| |
Collapse
|
5
|
Pekar K, Young RT, Sensale S. Optimizing Binding among Bimolecular Tethered Complexes. J Phys Chem B 2024; 128:5506-5512. [PMID: 38786364 DOI: 10.1021/acs.jpcb.4c01088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Tethered motion is ubiquitous in nature, offering controlled movement and spatial constraints to otherwise chaotic systems. The enhanced functionality and practical utility of tethers has been exploited in biotechnology, catalyzing the design of novel biosensors and molecular assembly techniques. While notable technological advances incorporating tethered motifs have been made, a theoretical gap persists within the paradigm, hindering a comprehensive understanding of tethered-based technologies. In this work, we focus on the characterization of the binding kinetics of two tethered molecules functionalized to a hard surface. Using a mean-field approximation, the binding time of such bimolecular system is determined analytically. Furthermore, estimates of the grafting site separation and polymer lengths which expedite binding are provided. These estimates, along with the analytical theories and frameworks established here, have the potential to improve efficacy in self-assembly methods in DNA nanotechnology and can be extended to more biologically specific endeavors including targeted drug-delivery and molecular sensing.
Collapse
Affiliation(s)
- Kyle Pekar
- Department of Mechanical Engineering, Cleveland State University, Cleveland, Ohio 44115-2214, United States
| | - Robert T Young
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115-2214, United States
| | - Sebastian Sensale
- Department of Physics, Cleveland State University, Cleveland, Ohio 44115-2214, United States
| |
Collapse
|
6
|
Itatani M, Onishi Y, Suematsu NJ, Lagzi I. Periodic Precipitation in a Confined Liquid Layer. J Phys Chem Lett 2024; 15:4948-4957. [PMID: 38687169 PMCID: PMC11089569 DOI: 10.1021/acs.jpclett.4c00832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
Pattern formation is a ubiquitous phenomenon in animate and inanimate systems generated by mass transport and reaction of chemical species. The Liesegang phenomenon is a self-organized periodic precipitation pattern always studied in porous media such as hydrogels and aerogels for over a century. The primary consideration of applying the porous media is to prevent the disintegration of the precipitation structures due to the sedimentation of the precipitate and induced fluid flow. Here, we show that the periodic precipitation patterns can be engineered using a Hele-Shaw cell in a confined liquid phase, restricting hydrodynamic instability. The patterns generated in several precipitation reaction systems exhibit spatiotemporal properties consistent with patterns obtained in solid hydrogels. Furthermore, analysis considering the Rayleigh-Darcy number emphasizes the crucial role of fluidity in generating periodic precipitation structures in a thin liquid film. This exploration promises breakthroughs at the intersection of fundamental understanding and practical applications.
Collapse
Affiliation(s)
- Masaki Itatani
- Department
of Physics, Institute of Physics, Budapest
University of Technology and Economics, Műegyetem rkp. 3, Budapest H-1111, Hungary
| | - Yuhei Onishi
- Graduate
School of Advanced Mathematical Sciences, Meiji University, 4-21-1 Nakano, Tokyo 164-8525, Japan
| | - Nobuhiko J. Suematsu
- Graduate
School of Advanced Mathematical Sciences, Meiji University, 4-21-1 Nakano, Tokyo 164-8525, Japan
- Meiji
Institute for Advanced Study of Mathematical Sciences (MIMS), Meiji University, 4-21-1
Nakano, Tokyo 164-8525, Japan
| | - István Lagzi
- Department
of Physics, Institute of Physics, Budapest
University of Technology and Economics, Műegyetem rkp. 3, Budapest H-1111, Hungary
- HU-REN-BME
Condensed Matter Physics Research Group, Budapest University of Technology and Economics, Műegyetem rkp. 3, Budapest H-1111, Hungary
| |
Collapse
|
7
|
Liu Z, Chen J, Li B, Jiang DE, Wang L, Yao Q, Xie J. Enzyme-Inspired Ligand Engineering of Gold Nanoclusters for Electrocatalytic Microenvironment Manipulation. J Am Chem Soc 2024; 146:11773-11781. [PMID: 38648616 DOI: 10.1021/jacs.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Natural enzymes intricately regulate substrate accessibility through specific amino acid sequences and folded structures at their active sites. Achieving such precise control over the microenvironment has proven to be challenging in nanocatalysis, especially in the realm of ligand-stabilized metal nanoparticles. Here, we use atomically precise metal nanoclusters (NCs) as model catalysts to demonstrate an effective ligand engineering strategy to control the local concentration of CO2 on the surface of gold (Au) NCs during electrocatalytic CO2 reduction reactions (CO2RR). The precise incorporation of two 2-thiouracil-5-carboxylic acid (TCA) ligands within the pocket-like cavity of [Au25(pMBA)18]- NCs (pMBA = para-mercaptobenzoic acid) leads to a substantial acceleration in the reaction kinetics of CO2RR. This enhancement is attributed to a more favorable microenvironment in proximity to the active site for CO2, facilitated by supramolecular interactions between the nucleophilic Nδ- of the pyrimidine ring of the TCA ligand and the electrophilic Cδ+ of CO2. A comprehensive investigation employing absorption spectroscopy, mass spectrometry, isotopic labeling measurements, electrochemical analyses, and quantum chemical computation highlights the pivotal role of local CO2 enrichment in enhancing the activity and selectivity of TCA-modified Au25 NCs for CO2RR. Notably, a high Faradaic efficiency of 98.6% toward CO has been achieved. The surface engineering approach and catalytic fundamentals elucidated in this study provide a systematic foundation for the molecular-level design of metal-based electrocatalysts.
Collapse
Affiliation(s)
- Zhihe Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
- Joint School of National University of Singapore and Tianjin University International Campus of Tianjin University Binhai New City, Fuzhou 350207, P. R. China
| | - Junmei Chen
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Bo Li
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - De-En Jiang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Lei Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Qiaofeng Yao
- Key Laboratory of Organic Integrated Circuits, Ministry of Education & Tianjin Key Laboratory of Molecular Optoelectronic Sciences, Department of Chemistry, School of Science, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Jianping Xie
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
- Joint School of National University of Singapore and Tianjin University International Campus of Tianjin University Binhai New City, Fuzhou 350207, P. R. China
| |
Collapse
|
8
|
Shandilya E, Rallabandi B, Maiti S. In situ enzymatic control of colloidal phoresis and catalysis through hydrolysis of ATP. Nat Commun 2024; 15:3603. [PMID: 38684662 PMCID: PMC11059368 DOI: 10.1038/s41467-024-47912-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
The ability to sense chemical gradients and respond with directional motility and chemical activity is a defining feature of complex living systems. There is a strong interest among scientists to design synthetic systems that emulate these properties. Here, we realize and control such behaviors in a synthetic system by tailoring multivalent interactions of adenosine nucleotides with catalytic microbeads. We first show that multivalent interactions of the bead with gradients of adenosine mono-, di- and trinucleotides (AM/D/TP) control both the phoretic motion and a proton-transfer catalytic reaction, and find that both effects are diminished greatly with increasing valence of phosphates. We exploit this behavior by using enzymatic hydrolysis of ATP to AMP, which downregulates multivalent interactivity in situ. This produces a sudden increase in transport of the catalytic microbeads (a phoretic jump), which is accompanied by increased catalytic activity. Finally, we show how this enzymatic activity can be systematically tuned, leading to simultaneous in situ spatial and temporal control of the location of the microbeads, as well as the products of the reaction that they catalyze. These findings open up new avenues for utilizing multivalent interaction-mediated programming of complex chemo-mechanical behaviors into active systems.
Collapse
Affiliation(s)
- Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Manauli, 140306, India
| | - Bhargav Rallabandi
- Department of Mechanical Engineering, University of California, Riverside, CA, 92521, USA.
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Manauli, 140306, India.
| |
Collapse
|
9
|
Lee WJ, Kim SJ, Ahn Y, Park J, Jin S, Jang J, Jeong J, Park M, Lee YS, Lee J, Seo D. From Homogeneity to Turing Pattern: Kinetically Controlled Self-Organization of Transmembrane Protein. NANO LETTERS 2024; 24:1882-1890. [PMID: 38198287 DOI: 10.1021/acs.nanolett.3c03637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Understanding the spatial organization of membrane proteins is crucial for unraveling key principles in cell biology. The reaction-diffusion model is commonly used to understand biochemical patterning; however, applying reaction-diffusion models to subcellular phenomena is challenging because of the difficulty in measuring protein diffusivity and interaction kinetics in the living cell. In this work, we investigated the self-organization of the plasmalemma vesicle-associated protein (PLVAP), which creates regular arrangements of fenestrated ultrastructures, using single-molecule tracking. We demonstrated that the spatial organization of the ultrastructures is associated with a decrease in the association rate by actin destabilization. We also constructed a reaction-diffusion model that accurately generates a hexagonal array with the same 130 nm spacing as the actual scale and informs the stoichiometry of the ultrastructure, which can be discerned only through electron microscopy. Through this study, we integrated single-molecule experiments and reaction-diffusion modeling to surpass the limitations of static imaging tools and proposed emergent properties of the PLVAP ultrastructure.
