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Article ; Online: Emergence of catalytic function in prebiotic information-coding polymers.

Tkachenko, Alexei V / Maslov, Sergei

2024 Volume 12

Abstract: Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early ... ...

Abstract	Life as we know it relies on the interplay between catalytic activity and information processing carried out by biological polymers. Here we present a plausible pathway by which a pool of prebiotic information-coding oligomers could acquire an early catalytic function, namely sequence-specific cleavage activity. Starting with a system capable of non-enzymatic templated replication, we demonstrate that even non-catalyzed spontaneous cleavage would promote proliferation by generating short fragments that act as primers. Furthermore, we show that catalytic cleavage function can naturally emerge and proliferate in this system. Specifically, a cooperative catalytic network with four subpopulations of oligomers is selected by the evolution in competition with chains lacking catalytic activity. The cooperative system emerges through the functional differentiation of oligomers into catalysts and their substrates. The model is inspired by the structure of the hammerhead RNA enzyme as well as other DNA- and RNA-based enzymes with cleavage activity that readily emerge through natural or artificial selection. We identify the conditions necessary for the emergence of the cooperative catalytic network. In particular, we show that it requires the catalytic rate enhancement over the spontaneous cleavage rate to be at least 10
MeSH term(s)	Catalysis ; Cognition ; Polymers ; Prebiotics ; RNA
Chemical Substances	Polymers ; Prebiotics ; RNA (63231-63-0)
Language	English
Publishing date	2024-03-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.91397
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Geometric and topological entropies of sphere packing.

Logan, Jack A / Tkachenko, Alexei V

Physical review. E

2022 Volume 105, Issue 1-1, Page(s) 14117

Abstract: We present a statistical mechanical description of randomly packed spherical particles, where the average coordination number is treated as a macroscopic thermodynamic variable. The overall packing entropy is shown to have two contributions: geometric, ... ...

Abstract	We present a statistical mechanical description of randomly packed spherical particles, where the average coordination number is treated as a macroscopic thermodynamic variable. The overall packing entropy is shown to have two contributions: geometric, reflecting statistical weights of individual configurations, and topological, which corresponds to the number of topologically distinct states. Both of them are computed in the thermodynamic limit for isostatic and weakly underconstrained packings in 2D and 3D. The theory generalizes concepts of granular and glassy configurational entropies for the case of nonjammed systems. It is directly applicable to sticky colloids and predicts an asymptotic phase behavior of sticky spheres in the limit of strong binding.
Language	English
Publishing date	2022-02-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.105.014117
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Article ; Online: Symmetry-specific characterization of bond orientation order in DNA-assembled nanoparticle lattices.

Logan, Jack A / Michelson, Aaron / Pattammattel, Ajith / Yan, Hanfei / Gang, Oleg / Tkachenko, Alexei V

The Journal of chemical physics

2023 Volume 159, Issue 15

Abstract: Bond-orientational order in DNA-assembled nanoparticles lattices is explored with the help of recently introduced Symmetry-specific Bond Order Parameters (SymBOPs). This approach provides a more sensitive analysis of local order than traditional scalar ... ...

Abstract	Bond-orientational order in DNA-assembled nanoparticles lattices is explored with the help of recently introduced Symmetry-specific Bond Order Parameters (SymBOPs). This approach provides a more sensitive analysis of local order than traditional scalar BOPs, facilitating the identification of coherent domains at the single bond level. The present study expands the method initially developed for assemblies of anisotropic particles to the isotropic ones or cases where particle orientation information is unavailable. The SymBOP analysis was applied to experiments on DNA-frame-based assembly of nanoparticle lattices. It proved highly sensitive in identifying coherent crystalline domains with different orientations, as well as detecting topological defects, such as dislocations. Furthermore, the analysis distinguishes individual sublattices within a single crystalline domain, such as pair of interpenetrating FCC lattices within a cubic diamond. The results underscore the versatility and robustness of SymBOPs in characterizing ordering phenomena, making them valuable tools for investigating structural properties in various systems.
MeSH term(s)	DNA/chemistry ; Nanoparticles/chemistry ; Anisotropy
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-10-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0168604
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Article ; Online: Generic phase diagram of binary superlattices.