Collapse
Affiliation(s)
- Wonhee John Lee
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Soo Jin Kim
- Department of Medical Science, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
- Department of Ophthalmology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Yongdeok Ahn
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Jiseong Park
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Siwoo Jin
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Juhee Jang
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Jinju Jeong
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Minsoo Park
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Young-Sam Lee
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Junyeop Lee
- Department of Ophthalmology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
- Translational Biomedical Research Group, Asan Institute for Life Science, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Daeha Seo
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| |
Collapse
|
10
|
Kubota R, Hamachi I. Cell-Like Synthetic Supramolecular Soft Materials Realized in Multicomponent, Non-/Out-of-Equilibrium Dynamic Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306830. [PMID: 38018341 PMCID: PMC10885657 DOI: 10.1002/advs.202306830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/30/2023] [Indexed: 11/30/2023]
Abstract
Living cells are complex, nonequilibrium supramolecular systems capable of independently and/or cooperatively integrating multiple bio-supramolecules to execute intricate physiological functions that cannot be accomplished by individual biomolecules. These biological design strategies offer valuable insights for the development of synthetic supramolecular systems with spatially controlled hierarchical structures, which, importantly, exhibit cell-like responses and functions. The next grand challenge in supramolecular chemistry is to control the organization of multiple types of supramolecules in a single system, thus integrating the functions of these supramolecules in an orthogonal and/or cooperative manner. In this perspective, the recent progress in constructing multicomponent supramolecular soft materials through the hybridization of supramolecules, such as self-assembled nanofibers/gels and coacervates, with other functional molecules, including polymer gels and enzymes is highlighted. Moreover, results show that these materials exhibit bioinspired responses to stimuli, such as bidirectional rheological responses of supramolecular double-network hydrogels, temporal stimulus pattern-dependent responses of synthetic coacervates, and 3D hydrogel patterning in response to reaction-diffusion processes are presented. Autonomous active soft materials with cell-like responses and spatially controlled structures hold promise for diverse applications, including soft robotics with directional motion, point-of-care disease diagnosis, and tissue regeneration.
Collapse
Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological ChemistryGraduate School of EngineeringKyoto UniversityKatsuraNishikyo‐kuKyoto615‐8510Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological ChemistryGraduate School of EngineeringKyoto UniversityKatsuraNishikyo‐kuKyoto615‐8510Japan
- JST‐ERATOHamachi Innovative Molecular Technology for NeuroscienceKyoto UniversityNishikyo‐kuKatsura615‐8530Japan
| |
Collapse
|
11
|
Zhang H, Xu T, Liang J, Wu B, Yang X, Wang J, Zhou Z, Wang H. Controlling Supramolecular Fiber Formation of Nucleopeptide by Guanosine Triphosphate. Biomacromolecules 2023; 24:5678-5686. [PMID: 37934694 DOI: 10.1021/acs.biomac.3c00674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Cells use dynamic self-assembly to construct functional structures for maintaining cellular homeostasis. However, using a natural biological small molecule to mimic this phenomenon remains challenging. This work reports the dynamic microfiber formation of nucleopeptide driven by guanosine triphosphate, the small molecule that controls microtubule polymerization in living cells. Deactivation of GTP by enzyme dissociates the fibers, which could be reactivated by adding GTP. Molecular dynamic simulation unveils the mystery of microfiber formation of GBM-1 and GTP. Moreover, the microfiber formation can also be controlled by diffusion-driven GTP gradients across a semipermeable membrane in bulk conditions and the microfluidic method in the defined droplets. This study provides a new platform to construct dynamic self-assembly materials of molecular building blocks driven by GTP.
Collapse
Affiliation(s)
- Hongyue Zhang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, P. R. China
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Tengyan Xu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Juan Liang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Bihan Wu
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Xuejiao Yang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Jing Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Ziao Zhou
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| | - Huaimin Wang
- Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou 310024, Zhejiang Province, China
| |
Collapse
|
12
|
Sangchai T, Al Shehimy S, Penocchio E, Ragazzon G. Artificial Molecular Ratchets: Tools Enabling Endergonic Processes. Angew Chem Int Ed Engl 2023; 62:e202309501. [PMID: 37545196 DOI: 10.1002/anie.202309501] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/08/2023]
Abstract
Non-equilibrium chemical systems underpin multiple domains of contemporary interest, including supramolecular chemistry, molecular machines, systems chemistry, prebiotic chemistry, and energy transduction. Experimental chemists are now pioneering the realization of artificial systems that can harvest energy away from equilibrium. In this tutorial Review, we provide an overview of artificial molecular ratchets: the chemical mechanisms enabling energy absorption from the environment. By focusing on the mechanism type-rather than the application domain or energy source-we offer a unifying picture of seemingly disparate phenomena, which we hope will foster progress in this fascinating domain of science.
Collapse
Affiliation(s)
- Thitiporn Sangchai
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Shaymaa Al Shehimy
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Emanuele Penocchio
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Giulio Ragazzon
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
| |
Collapse
|
13
|
Ramnarine-Sanchez RS, Kanczler JM, Evans ND, Oreffo ROC, Dawson JI. Self-Assembly of Structured Colloidal Gels for High-Resolution 3D Micropatterning of Proteins at Scale. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2304461. [PMID: 37658732 DOI: 10.1002/adma.202304461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Indexed: 09/05/2023]
Abstract
Self-assembly, the spontaneous ordering of components into patterns, is widespread in nature and fundamental to generating function across length scales. Morphogen gradients in biological development are paradigmatic as both products and effectors of self-assembly and various attempts have been made to reproduce such gradients in biomaterial design. To date, approaches have typically utilized top-down fabrication techniques that, while allowing high-resolution control, are limited by scale and require chemical cross-linking steps to stabilize morphogen patterns in time. Here, a bottom-up approach to protein patterning is developed based on a novel binary reaction-diffusion process where proteins function as diffusive reactants to assemble a nanoclay-protein composite hydrogel. Using this approach, it is possible to generate scalable and highly stable 3D patterns of target proteins down to sub-cellular resolution through only physical interactions between clay nanoparticles and the proteins and ions present in blood. Patterned nanoclay gels are able to guide cell behavior to precisely template bone tissue formation in vivo. These results demonstrate the feasibility of stabilizing 3D gradients of biological signals through self-assembly processes and open up new possibilities for morphogen-based therapeutic strategies and models of biological development and repair.
Collapse
Affiliation(s)
- Roxanna S Ramnarine-Sanchez
- Faculty of Medicine, Department of Human Development and Health, University of Southampton, Southampton, SO16 6YD, UK
| | - Janos M Kanczler
- Faculty of Medicine, Department of Human Development and Health, University of Southampton, Southampton, SO16 6YD, UK
| | - Nicholas D Evans
- Faculty of Medicine, Department of Human Development and Health, University of Southampton, Southampton, SO16 6YD, UK
| | - Richard O C Oreffo
- Faculty of Medicine, Department of Human Development and Health, University of Southampton, Southampton, SO16 6YD, UK
| | - Jonathan I Dawson
- Faculty of Medicine, Department of Human Development and Health, University of Southampton, Southampton, SO16 6YD, UK
| |
Collapse
|
14
|
Milinkovitch MC, Jahanbakhsh E, Zakany S. The Unreasonable Effectiveness of Reaction Diffusion in Vertebrate Skin Color Patterning. Annu Rev Cell Dev Biol 2023; 39:145-174. [PMID: 37843926 DOI: 10.1146/annurev-cellbio-120319-024414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
In 1952, Alan Turing published the reaction-diffusion (RD) mathematical framework, laying the foundations of morphogenesis as a self-organized process emerging from physicochemical first principles. Regrettably, this approach has been widely doubted in the field of developmental biology. First, we summarize Turing's line of thoughts to alleviate the misconception that RD is an artificial mathematical construct. Second, we discuss why phenomenological RD models are particularly effective for understanding skin color patterning at the meso/macroscopic scales, without the need to parameterize the profusion of variables at lower scales. More specifically, we discuss how RD models (a) recapitulate the diversity of actual skin patterns, (b) capture the underlying dynamics of cellular interactions, (c) interact with tissue size and shape, (d) can lead to ordered sequential patterning, (e) generate cellular automaton dynamics in lizards and snakes, (f) predict actual patterns beyond their statistical features, and (g) are robust to model variations. Third, we discuss the utility of linear stability analysis and perform numerical simulations to demonstrate how deterministic RD emerges from the underlying chaotic microscopic agents.
Collapse
Affiliation(s)
- Michel C Milinkovitch
- Laboratory of Artificial and Natural Evolution, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland;
| | - Ebrahim Jahanbakhsh
- Laboratory of Artificial and Natural Evolution, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland;
| | - Szabolcs Zakany
- Laboratory of Artificial and Natural Evolution, Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland;
| |
Collapse
|
15
|
Gu J, Li L, Xie Y, Chen B, Tian F, Wang Y, Zhong J, Shen J, Lu J. Turing structuring with multiple nanotwins to engineer efficient and stable catalysts for hydrogen evolution reaction. Nat Commun 2023; 14:5389. [PMID: 37666814 PMCID: PMC10477283 DOI: 10.1038/s41467-023-40972-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023] Open
Abstract
Low-dimensional nanocrystals with controllable defects or strain modifications are newly emerging active electrocatalysts for hydrogen-energy conversion and utilization; however, a crucial challenge remains in insufficient stability due to spontaneous structural degradation and strain relaxation. Here we report a Turing structuring strategy to activate and stabilize superthin metal nanosheets by incorporating high-density nanotwins. Turing configuration, realized by constrained orientation attachment of nanograins, yields intrinsically stable nanotwin network and straining effects, which synergistically reduce the energy barrier of water dissociation and optimize the hydrogen adsorption free energy for hydrogen evolution reaction. Turing PtNiNb nanocatalyst achieves 23.5 and 3.1 times increase in mass activity and stability index, respectively, compared against commercial 20% Pt/C. The Turing PtNiNb-based anion-exchange-membrane water electrolyser with a low Pt mass loading of 0.05 mg cm-2 demonstrates at least 500 h stability at 1000 mA cm-2, disclosing the stable catalysis. Besides, this new paradigm can be extended to Ir/Pd/Ag-based nanocatalysts, illustrating the universality of Turing-type catalysts.
Collapse
Affiliation(s)
- Jialun Gu
- Centre for Advanced Structural Materials, City University of Hong Kong Shenzhen Research Institute, Greater Bay Joint Division, Shenyang National Laboratory for Materials Science, Shenzhen, China
- Department of Mechanical Engineering, City University of Hong Kong, Hong Kong, China
- CityU-Shenzhen Futian Research Institute, Shenzhen, China
- Hong Kong Branch of National Precious Metals Material Engineering Research Centre, City University of Hong Kong, Hong Kong, China
| | - Lanxi Li
- Centre for Advanced Structural Materials, City University of Hong Kong Shenzhen Research Institute, Greater Bay Joint Division, Shenyang National Laboratory for Materials Science, Shenzhen, China
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
- Hong Kong Branch of National Precious Metals Material Engineering Research Centre, City University of Hong Kong, Hong Kong, China
| | - Youneng Xie
- Centre for Advanced Structural Materials, City University of Hong Kong Shenzhen Research Institute, Greater Bay Joint Division, Shenyang National Laboratory for Materials Science, Shenzhen, China
- Department of Mechanical Engineering, City University of Hong Kong, Hong Kong, China
- Hong Kong Branch of National Precious Metals Material Engineering Research Centre, City University of Hong Kong, Hong Kong, China
| | - Bo Chen
- Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Fubo Tian
- State Key Laboratory of Superhard Materials, College of Physics, Jilin University, Changchun, China
| | - Yanju Wang
- Centre for Advanced Structural Materials, City University of Hong Kong Shenzhen Research Institute, Greater Bay Joint Division, Shenyang National Laboratory for Materials Science, Shenzhen, China
- Department of Mechanical Engineering, City University of Hong Kong, Hong Kong, China
- Hong Kong Branch of National Precious Metals Material Engineering Research Centre, City University of Hong Kong, Hong Kong, China
| | - Jing Zhong
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
| | - Junda Shen
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China
- Hong Kong Branch of National Precious Metals Material Engineering Research Centre, City University of Hong Kong, Hong Kong, China
| | - Jian Lu
- Centre for Advanced Structural Materials, City University of Hong Kong Shenzhen Research Institute, Greater Bay Joint Division, Shenyang National Laboratory for Materials Science, Shenzhen, China.
- Department of Mechanical Engineering, City University of Hong Kong, Hong Kong, China.
- Department of Materials Science and Engineering, City University of Hong Kong, Hong Kong, China.
- CityU-Shenzhen Futian Research Institute, Shenzhen, China.
- Hong Kong Branch of National Precious Metals Material Engineering Research Centre, City University of Hong Kong, Hong Kong, China.
| |
Collapse
|
16
|
Guo J, Wang F, Huang Y, He H, Tan W, Yi M, Egelman EH, Xu B. Cell spheroid creation by transcytotic intercellular gelation. NATURE NANOTECHNOLOGY 2023; 18:1094-1104. [PMID: 37217766 PMCID: PMC10525029 DOI: 10.1038/s41565-023-01401-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/14/2023] [Indexed: 05/24/2023]
Abstract
Cell spheroids bridge the discontinuity between in vitro systems and in vivo animal models. However, inducing cell spheroids by nanomaterials remains an inefficient and poorly understood process. Here we use cryogenic electron microscopy to determine the atomic structure of helical nanofibres self-assembled from enzyme-responsive D-peptides and fluorescent imaging to show that the transcytosis of D-peptides induces intercellular nanofibres/gels that potentially interact with fibronectin to enable cell spheroid formation. Specifically, D-phosphopeptides, being protease resistant, undergo endocytosis and endosomal dephosphorylation to generate helical nanofibres. On secretion to the cell surface, these nanofibres form intercellular gels that act as artificial matrices and facilitate the fibrillogenesis of fibronectins to induce cell spheroids. No spheroid formation occurs without endo- or exocytosis, phosphate triggers or shape switching of the peptide assemblies. This study-coupling transcytosis and morphological transformation of peptide assemblies-demonstrates a potential approach for regenerative medicine and tissue engineering.
Collapse
Affiliation(s)
- Jiaqi Guo
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Yimeng Huang
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Hongjian He
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Weiyi Tan
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Meihui Yi
- Department of Chemistry, Brandeis University, Waltham, MA, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
| | - Bing Xu
- Department of Chemistry, Brandeis University, Waltham, MA, USA.
| |
Collapse
|
17
|
Winkens M, Vilcan A, de Visser PJ, de Graaf FV, Korevaar PA. Orbiting Self-Organization of Filament-Tethered Surface-Active Droplets. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206800. [PMID: 36799188 DOI: 10.1002/smll.202206800] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/17/2023] [Indexed: 05/18/2023]
Abstract
Dissipative chemical systems hold the potential to enable life-like behavior in synthetic matter, such as self-organization, motility, and dynamic switching between different states. Here, out-of-equilibrium self-organization is demonstrated by interconnected source and drain droplets at an air-water interface, which display dynamic behavior due to a hydrolysis reaction that generates a concentration gradient around the drain droplets. This concentration gradient interferes with the adhesion of self-assembled amphiphile filaments that grow from a source droplet. The chemical gradient sustains a unique orbiting of the drain droplet, which is proposed to be driven by the selective adhesion of the filaments to the front of the moving droplet, while filaments approaching from behind are destabilized upon contact with the hydrolysis product in the trail of the droplet. Potential applications are foreseen in the transfer of chemical signals amongst communicating droplets in rearranging networks, and the implementation of chemical reactions to drive complex positioning routines in life-like systems.
Collapse
Affiliation(s)
- Mitch Winkens
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Alexandru Vilcan
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Pieter J de Visser
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Freek V de Graaf
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Peter A Korevaar
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| |
Collapse
|
18
|
Penocchio E, Ragazzon G. Kinetic Barrier Diagrams to Visualize and Engineer Molecular Nonequilibrium Systems. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206188. [PMID: 36703505 DOI: 10.1002/smll.202206188] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/11/2022] [Indexed: 06/18/2023]
Abstract
Molecular nonequilibrium systems hold great promises for the nanotechnology of the future. Yet, their development is slowed by the absence of an informative representation. Indeed, while potential energy surfaces comprise in principle all the information, they hide the dynamic interplay of multiple reaction pathways underlying nonequilibrium systems, i.e., the degree of kinetic asymmetry. To offer an insightful visual representation of kinetic asymmetry, we extended an approach pertaining to catalytic networks, the energy span model, by focusing on system dynamics - rather than thermodynamics. Our approach encompasses both chemically and photochemically driven systems, ranging from unimolecular motors to simple self-assembly schemes. The obtained diagrams give immediate access to information needed to guide experiments, such as states' population, rate of machine operation, maximum work output, and effects of design changes. The proposed kinetic barrier diagrams offer a unifying graphical tool for disparate nonequilibrium phenomena.
Collapse
Affiliation(s)
- Emanuele Penocchio
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg, L-1511, Luxembourg
- Department of Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Giulio Ragazzon
- University of Strasbourg, CNRS, Institut de Science et d'Ingégnierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, Strasbourg, F-67000, France
| |
Collapse
|
19
|
Switching-Like Event-Triggered State Estimation for Reaction–Diffusion Neural Networks Against DoS Attacks. Neural Process Lett 2023. [DOI: 10.1007/s11063-023-11189-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
|
20
|
Chowdhuri S, Das S, Kushwaha R, Das T, Das BK, Das D. Cumulative Effect of pH and Redox Triggers on Highly Adaptive Transient Coacervates. Chemistry 2023; 29:e202203820. [PMID: 36786201 DOI: 10.1002/chem.202203820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/15/2023]
Abstract
An intricate synergism between multiple biochemical processes and physical conditions determines the formation and function of various biological self-assemblies. Thus, a complex set of variables dictate the far-from-equilibrium nature of these biological assemblies. Mimicking such systems synthetically is a challenging task. We report multi-stimuli responsive transient coacervation of an aldehyde-appended polymer and a short peptide. The coacervates are formed by the disulphide linkages between the peptide molecules and the imine bond between the polymer and the peptide. Imines are susceptible to pH changes and the disulphide bonds can be tuned by oxidation/reduction processes. Thus, the coacervation is operational only under the combined effect of appropriate pH and oxidative conditions. Taking advantage of these facts, the coacervates are transiently formed under a pH cycle (urea-urease/gluconolactone) and a non-equilibrium redox cycle (TCEP/H2 O2 ). Importantly, the system showed high adaptability toward environmental changes. The transient existence of the coacervates can be generated without any apparent change in size and shape within the same system through the sequential application of the above-mentioned nonequilibrium reaction cycles. Additionally, the coacervation allows for efficient encapsulation/stabilisation of proteins. Thus, the system has the potential to be used for protein/drug delivery purposes in the future.
Collapse
Affiliation(s)
- Sumit Chowdhuri
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India
| | - Saurav Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India
| | - Ritvika Kushwaha
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India
| | - Tanushree Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India
| | - Basab Kanti Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India
| | - Debapratim Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India
| |
Collapse
|
21
|
Cao Y, Gabrielli L, Frezzato D, Prins LJ. Persistent ATP-Concentration Gradients in a Hydrogel Sustained by Chemical Fuel Consumption. Angew Chem Int Ed Engl 2023; 62:e202215421. [PMID: 36420591 DOI: 10.1002/anie.202215421] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/19/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022]
Abstract
We show the formation of macroscopic ATP-concentrations in an agarose gel and demonstrate that these gradients can be sustained in time at the expense of the consumption of a chemical fuel. The approach relies on the spatially controlled activation of ATP-producing and ATP-consuming reactions through the local injection of enzymes in the matrix. The reaction-diffusion system is maintained in a stationary non-equilibrium state as long as chemical fuel, phosphocreatine, is present. The reaction-diffusion system is coupled to a supramolecular system composed of monolayer protected gold nanoparticles and a fluorescent probe. As a result of this coupling, fluorescence signals emerge spontaneously in response to the ATP-concentration gradients. We show that the approach permits the rational formation of complex fluorescence patterns that change over time as a function of the evolution of the ATP-concentrations present in the system.