Tkachenko, Alexei V

Proceedings of the National Academy of Sciences of the United States of America

2016 Volume 113, Issue 37, Page(s) 10269–10274

Abstract: Emergence of a large variety of self-assembled superlattices is a dramatic recent trend in the fields of nanoparticle and colloidal sciences. Motivated by this development, we propose a model that combines simplicity with a remarkably rich phase behavior ...

Abstract	Emergence of a large variety of self-assembled superlattices is a dramatic recent trend in the fields of nanoparticle and colloidal sciences. Motivated by this development, we propose a model that combines simplicity with a remarkably rich phase behavior applicable to a wide range of such self-assembled systems. Those systems include nanoparticle and colloidal assemblies driven by DNA-mediated interactions, electrostatics, and possibly, controlled drying. In our model, a binary system of large and small hard spheres (L and S, respectively) interacts via selective short-range ("sticky") attraction. In its simplest version, this binary sticky sphere model features attraction only between S and L particles. We show that, in the limit when this attraction is sufficiently strong compared with [Formula: see text], the problem becomes purely geometrical: the thermodynamically preferred state should maximize the number of [Formula: see text] contacts. A general procedure for constructing the phase diagram as a function of system composition f and particle size ratio r is outlined. In this way, the global phase behavior can be calculated very efficiently for a given set of plausible candidate phases. Furthermore, the geometric nature of the problem enables us to generate those candidate phases through a well-defined and intuitive construction. We calculate the phase diagrams for both 2D and 3D systems and compare the results with existing experiments. Most of the 3D superlattices observed to date are featured in our phase diagram, whereas several more are predicted for future discovery.
Language	English
Publishing date	2016-09-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1525358113
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Article ; Online: Controlling morphology in hybrid isotropic/patchy particle assemblies.

Mushnoori, Srinivas / Logan, Jack A / Tkachenko, Alexei V / Dutt, Meenakshi

The Journal of chemical physics

2022 Volume 156, Issue 2, Page(s) 24501

Abstract: Brownian dynamics is used to study self-assembly in a hybrid system of isotropic particles (IPs), combined with anisotropic building blocks that represent special "designer particles." Those are modeled as spherical patchy particles (PPs) with binding ... ...

Abstract	Brownian dynamics is used to study self-assembly in a hybrid system of isotropic particles (IPs), combined with anisotropic building blocks that represent special "designer particles." Those are modeled as spherical patchy particles (PPs) with binding only allowed between their patches and IPs. In this study, two types of PPs are considered: Octahedral PPs (Oh-PPs) and Square PPs (Sq-PPs), with octahedral and square arrangements of patches, respectively. The self-assembly is additionally facilitated by the simulated annealing procedure. The resultant structures are characterized by a combination of local correlations in cubatic ordering and a symmetry-specific variation of bond orientation order parameters (SymBOPs). By varying the PP/IP size ratio, we detected a sharp crossover between two distinct morphologies in both types of systems. High symmetry phases, NaCl crystal for Oh-PP and square lattice for Sq-PP, are observed for larger size ratios. For the smaller ones, the dominant morphologies are significantly different, e.g., Oh-PPs form a compact amorphous structure with predominantly face-to-face orientation of neighboring PPs. Unusually, for a morphology without a long-range order, it is still possible to identify well organized coherent clusters of this structure, thanks to the adoption of our SymBOP-based characterization.
Language	English
Publishing date	2022-01-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0076914
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Article ; Online: Onset of natural selection in populations of autocatalytic heteropolymers.

Tkachenko, Alexei V / Maslov, Sergei

The Journal of chemical physics

2018 Volume 149, Issue 13, Page(s) 134901

Abstract: Reduction of information entropy along with ever-increasing complexity is among the key signatures of life. Understanding the onset of such behavior in the early prebiotic world is essential for solving the problem of the origin of life. Here we study a ... ...

Abstract	Reduction of information entropy along with ever-increasing complexity is among the key signatures of life. Understanding the onset of such behavior in the early prebiotic world is essential for solving the problem of the origin of life. Here we study a general problem of heteropolymers capable of template-assisted ligation based on Watson-Crick-like hybridization. The system is driven off-equilibrium by cyclic changes in the environment. We model the dynamics of 2-mers, i.e., sequential pairs of specific monomers within the heteropolymer population. While the possible number of them is
MeSH term(s)	Algorithms ; Biopolymers/chemistry ; Catalysis ; Computer Graphics ; Computer Simulation ; Entropy ; Models, Chemical ; Nucleic Acid Hybridization ; Origin of Life ; Polymerization
Chemical Substances	Biopolymers
Language	English
Publishing date	2018-09-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.5048488
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Article ; Online: Communication: Programmable self-assembly of thin-shell mesostructures.