Collapse
Affiliation(s)
- Yingjuan Cao
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Luca Gabrielli
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Diego Frezzato
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| |
Collapse
|
22
|
Das K, Kar H, Chen R, Fortunati I, Ferrante C, Scrimin P, Gabrielli L, Prins LJ. Formation of Catalytic Hotspots in ATP-Templated Assemblies. J Am Chem Soc 2022; 145:898-904. [PMID: 36576874 PMCID: PMC9853849 DOI: 10.1021/jacs.2c09343] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The self-assembly of surfactant-based structures that rely for their formation on the combination of a thermodynamically controlled and a dissipative pathway is described. Adenosine triphosphate (ATP) acts as a high-affinity template and triggers assembly formation at low surfactant concentrations. The presence of these assemblies creates the conditions for the activation of a dissipative self-assembly process by a weak-affinity substrate. The substrate-induced recruitment of additional surfactants leads to the spontaneous formation of catalytic hotspots in the ATP-stabilized assemblies that cleave the substrate. As a result of the two self-assembly processes, catalysis can be observed at a surfactant concentration at which low catalytic activity is observed in the absence of ATP.
Collapse
|
23
|
Shevchenko VY, Makogon AI, Sychov MM, Nosonovsky M, Skorb EV. Reaction-Diffusion Pathways for a Programmable Nanoscale Texture of the Diamond-SiC Composite. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15220-15225. [PMID: 36442157 PMCID: PMC10168640 DOI: 10.1021/acs.langmuir.2c02184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The diamond-SiC composite has a low density and the highest possible speed of sound among existing materials except for diamond. The composite is synthesized by a complex exothermic chemical reaction between diamond powder and liquid Si. This makes it an ideal material for protection against impact loading. Experiments show that a system of patterns is formed at the diamond-SiC interface. Modeling of reaction-diffusion processes of composite synthesis proves a formation of ceramic materials with a regular (periodic) interconnected microstructure in a given system. The composite material with interconnected structures at the interface has very high mechanical properties and resistance to impact since its fractioning is intercrystallite.
Collapse
Affiliation(s)
- Vladimir Ya Shevchenko
- Institute of Silicate Chemistry, Russian Academy of Sciences, St. Petersburg199034, Russia
- NRC Kurchatov Institute - CRISM Prometey, 49 Shpalernaya str., St. Petersburg191015, Russia
| | - Aleksei I Makogon
- Institute of Silicate Chemistry, Russian Academy of Sciences, St. Petersburg199034, Russia
- St. Petersburg State Institute of Technology, St. Petersburg190013, Russia
| | - Maxim M Sychov
- Institute of Silicate Chemistry, Russian Academy of Sciences, St. Petersburg199034, Russia
- St. Petersburg State Institute of Technology, St. Petersburg190013, Russia
| | - Michael Nosonovsky
- ITMO University, 9 Lomonosov St., St. Petersburg191002, Russia
- University of Wisconsin-Milwaukee, 3200 N Cramer St., Milwaukee, Wisconsin53210, United States
| | | |
Collapse
|
24
|
Priming self-assembly pathways by stacking block copolymers. Nat Commun 2022; 13:6947. [PMID: 36376380 PMCID: PMC9663688 DOI: 10.1038/s41467-022-34729-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022] Open
Abstract
Block copolymers spontaneously self-assemble into well-defined nanoscale morphologies. Yet equilibrium assembly gives rise to a limited set of structures. Non-equilibrium strategies can, in principle, expand diversity by exploiting self-assembly's responsive nature. In this vein, we developed a pathway priming strategy combining control of thin film initial configurations and ordering history. We sequentially coat distinct materials to form prescribed initial states, and use thermal annealing to evolve these manifestly non-equilibrium states through the assembly landscape, traversing normally inaccessible transient structures. We explore the enormous associated hyperspace, spanning processing (annealing temperature and time), material (composition and molecular weight), and layering (thickness and order) dimensions. We demonstrate a library of exotic non-native morphologies, including vertically-oriented perforated lamellae, aqueduct structures (vertical lamellar walls with substrate-pinned perforations), parapets (crenellated lamellae), and networks of crisscrossing lamellae. This enhanced structural control can be used to modify functional properties, including accessing regimes that surpass their equilibrium analogs.
Collapse
|
25
|
Takada S, Yoshinaga N, Doi N, Fujiwara K. Controlling the Periodicity of a Reaction-Diffusion Wave in Artificial Cells by a Two-Way Energy Supplier. ACS NANO 2022; 16:16853-16861. [PMID: 36214379 DOI: 10.1021/acsnano.2c06756] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Reaction-diffusion (RD) waves, which are dynamic self-organization structures generated by nanosize molecules, are a fundamental mechanism from patterning in nano- and micromaterials to spatiotemporal regulations in living cells, such as cell division and motility. Although the periods of RD waves are the critical element for these functions, the development of a system to control their period is challenging because RD waves result from nonlinear physical dynamics under far-from-equilibrium conditions. Here, we developed an artificial cell system with tunable period of an RD-driven wave (Min protein wave), which determines a cell division site plane in living bacterial cells. The developed system is based on our finding that Min waves are generated by energy consumption of either ATP or dATP, and the period of the wave is different between these two energy suppliers. We showed that the Min-wave period was modulated linearly by the mixing ratio of ATP and dATP and that it was also possible to estimate the mixing ratio of ATP and dATP from the period. Our findings illuminated a previously unidentified principle to control the dissipative dynamics of biomolecules and, simultaneously, built an important framework to construct molecular robots with spatiotemporal units.
Collapse
Affiliation(s)
- Sakura Takada
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University Katahira 2-1-1, Aoba-Ku, Sendai 9808577, Japan
- MathAM-OIL, AIST, Sendai 980-8577, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| |
Collapse
|
26
|
Holló G, Zámbó D, Deák A, Rossi F, Cucciniello R, Lo Nostro P, Nabika H, Baytekin B, Lagzi I, Itatani M. Effect of the Polarity of Solvents on Periodic Precipitation: Formation of Hierarchical Revert Liesegang Patterns. J Phys Chem B 2022; 126:8322-8330. [PMID: 36219566 PMCID: PMC9589725 DOI: 10.1021/acs.jpcb.2c05810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Liesegang pattern (LP) is one example of self-organized periodic precipitation patterns in nonequilibrium systems. Several studies have demonstrated that the LP morphology can track physicochemical environmental conditions (e.g., temperature); however, the polarity effect has not been explored to date. In this study, a copper chromate system is used to reveal the impact of solvent polarity on the evolving LP structure using water/organic solvent mixtures. In the typical case of using water/dimethyl sulfoxide (DMSO) mixtures, two drastic changes in LP morphology with increasing DMSO contents were found: (i) increasing frequency of the original structure and (ii) formation of a hierarchical pattern with the appearance of another, lower-frequency structure. Furthermore, the simulation model operating with a bimodal size distribution, allowing both homogeneous and heterogeneous precipitations showed good agreement with the experimental results. Therefore, this study demonstrated that LP can be tailored by solvent polarity and can be used for designing hierarchical precipitation patterns in a straightforward manner.
Collapse
Affiliation(s)
- Gábor Holló
- ELKH-BME
Condensed Matter Research Group, Budapest
University of Technology and Economics, Műegyetem rakpart 3, Budapest1111, Hungary
| | - Dániel Zámbó
- Institute
of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, H-1121Budapest, Hungary
| | - András Deák
- Institute
of Technical Physics and Materials Science, Centre for Energy Research, Konkoly-Thege Miklós út 29-33, H-1121Budapest, Hungary
| | - Federico Rossi
- Department
of Earth, Environmental and Physical Sciences—DEEP Sciences, University of Siena, Pian dei Mantellini 44, 53100Siena, Italy
| | - Raffaele Cucciniello
- Department
of Chemistry and Biology “Adolfo Zambelli”, University of Salerno, Viale Via Giovanni Paolo II 132, 84084Fisciano, Salerno, Italy
| | - Pierandrea Lo Nostro
- Department
of Chemistry ‘Ugo Schiff”, University of Florence, Via della Lastruccia 3, 50019Sesto Fiorentino, Florence, Italy
| | - Hideki Nabika
- Faculty of
Science, Yamagata University, 1-4-12, Kojirakawa, Yamagata990-8560, Japan
| | - Bilge Baytekin
- Department
of Chemistry and UNAM, Bilkent University, 06800Ankara, Turkey
| | - István Lagzi
- ELKH-BME
Condensed Matter Research Group, Budapest
University of Technology and Economics, Műegyetem rakpart 3, Budapest1111, Hungary,Department
of Physics, Institute of Physics, Budapest
University of Technology and Economics, Budafoki út 8, Budapest1111, Hungary,
| | - Masaki Itatani
- Department
of Physics, Institute of Physics, Budapest
University of Technology and Economics, Budafoki út 8, Budapest1111, Hungary,
| |
Collapse
|
27
|
Yanagisawa M, Watanabe C, Yoshinaga N, Fujiwara K. Cell-Size Space Regulates the Behavior of Confined Polymers: From Nano- and Micromaterials Science to Biology. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11811-11827. [PMID: 36125172 DOI: 10.1021/acs.langmuir.2c01397] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polymer micromaterials in a liquid or gel phase covered with a surfactant membrane are widely used materials in pharmaceuticals, cosmetics, and foods. In particular, cell-sized micromaterials of biopolymer solutions covered with a lipid membrane have been studied as artificial cells to understand cells from a physicochemical perspective. The characteristics and phase transitions of polymers confined to a microscopic space often differ from those in bulk systems. The effect that causes this difference is referred to as the cell-size space effect (CSE), but the specific physicochemical factors remain unclear. This study introduces the analysis of CSE on molecular diffusion, nanostructure transition, and phase separation and presents their main factors, i.e., short- and long-range interactions with the membrane surface and small volume (finite element nature). This serves as a guide for determining the dominant factors of CSE. Furthermore, we also introduce other factors of CSE such as spatial closure and the relationships among space size, the characteristic length of periodicity, the structure size, and many others produced by biomolecular assemblies through the analysis of protein reaction-diffusion systems and biochemical reactions.
Collapse
Affiliation(s)
- Miho Yanagisawa
- Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo 113-0033, Japan
| | - Chiho Watanabe
- School of Integrated Arts and Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima 739-8521, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai 9808577, Japan
- MathAM-OIL, National Institute of Advanced Industrial Science and Technology, Sendai 980-8577, Japan
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, Yokohama 223-8522, Japan
| |
Collapse
|
28
|
Nguindjel ADC, de Visser PJ, Winkens M, Korevaar PA. Spatial programming of self-organizing chemical systems using sustained physicochemical gradients from reaction, diffusion and hydrodynamics. Phys Chem Chem Phys 2022; 24:23980-24001. [PMID: 36172850 DOI: 10.1039/d2cp02542f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Living organisms employ chemical self-organization to build structures, and inspire new strategies to design synthetic systems that spontaneously take a particular form, via a combination of integrated chemical reactions, assembly pathways and physicochemical processes. However, spatial programmability that is required to direct such self-organization is a challenge to control. Thermodynamic equilibrium typically brings about a homogeneous solution, or equilibrium structures such as supramolecular complexes and crystals. This perspective addresses out-of-equilibrium gradients that can be driven by coupling chemical reaction, diffusion and hydrodynamics, and provide spatial differentiation in the self-organization of molecular, ionic or colloidal building blocks in solution. These physicochemical gradients are required to (1) direct the organization from the starting conditions (e.g. a homogeneous solution), and (2) sustain the organization, to prevent it from decaying towards thermodynamic equilibrium. We highlight four different concepts that can be used as a design principle to establish such self-organization, using chemical reactions as a driving force to sustain the gradient and, ultimately, program the characteristics of the gradient: (1) reaction-diffusion coupling; (2) reaction-convection; (3) the Marangoni effect and (4) diffusiophoresis. Furthermore, we outline their potential as attractive pathways to translate chemical reactions and molecular/colloidal assembly into organization of patterns in solution, (dynamic) self-assembled architectures and collectively moving swarms at the micro-, meso- and macroscale, exemplified by recent demonstrations in the literature.
Collapse
Affiliation(s)
| | - Pieter J de Visser
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
| | - Mitch Winkens
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
| | - Peter A Korevaar
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
| |
Collapse
|
29
|
Bartlett S, Louapre D. Provenance of life: Chemical autonomous agents surviving through associative learning. Phys Rev E 2022; 106:034401. [PMID: 36266823 DOI: 10.1103/physreve.106.034401] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/21/2022] [Indexed: 06/16/2023]
Abstract
We present a benchmark study of autonomous, chemical agents exhibiting associative learning of an environmental feature. Associative learning systems have been widely studied in cognitive science and artificial intelligence but are most commonly implemented in highly complex or carefully engineered systems, such as animal brains, artificial neural networks, DNA computing systems, and gene regulatory networks, among others. The ability to encode environmental information and use it to make simple predictions is a benchmark of biological resilience and underpins a plethora of adaptive responses in the living hierarchy, spanning prey animal species anticipating the arrival of predators to epigenetic systems in microorganisms learning environmental correlations. Given the ubiquitous and essential presence of learning behaviors in the biosphere, we aimed to explore whether simple, nonliving dissipative structures could also exhibit associative learning. Inspired by previous modeling of associative learning in chemical networks, we simulated simple systems composed of long- and short-term memory chemical species that could encode the presence or absence of temporal correlations between two external species. The ability to learn this association was implemented in Gray-Scott reaction-diffusion spots, emergent chemical patterns that exhibit self-replication and homeostasis. With the novel ability of associative learning, we demonstrate that simple chemical patterns can exhibit a broad repertoire of lifelike behavior, paving the way for in vitro studies of autonomous chemical learning systems, with potential relevance to artificial life, origins of life, and systems chemistry. The experimental realization of these learning behaviors in protocell or coacervate systems could advance a new research direction in astrobiology, since our system significantly reduces the lower bound on the required complexity for autonomous chemical learning.
Collapse
Affiliation(s)
- Stuart Bartlett
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California 91125, USA and Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - David Louapre
- Ubisoft Entertainment, 94160 Saint-Mandé, France and Science Étonnante, 75014 Paris, France†
| |
Collapse
|
30
|
Chen X, Xu Y, Lou K, Peng Y, Zhou C, Zhang HP, Wang W. Programmable, Spatiotemporal Control of Colloidal Motion Waves via Structured Light. ACS NANO 2022; 16:12755-12766. [PMID: 35857820 DOI: 10.1021/acsnano.2c04596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Traveling waves in a reaction-diffusion system are essential for long-range communication in living organisms and inspire biomimetic materials of similar capabilities. One recent example is the traveling motion waves among photochemically oscillating, silver (Ag)-containing colloids. Being able to manipulate these colloidal waves holds the key for potential applications. Here, we have discovered that these motion waves can be confined by light patterns and that the chemical clocks of silver particles are moved forward by reducing local light intensity. Using these discoveries as design principles, we have applied structured light technology for the precise and programmable control of colloidal motion waves, including their origins, propagation directions, paths, shapes, annihilation, frequency, and speeds. We have also used the controlled propagation of colloidal waves to guide chemical messages along a predefined path to activate a population of micromotors located far from the signal. Our demonstrated capabilities in manipulating colloidal waves in space and time offer physical insights on their operation and expand their usefulness in the fundamental study of reaction-diffusion processes. Moreover, our findings inspire biomimetic strategies for the directional transport of mass, energy, and information at micro- or even nanoscales.
Collapse
Affiliation(s)
- Xi Chen
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yankai Xu
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kai Lou
- Guangzhou Kayja-Optics Technology Co., Ltd., Guangzhou 511458, China
| | - Yixin Peng
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Chao Zhou
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Department of Mechanical and Energy Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - H P Zhang
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei Wang
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| |
Collapse
|
31
|
Kubota R, Torigoe S, Hamachi I. Temporal Stimulus Patterns Drive Differentiation of a Synthetic Dipeptide-Based Coacervate. J Am Chem Soc 2022; 144:15155-15164. [PMID: 35943765 DOI: 10.1021/jacs.2c05101] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The fate of living cells often depends on their processing of temporally modulated information, such as the frequency and duration of various signals. Synthetic stimulus-responsive systems have been intensely studied for >50 years, but it is still challenging for chemists to create artificial systems that can decode dynamically oscillating stimuli and alter the systems' properties/functions because of the lack of sophisticated reaction networks that are comparable with biological signal transduction. Here, we report morphological differentiation of synthetic dipeptide-based coacervates in response to temporally distinct patterns of the light pulse. We designed a simple cationic diphenylalanine peptide derivative to enable the formation of coacervates. The coacervates concentrated an anionic methacrylate monomer and a photoinitiator, which provided a unique reaction environment and facilitated light-triggered radical polymerization─even in air. Pulsed light irradiation at 9.0 Hz (but not at 0.5 Hz) afforded anionic polymers. This dependence on the light pulse patterns is attributable to the competition of reactive radical intermediates between the methacrylate monomer and molecular oxygen. The temporal pulse pattern-dependent polymer formation enabled the coacervates to differentiate in terms of morphology and internal viscosity, with an ultrasensitive switch-like mode. Our achievements will facilitate the rational design of smart supramolecular soft materials and are insightful regarding the synthesis of sophisticated chemical cells.
Collapse
Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo̅-ku, Kyoto 615-8510, Japan
| | - Shogo Torigoe
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo̅-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo̅-ku, Kyoto 615-8510, Japan.,JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Katsura, Nishikyo̅-ku, Kyoto 615-8530, Japan
| |
Collapse
|
32
|
Runser JY, Criado-Gonzalez M, Fneich F, Rabineau M, Senger B, Weiss P, Jierry L, Schaaf P. Non-monotonous enzyme-assisted self-assembly profiles resulting from reaction-diffusion processes in host gels. J Colloid Interface Sci 2022; 620:234-241. [DOI: 10.1016/j.jcis.2022.03.150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/16/2022]
|
33
|
Liu Y, Che P, Zhang B, Yang J, Gao H, Feng J, Wu Y, Jiang L. One-Step Patterning of Organic Semiconductors on Gold Electrodes via Capillary-Bridge Manipulation. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32761-32770. [PMID: 35816371 DOI: 10.1021/acsami.2c09346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Patterning organic semiconductors directly on Au electrodes possesses the advantages of eliminating metal atomic penetration effect, compatibility with fine lithography processes, and feasibility of work function modification on electrodes, and it is therefore of value in the commercial manufacturability application of optoelectronic devices with low cost, large scale, and high efficiency. Solution processing, is relatively inexpensive and is scalable to large areas. Nonetheless, conventional solution processing approaches have trade-offs among controllable morphology, regular alignment, precise position, and ordered molecular packing arising from the uncontrollable dewetting kinetics. Here, one-step patterning of 1D polymer nanowire arrays directly on Au source-drain electrodes with precise position, controlled orientation, regulated distribution, and tunable width size were realized by employing a capillary-bridge manipulation method to guide the processes of liquid dewetting and nanowire assembly. Organic field-effect transistors (OFETs) with mobility of 10.1 cm2 V-1 s-1 and on/off current ratio of 1.9 × 104 were fabricated. Moreover, we verified generality of our method by patterning different solution-processable optoelectronic materials, including small molecules, quantum dot (QD) nanoparticles, and metal-halide perovskites, into ordered structures directly on the target substrate. The work provides a novel insight into efficient manufacturing the regular aligned and precisely positioned 1D organic semiconductors directly on the channel region of prefabricated Au electrodes in one step and facilitates their applications in high-performance electronic devices.