Halverson, Jonathan D / Tkachenko, Alexei V

The Journal of chemical physics

2017 Volume 147, Issue 14, Page(s) 141103

Abstract: We study numerically the possibility of programmable self-assembly of various thin-shell architectures. They include clusters isomorphic to fullerenes ... ...

Abstract	We study numerically the possibility of programmable self-assembly of various thin-shell architectures. They include clusters isomorphic to fullerenes C
Language	English
Publishing date	2017-10-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/1.4999654
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Article ; Online: Symmetry-specific orientational order parameters for complex structures.

Logan, Jack A / Mushnoori, Srinivas / Dutt, Meenakshi / Tkachenko, Alexei V

The Journal of chemical physics

2021 Volume 156, Issue 5, Page(s) 54108

Abstract: A comprehensive framework of characterizing complex self-assembled structures with a set of orientational order parameters is presented. It is especially relevant in the context of using anisotropic building blocks with various symmetries. Two classes of ...

Abstract	A comprehensive framework of characterizing complex self-assembled structures with a set of orientational order parameters is presented. It is especially relevant in the context of using anisotropic building blocks with various symmetries. Two classes of tensor order parameters are associated with polyhedral nematic and bond orientational order. For the latter, a variation of classical bond order parameters (BOPs) is introduced, which takes advantage of the symmetry of constituent particles and/or expected crystalline phases. These symmetrized BOPs can be averaged over an entire system or assigned locally to an individual bond. By combining that with the bond percolation procedure, one is able to identify coherent domains within a self-assembled structure. As a demonstration of the proposed framework, we apply it to a simulated hybrid system that combines isotropic and patchy particles with octahedral symmetry. Not only does the methodology allow one to identify individual crystalline domains but also it detects coherent clusters of a peculiar compact amorphous structure that is not space-filling and lacks any long-range order.
Language	English
Publishing date	2021-12-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	3113-6
ISSN	1089-7690 ; 0021-9606
ISSN (online)	1089-7690
ISSN	0021-9606
DOI	10.1063/5.0076915
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Article ; Online: Layer-by-layer assembly of patchy particles as a route to nontrivial structures.

Patra, Niladri / Tkachenko, Alexei V

Physical review. E

2017 Volume 96, Issue 2-1, Page(s) 22601

Abstract: We propose a strategy for robust high-quality self-assembly of nontrivial periodic structures out of patchy particles and investigate it with Brownian dynamics simulations. Its first element is the use of specific patch-patch and shell-shell interactions ...

Abstract	We propose a strategy for robust high-quality self-assembly of nontrivial periodic structures out of patchy particles and investigate it with Brownian dynamics simulations. Its first element is the use of specific patch-patch and shell-shell interactions between the particles, which can be implemented through differential functionalization of patched and shell regions with specific DNA strands. The other key element of our approach is the use of a layer-by-layer protocol that allows one to avoid the formation of undesired random aggregates. As an example, we design and self-assemble in silico a version of a double diamond lattice in which four particle types are arranged into bcc crystal made of four fcc sublattices. The lattice can be further converted to cubic diamond by selective removal of the particles of certain types. Our results demonstrate that by combining the directionality, selectivity of interactions, and the layer-by-layer protocol, a high-quality robust self-assembly can be achieved.
MeSH term(s)	Computer Simulation ; DNA/chemistry ; DNA/metabolism ; Dimerization ; Freezing ; Models, Molecular ; Nucleic Acid Conformation
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2017-08-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.96.022601
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Article ; Online: Structured sequences emerge from random pool when replicated by templated ligation.

Kudella, Patrick W / Tkachenko, Alexei V / Salditt, Annalena / Maslov, Sergei / Braun, Dieter

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 8

Abstract: The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error ... ...

Abstract	The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error threshold to avoid that replicated specific sequences become random because of the incorporated replication errors [M. Eigen,
MeSH term(s)	DNA-Directed DNA Polymerase/metabolism ; Evolution, Molecular ; Nucleic Acid Conformation ; Oligonucleotides/chemistry ; Origin of Life ; Templates, Genetic
Chemical Substances	Oligonucleotides ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2021-01-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2018830118
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