Collapse
Affiliation(s)
- Yun Liu
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing 100191, P. R. China
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Pengda Che
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing 100191, P. R. China
| | - Bo Zhang
- Institute of Advanced Structure Technology, Beijing Key Laboratory of Lightweight Multi-Functional Composite Materials and Structures, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Jingrun Yang
- Department of General Surgery, First Medical Center, PLA General Hospital, Beijing 100853, P. R. China
| | - Hanfei Gao
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- Ji Hua Laboratory, Foshan, Guangdong 528000, P. R. China
| | - Jiangang Feng
- Department of Chemical and Biomolecular Sciences, National University of Singapore, 117585, Singapore
| | - Yuchen Wu
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- Ji Hua Laboratory, Foshan, Guangdong 528000, P. R. China
| | - Lei Jiang
- Key Laboratory of Bio-inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry, Beihang University, Beijing 100191, P. R. China
- Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- Ji Hua Laboratory, Foshan, Guangdong 528000, P. R. China
| |
Collapse
|
34
|
Escárcega-Bobadilla MV, Maldonado-Domínguez M, Romero-Ávila M, Zelada-Guillén GA. Turing patterns by supramolecular self-assembly of a single salphen building block. iScience 2022; 25:104545. [PMID: 35747384 PMCID: PMC9209723 DOI: 10.1016/j.isci.2022.104545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/15/2022] [Accepted: 06/02/2022] [Indexed: 11/02/2022] Open
Abstract
In the 1950s, Alan Turing showed that concerted reactions and diffusion of activating and inhibiting chemical species can autonomously generate patterns without previous positional information, thus providing a chemical basis for morphogenesis in Nature. However, access to these patterns from only one molecular component that contained all the necessary information to execute agonistic and antagonistic signaling is so far an elusive goal, since two or more participants with different diffusivities are a must. Here, we report on a single-molecule system that generates Turing patterns arrested in the solid state, where supramolecular interactions are used instead of chemical reactions, whereas diffusional differences arise from heterogeneously populated self-assembled products. We employ a family of hydroxylated organic salphen building blocks based on a bis-Schiff-base scaffold with portions responsible for either activation or inhibition of assemblies at different hierarchies through purely supramolecular reactions, only depending upon the solvent dielectric constant and evaporation as fuel.
Collapse
Affiliation(s)
- Martha V Escárcega-Bobadilla
- School of Chemistry, National Autonomous University of Mexico (UNAM), Circuito Escolar s/n, Ciudad Universitaria, 04510 Mexico City, Mexico
| | - Mauricio Maldonado-Domínguez
- School of Chemistry, National Autonomous University of Mexico (UNAM), Circuito Escolar s/n, Ciudad Universitaria, 04510 Mexico City, Mexico.,Department of Computational Chemistry, J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, 18223 Prague 8, Czech Republic
| | - Margarita Romero-Ávila
- School of Chemistry, National Autonomous University of Mexico (UNAM), Circuito Escolar s/n, Ciudad Universitaria, 04510 Mexico City, Mexico
| | - Gustavo A Zelada-Guillén
- School of Chemistry, National Autonomous University of Mexico (UNAM), Circuito Escolar s/n, Ciudad Universitaria, 04510 Mexico City, Mexico
| |
Collapse
|
35
|
Mahato RR, Shandilya E, Not Applicable S, Maiti S. Regulating Spatial Localization and Reactivity Biasness of DNAzymes by Metal Ions and Oligonucleotides. Chembiochem 2022; 23:e202200154. [PMID: 35762518 DOI: 10.1002/cbic.202200154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 06/08/2022] [Indexed: 11/09/2022]
Abstract
Chemical gradient sensing behavior of catalytically active colloids and enzymes is an area of immense interest owing to their importance in understanding fundamental spatiotemporal complexity pattern in living systems and designing of dynamic materials. Herein, we have shown peroxidase activity of DNAzyme (G-quadruplex-hemin complex tagged in a micron-sized glass bead) can be modulated by metal ions and metal ion-binding oligonucleotides. Next we demonstrated both experimentally and theoretically that the localization and product formation ability of the DNAzyme containing particle remains biased to the more catalytically active zone where concentration of metal ion (Hg2+) inhibitor is low. Interestingly, this biased localization can be broken by introduction of Hg2+ binding oligonucleotide in the system. Additionally, macroscopically asymmetric catalytic product distributed zone has also been achieved on this process, showing possibility in regulation in autonomous spatially controlled chemical process. This demonstration of autonomous modulation of the localization pattern and spatially specific enhanced product forming ability of DNAzymes will further enable in designing of responsive nucleic acid-based motile materials and surfaces.
Collapse
Affiliation(s)
- Rishi Ram Mahato
- Indian Institute of Science Education and Research Mohali, Chemical Sciences, INDIA
| | - Ekta Shandilya
- Indian Institute of Science Education and Research Mohali, Chemical Sciences, INDIA
| | | | - Subhabrata Maiti
- Indian Institute of Science Education and Research Mohali, Chemical Sciences, Knowledge City, Sector-81, S.A.S. Nagar, Manauli P.O., 140306, Mohali, INDIA
| |
Collapse
|
36
|
Chen X, Xu Y, Zhou C, Lou K, Peng Y, Zhang HP, Wang W. Unraveling the physiochemical nature of colloidal motion waves among silver colloids. SCIENCE ADVANCES 2022; 8:eabn9130. [PMID: 35613263 PMCID: PMC9132452 DOI: 10.1126/sciadv.abn9130] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Traveling waves are common in biological and synthetic systems, including the recent discovery that silver (Ag) colloids form traveling motion waves in H2O2 and under light. Here, we show that this colloidal motion wave is a heterogeneous excitable system. The Ag colloids generate traveling chemical waves via reaction-diffusion, and either self-propel through self-diffusiophoresis ("ballistic waves") or are advected by diffusio-osmotic flows from gradients of neutral molecules ("swarming waves"). Key results include the experimental observation of traveling waves of OH- with pH-sensitive fluorescent dyes and a Rogers-McCulloch model that qualitatively and quantitatively reproduces the key features of colloidal waves. These results are a step forward in elucidating the Ag-H2O2-light oscillatory system at individual and collective levels. In addition, they pave the way for using colloidal waves either as a platform for studying nonlinear phenomena, or as a tool for colloidal transport and for information transmission in microrobot ensembles.
Collapse
Affiliation(s)
- Xi Chen
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yankai Xu
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chao Zhou
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Kai Lou
- Guangzhou Kayja-Optics Technology Co. Ltd., Guangzhou 511458, China
| | - Yixin Peng
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - H. P. Zhang
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Corresponding author. (W.W.); (H.P.Z.)
| | - Wei Wang
- Sauvage Laboratory for Smart Materials, School of Materials Science and Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
- Corresponding author. (W.W.); (H.P.Z.)
| |
Collapse
|
37
|
Paikar A, Novichkov AI, Hanopolskyi AI, Smaliak VA, Sui X, Kampf N, Skorb EV, Semenov SN. Spatiotemporal Regulation of Hydrogel Actuators by Autocatalytic Reaction Networks. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2106816. [PMID: 34910837 DOI: 10.1002/adma.202106816] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/26/2021] [Indexed: 06/14/2023]
Abstract
Regulating hydrogel actuators with chemical reaction networks is instrumental for constructing life-inspired smart materials. Herein, hydrogel actuators are engineered that are regulated by the autocatalytic front of thiols. The actuators consist of two layers. The first layer, which is regular polyacrylamide hydrogel, is in a strained conformation. The second layer, which is polyacrylamide hydrogel with disulfide crosslinks, maintains strain in the first layer. When thiols released by the autocatalytic front reduce disulfide crosslinks, the hydrogel actuates by releasing the mechanical strain in the first layer. The autocatalytic front is sustained by the reaction network, which uses thiouronium salts, disulfides of β-aminothiols, and maleimide as starting components. The gradual actuation by the autocatalytic front enables movements such as gradual unrolling, screwing, and sequential closing of "fingers." This actuation also allows the transmission of chemical signals in a relay fashion and the conversion of a chemical signal to an electrical signal. Locations and times of spontaneous initiation of autocatalytic fronts can be preprogrammed in the spatial distribution of the reactants in the hydrogel. To approach the functionality of living matter, the actuators triggered by an autocatalytic front can be integrated into smart materials regulated by chemical circuits.
Collapse
Affiliation(s)
- Arpita Paikar
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Alexander I Novichkov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Anton I Hanopolskyi
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Viktoryia A Smaliak
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Xiaomeng Sui
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir Kampf
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ekaterina V Skorb
- Infochemistry Scientific Center, ITMO University, Saint Petersburg, 191002, Russia
| | - Sergey N Semenov
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| |
Collapse
|
38
|
Iodine clocks: applications and untapped opportunities in materials science. REACTION KINETICS MECHANISMS AND CATALYSIS 2022. [DOI: 10.1007/s11144-022-02202-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
AbstractIodine clocks are fascinating nonlinear chemical systems with a glorious past and a promising future. The dynamic removal of iodine from these systems by different means can have important consequences for their reaction dynamics, and could be exploited for time-controlled autonomous dissipative self-assembly. Here, the untapped opportunities offered by iodine clocks for materials science, especially for the time-programming of supramolecular assembly and sol–gel transition, are reviewed and discussed with the hope of arousing the interest on the subject and stimulating new research directions.
Collapse
|
39
|
Feng J, Qiu Y, Jiang L, Wu Y. Long-Range-Ordered Assembly of Micro-/Nanostructures at Superwetting Interfaces. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2106857. [PMID: 34908188 DOI: 10.1002/adma.202106857] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/03/2021] [Indexed: 06/14/2023]
Abstract
On-chip integration of solution-processable materials imposes stringent and simultaneous requirements of controlled nucleation and growth, tunable geometry and dimensions, and long-range-ordered assembly, which is challenging in solution process far from thermodynamic equilibrium. Superwetting interfaces, underpinned by programmable surface chemistry and topography, are promising for steering transport, dewetting, and microfluid dynamics of liquids, thus opening a new paradigm for micro-/nanostructure assembly in solution process. Herein, assembly methods on the basis of superwetting interfaces are reviewed for constructing long-range-ordered micro-/nanostructures. Confined capillary liquids, including capillary bridges and capillary corner menisci realized by controlling local wettability and surface topography, are highlighted for simultaneously attained deterministic patterning and long-range order. The versatility and robustness of confined capillary liquids are discussed with assembly of single-crystalline micro-/nanostructures of organic semiconductors, metal-halide perovskites, and colloidal-nanoparticle superlattices, which lead to enhanced device performances and exotic functionalities. Finally, a perspective for promising directions in this realm is provided.
Collapse
Affiliation(s)
- Jiangang Feng
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Department of Chemical and Biomolecular Sciences, National University of Singapore, Singapore, 117585, Singapore
| | - Yuchen Qiu
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lei Jiang
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- School of Chemistry, Beihang University, Beijing, 100191, P. R. China
| | - Yuchen Wu
- Key Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| |
Collapse
|
40
|
Chen Z, Suzuki Y, Imayoshi A, Ji X, Rao KV, Omata Y, Miyajima D, Sato E, Nihonyanagi A, Aida T. Solvent-free autocatalytic supramolecular polymerization. NATURE MATERIALS 2022; 21:253-261. [PMID: 34650229 DOI: 10.1038/s41563-021-01122-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Solvent-free chemical manufacturing is one of the awaited technologies for addressing an emergent issue of environmental pollution. Here, we report solvent-free autocatalytic supramolecular polymerization (SF-ASP), which provides an inhibition-free template-assisted catalytic organic transformation that takes great advantage of the fact that the product (template) undergoes a termination-free nucleation-elongation assembly (living supramolecular polymerization) under solvent-free conditions. SF-ASP allows for reductive cyclotetramerization of hydrogen-bonding phthalonitriles into the corresponding phthalocyanines in exceptionally high yields (>80%). SF-ASP requires the growing polymer to form hexagonally packed crystalline fibres, which possibly preorganize the phthalonitriles at their cross-sectional edges for their efficient transformation. With metal oleates, SF-ASP produces single-crystalline fibres of metallophthalocyanines again in exceptionally high yields, which grow in both directions without terminal coupling until the phthalonitrile precursors are completely consumed. By taking advantage of this living nature of polymerization, multistep SF-ASP without/with metal oleates allows for the precision synthesis of multi-block supramolecular copolymers.
Collapse
Affiliation(s)
- Zhen Chen
- RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Yukinaga Suzuki
- RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ayumi Imayoshi
- RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan
| | - Xiaofan Ji
- RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan
| | | | - Yuki Omata
- RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan
| | - Daigo Miyajima
- RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan.
| | - Emiko Sato
- RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan
| | | | - Takuzo Aida
- RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| |
Collapse
|
41
|
Itatani M, Fang Q, Lagzi I, Nabika H. Phase separation mechanism for a unified understanding of dissipative pattern formation in a Liesegang system. Phys Chem Chem Phys 2022; 24:2088-2094. [PMID: 35018927 DOI: 10.1039/d1cp05184a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Dissipative patterns with solid-phase transitions are ubiquitous in nature. Despite their ubiquitous nature, there is no unified understanding of the non-equilibrium self-assembly mechanisms of such pattern formation. The Liesegang pattern (LP) is a typical model that has the potential to describe dissipative pattern formation arising from the nonlinear coupling of directional mass transport of water-soluble substances into a porous media with their solid-phase transition processes. However, the conventional mechanism in a Liesegang system lacks practicality because most of the existing studies have focused only on the transition mechanism of nucleation from the molecular to the solid state. In this study, we demonstrate a novel experimental system based on a phase transition and separation mechanism that does not require nucleation, namely, the pH-induced aggregation of gold nanoparticles modified with 11-mercaptoundecanoic acid (MUA-Au NPs) by H+ diffusion in a solid hydrogel. Combined experiments and numerical simulations reveal that pattern formation is driven by the macroscopic phase-separation mechanism. Furthermore, the pattern periodicity obtained from both experiments and simulations follows the classical spacing law of LP, namely, the LP morphology is determined without the need for nucleation. Therefore, we can show that the formation of LPs can be described in a unified mechanism, regardless of whether nucleation occurs. This finding opens the possibility that the chemical Liesegang system can be applied as a practical model for proving the mechanisms of similar dissipative pattern formation.
Collapse
Affiliation(s)
- Masaki Itatani
- Graduate School of Science and Engineering, Yamagata University, 1-4-12, Kojirakawa, Yamagata 990-8560, Japan
| | - Qing Fang
- Faculty of Science, Yamagata University, 1-4-12, Kojirakawa, Yamagata 990-8560, Japan.
| | - István Lagzi
- Department of Physics, Budapest University of Technology and Economics, Budafoki út 8, Budapest 1111, Hungary.,MTA-BME Condensed Matter Physics Research Group, Budapest University of Technology and Economics, Budafoki út 8, Budapest 1111, Hungary
| | - Hideki Nabika
- Faculty of Science, Yamagata University, 1-4-12, Kojirakawa, Yamagata 990-8560, Japan.
| |
Collapse
|
42
|
Chen R, Das K, Cardona MA, Gabrielli L, Prins LJ. Progressive Local Accumulation of Self-Assembled Nanoreactors in a Hydrogel Matrix through Repetitive Injections of ATP. J Am Chem Soc 2022; 144:2010-2018. [PMID: 35061942 PMCID: PMC8815075 DOI: 10.1021/jacs.1c13504] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cellular functions
are regulated with high spatial control through
the local activation of chemical processes in a complex inhomogeneous
matrix. The development of synthetic macroscopic systems with a similar
capacity allows fundamental studies aimed at understanding the relationship
between local molecular events and the emergence of functional properties
at the macroscopic level. Here, we show that a kinetically stable
inhomogeneous hydrogel matrix is spontaneously formed upon the local
injection of ATP. Locally, ATP templates the self-assembly of amphiphiles
into large nanoreactors with a much lower diffusion rate compared
to unassembled amphiphiles. The local depletion of unassembled amphiphiles
near the injection point installs a concentration gradient along which
unassembled amphiphiles diffuse from the surroundings to the center.
This allows for a progressive local accumulation of self-assembled
nanoreactors in the matrix upon repetitive cycles of ATP injection
separated by time intervals during which diffusion of unassembled
amphiphiles takes place. Contrary to the homogeneous matrix containing
the same components, in the inhomogeneous matrix the local upregulation
of a chemical reaction occurs. Depending on the way the same amount
of injected ATP is administered to the hydrogel matrix different macroscopic
distributions of nanoreactors are obtained, which affect the location
in the matrix where the chemical reaction is upregulated.
Collapse
Affiliation(s)
- Rui Chen
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Krishnendu Das
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Maria A. Cardona
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Luca Gabrielli
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| | - Leonard J. Prins
- Department of Chemical Sciences, University of Padova, Padova, 35131, Italy
| |
Collapse
|
43
|
Deshwal A, Shikha, Maiti S. Trade-off between carbohydrates and metal ions regulates the chemotactic directionality of alkaline phosphatase. Chem Commun (Camb) 2022; 58:12851-12854. [DOI: 10.1039/d2cc04360b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of the Hofmeister interaction in governing the chemotactic behavior of alkaline phosphatase in the presence of carbohydrate and metal ion gradients has been established.
Collapse
Affiliation(s)
- Akshi Deshwal
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Shikha
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli 140306, India
| |
Collapse
|
44
|
Priyanka, Shandilya E, Brar SK, Mahato RR, Maiti S. Spatiotemporal dynamics of self-assembled structures in enzymatically induced agonistic and antagonistic conditions. Chem Sci 2021; 13:274-282. [PMID: 35059177 PMCID: PMC8694342 DOI: 10.1039/d1sc05353a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/20/2021] [Indexed: 12/20/2022] Open
Abstract
Predicting and designing systems with dynamic self-assembly properties in a spatiotemporal fashion is an important research area across disciplines ranging from understanding the fundamental non-equilibrium features of life to the fabrication of next-generation materials with life-like properties. Herein, we demonstrate a spatiotemporal dynamics pattern in the self-assembly behavior of a surfactant from an unorganized assembly, induced by adenosine triphosphate (ATP) and enzymes responsible for the degradation or conversion of ATP. We report the different behavior of two enzymes, alkaline phosphatase (ALP) and hexokinase (HK), towards adenosine triphosphate (ATP)-driven surfactant assembly, which also results in contrasting spatiotemporal dynamic assembly behavior. Here, ALP acts antagonistically, resulting in transient self-assemblies, whereas HK shows agonistic action with the ability to sustain the assemblies. This dynamic assembly behavior was then used to program the time-dependent emergence of a self-assembled structure in a two-dimensional space by maintaining concentration gradients of the enzymes and surfactant at different locations, demonstrating a new route for obtaining 'spatial' organizational adaptability in a self-organized system of interacting components for the incorporation of programmed functionality.
Collapse
Affiliation(s)
- Priyanka
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City Manauli 140306 India
| | - Ekta Shandilya
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City Manauli 140306 India
| | - Surinder Kaur Brar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City Manauli 140306 India
| | - Rishi Ram Mahato
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City Manauli 140306 India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali Knowledge City Manauli 140306 India
| |
Collapse
|
45
|
Nakamura K, Tanaka W, Sada K, Kubota R, Aoyama T, Urayama K, Hamachi I. Phototriggered Spatially Controlled Out-of-Equilibrium Patterns of Peptide Nanofibers in a Self-Sorting Double Network Hydrogel. J Am Chem Soc 2021; 143:19532-19541. [PMID: 34767720 DOI: 10.1021/jacs.1c09172] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Out-of-equilibrium patterns arising from diffusion processes are ubiquitous in nature, although they have not been fully exploited for the design of artificial materials. Here, we describe the formation of phototriggered out-of-equilibrium patterns using photoresponsive peptide-based nanofibers in a self-sorting double network hydrogel. Light irradiation using a photomask followed by thermal incubation induced the spatially controlled condensation of peptide nanofibers. According to confocal images and spectroscopic analyses, metastable nanofibers photodecomposed in the irradiated areas, where thermodynamically stable nanofibers reconstituted and condensed with a supply of monomers from the nonirradiated areas. These supramolecular events were regulated by light and diffusion to facilitate the creation of unique out-of-equilibrium patterns, including two lines from a one-line photomask and a line pattern of a protein immobilized in the hydrogel.
Collapse
Affiliation(s)
- Keisuke Nakamura
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Wataru Tanaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kei Sada
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takuma Aoyama
- Department of Macromolecular Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan
| | - Kenji Urayama
- Department of Macromolecular Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan.,JST-ERATO, Hamachi Innovative Molecular Technology for Neuroscience, Nishikyo-ku, Kyoto 615-8530, Japan
| |
Collapse
|
46
|
Mallphanov IL, Vanag VK. Chemical micro-oscillators based on the Belousov–Zhabotinsky reaction. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Abstract
The results of studies on the development of micro-oscillators (MOs) based on the Belousov –Zhabotinsky (BZ) oscillatory chemical reaction are integrated and systematized. The mechanisms of the BZ reaction and the methods of immobilization of the catalyst of the BZ reaction in micro-volumes are briefly discussed. Methods for creating BZ MOs based on water microdroplets in the oil phase and organic and inorganic polymer microspheres are considered. Methods of control and management of the dynamics of BZ MO networks are described, including methods of MO synchronization. The prospects for the design of neural networks of MOs with intelligent-like behaviour are outlined. Such networks present a new area of nonlinear chemistry, including, in particular, the creation of a chemical ‘computer’.
The bibliography includes 250 references.
Collapse
|
47
|
|
48
|
Fang Y, Yang X, Lin Y, Shi J, Prominski A, Clayton C, Ostroff E, Tian B. Dissecting Biological and Synthetic Soft-Hard Interfaces for Tissue-Like Systems. Chem Rev 2021; 122:5233-5276. [PMID: 34677943 DOI: 10.1021/acs.chemrev.1c00365] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Soft and hard materials at interfaces exhibit mismatched behaviors, such as mismatched chemical or biochemical reactivity, mechanical response, and environmental adaptability. Leveraging or mitigating these differences can yield interfacial processes difficult to achieve, or inapplicable, in pure soft or pure hard phases. Exploration of interfacial mismatches and their associated (bio)chemical, mechanical, or other physical processes may yield numerous opportunities in both fundamental studies and applications, in a manner similar to that of semiconductor heterojunctions and their contribution to solid-state physics and the semiconductor industry over the past few decades. In this review, we explore the fundamental chemical roles and principles involved in designing these interfaces, such as the (bio)chemical evolution of adaptive or buffer zones. We discuss the spectroscopic, microscopic, (bio)chemical, and computational tools required to uncover the chemical processes in these confined or hidden soft-hard interfaces. We propose a soft-hard interaction framework and use it to discuss soft-hard interfacial processes in multiple systems and across several spatiotemporal scales, focusing on tissue-like materials and devices. We end this review by proposing several new scientific and engineering approaches to leveraging the soft-hard interfacial processes involved in biointerfacing composites and exploring new applications for these composites.
Collapse
Affiliation(s)
- Yin Fang
- The James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States
| | - Xiao Yang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yiliang Lin
- The James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States.,Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States.,The Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Jiuyun Shi
- The James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States.,Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States.,The Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Aleksander Prominski
- The James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States.,Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States.,The Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| | - Clementene Clayton
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Ellie Ostroff
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Bozhi Tian
- The James Franck Institute, University of Chicago, Chicago, Illinois 60637, United States.,Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States.,The Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|
49
|
Amano S, Borsley S, Leigh DA, Sun Z. Chemical engines: driving systems away from equilibrium through catalyst reaction cycles. NATURE NANOTECHNOLOGY 2021; 16:1057-1067. [PMID: 34625723 DOI: 10.1038/s41565-021-00975-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
Biological systems exhibit a range of complex functions at the micro- and nanoscales under non-equilibrium conditions (for example, transportation and motility, temporal control, information processing and so on). Chemists also employ out-of-equilibrium systems, for example in kinetic selection during catalysis, self-replication, dissipative self-assembly and synthetic molecular machinery, and in the form of chemical oscillators. Key to non-equilibrium behaviour are the mechanisms through which systems are able to extract energy from the chemical reactants ('fuel') that drive such processes. In this Perspective we relate different examples of such powering mechanisms using a common conceptual framework. We discuss how reaction cycles can be coupled to other dynamic processes through positive (acceleration) or negative (inhibition) catalysis to provide the thermodynamic impetus for diverse non-equilibrium behaviour, in effect acting as a 'chemical engine'. We explore the way in which the energy released from reaction cycles is harnessed through kinetic selection in a series of what have sometimes been considered somewhat disparate fields (systems chemistry, molecular machinery, dissipative assembly and chemical oscillators), highlight common mechanistic principles and the potential for the synchronization of chemical reaction cycles, and identify future challenges for the invention and application of non-equilibrium systems. Explicit recognition of the use of fuelling reactions to power structural change in catalysts may stimulate the investigation of known catalytic cycles as potential elements for chemical engines, a currently unexplored area of catalysis research.
Collapse
Affiliation(s)
- Shuntaro Amano
- Department of Chemistry, University of Manchester, Manchester, UK
| | - Stefan Borsley
- Department of Chemistry, University of Manchester, Manchester, UK
| | - David A Leigh
- Department of Chemistry, University of Manchester, Manchester, UK.
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Zhanhu Sun
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China
| |
Collapse
|
50
|
Mehan S, Herrmann L, Chapel JP, Jestin J, Berret JF, Cousin F. The desalting/salting pathway: a route to form metastable aggregates with tuneable morphologies and lifetimes. SOFT MATTER 2021; 17:8496-8505. [PMID: 34474458 DOI: 10.1039/d1sm00260k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We investigate the formation/re-dissociation mechanisms of hybrid complexes made from negatively charged PAA2k coated γ-Fe2O3 nanoparticles (NP) and positively charged polycations (PDADMAC) in aqueous solution in the regime of very high ionic strength (I). When the building blocks are mixed at large ionic strength (1 M NH4Cl), the electrostatic interaction is screened and complexation does not occur. If the ionic strength is then lowered down to a targeted ionic strength Itarget, there is a critical threshold Ic = 0.62 M at which complexation occurs, that is independent of the charge ratio Z and the pathway used to reduce salinity (drop-by-drop mixing or fast mixing). If salt is added back up to 1 M, the transition is not reversible and persistent out-of-equilibrium aggregates are formed. The lifetimes of such aggregates depends on Itarget: the closer Itarget to Ic is, the more difficult it is to dissolve the aggregates. Such peculiar behavior is driven by the inner structure of the complexes that are formed after desalting. When Itarget is far below Ic, strong electrostatic interactions induce the formation of dense, compact and frozen aggregates. Such aggregates can only poorly reorganize further on with time, which makes their dissolution upon resalting almost reversible. Conversely, when Itarget is close to Ic more open aggregates are formed due to weaker electrostatic interactions upon desalting. The system can thus rearrange with time to lower its free energy and reach more stable out-of-equilibrium states which are very difficult to dissociate back upon resalting, even at very high ionic strength.
Collapse
Affiliation(s)
- Sumit Mehan
- Laboratoire Léon Brillouin, Université Paris-Saclay, CEA Saclay, 91191 Gif sur Yvette Cedex, France.
| | - Laure Herrmann
- Université de Paris, CNRS, Matière et systèmes complexes, 75013 Paris, France
| | - Jean-Paul Chapel
- Centre de Recherche Paul Pascal (CRPP), UMR CNRS 5031, Université de Bordeaux, 33600 Pessac, France
| | - Jacques Jestin
- Laboratoire Léon Brillouin, Université Paris-Saclay, CEA Saclay, 91191 Gif sur Yvette Cedex, France.
| | | | - Fabrice Cousin
- Laboratoire Léon Brillouin, Université Paris-Saclay, CEA Saclay, 91191 Gif sur Yvette Cedex, France.
| |
Collapse
|