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result(s) for
"pathway complexity"
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A probabilistic framework for identifying biosignatures using Pathway Complexity
by
Cronin, Leroy
,
Murray, Alastair R. G.
,
Marshall, Stuart M.
in
Abundance
,
Biological activity
,
Biology
2017
One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from non-living material assemblies. Many complex artefacts, from ordinary bioproducts to human tools, though they are not living things, are ultimately produced by biological processes-whether those processes occur at the scale of cells or societies, they are the consequences of living systems. While these objects are not living, they cannot randomly form, as they are the product of a biological organism and hence are either technological or cultural biosignatures. A generalized approach that aims to evaluate complex objects as possible biosignatures could be useful to explore the cosmos for new life forms. However, it is not obvious how it might be possible to create such a self-contained approach. This would require us to prove rigorously that a given artefact is too complex to have formed by chance. In this paper, we present a new type of complexity measure, which we call 'Pathway Complexity', that allows us not only to threshold the abiotic-biotic divide, but also to demonstrate a probabilistic approach based on object abundance and complexity which can be used to unambiguously assign complex objects as biosignatures. We hope that this approach will not only open up the search for biosignatures beyond the Earth, but also allow us to explore the Earth for new types of biology, and to determine when a complex chemical system discovered in the laboratory could be considered alive.
This article is part of the themed issue ‘Reconceptualizing the origins of life’.
Journal Article
Progress in Precision Synthesis of Supramolecular Copolymers
by
Satheesan, Sudheeshma
,
Kalathil, Krishnan Kartha
,
Gopalakrishnan, Anjali K.
in
copolymers
,
donor–acceptor
,
pathway complexity
2025
Supramolecular copolymerization has emerged as a promising tool to organize multiple components in solution. Theoretically, mixing more than one component in solution can lead to different architectures, such as narcissistic, social, blocky, and random. However, controlling the formation of a specific copolymer structure during supramolecular copolymerization remains elusive, owing to the dynamic and reversible nature of non‐covalent interactions between the constituent monomers, which facilitate rapid monomer exchange and reorganization in solution. Recent breakthroughs in the synthesis of supramolecular polymers have provided detailed mechanistic insights into supramolecular polymerization, enabling precise control over the size and morphology of the resulting assemblies. Leveraging these mechanistic insights, several attempts have been made to control supramolecular copolymerization. Rational molecular design strategies have been employed to achieve the exclusive synthesis of social and narcissistic copolymers. Conversely, tuning the subtle interplay between homo‐ and hetero‐recognition of structurally matched monomers enabled the selective formation of block copolymers. In this review, we provide an overview of rational design principles and synthetic strategies enabling the precision synthesis of supramolecular copolymers.
Supramolecular copolymerization is a promising strategy for developing functional organic materials with emergent properties and applications, which are inaccessible from single‐component self‐assembly. In this proposed review, we summarize the recent advancements in the precision synthesis of supramolecular copolymers in solution.
Journal Article
The Mastigamoeba balamuthi Genome and the Nature of the Free-Living Ancestor of Entamoeba
2021
The transition of free-living organisms to parasitic organisms is a mysterious process that occurs in all major eukaryotic lineages. Parasites display seemingly unique features associated with their pathogenicity; however, it is important to distinguish ancestral preconditions to parasitism from truly new parasite-specific functions. Here, we sequenced the genome and transcriptome of anaerobic free-living Mastigamoeba balamuthi and performed phylogenomic analysis of four related members of the Archamoebae, including Entamoeba histolytica, an important intestinal pathogen of humans. We aimed to trace gene histories throughout the adaptation of the aerobic ancestor of Archamoebae to anaerobiosis and throughout the transition from a free-living to a parasitic lifestyle. These events were associated with massive gene losses that, in parasitic lineages, resulted in a reduction in structural features, complete losses of some metabolic pathways, and a reduction in metabolic complexity. By reconstructing the features of the common ancestor of Archamoebae, we estimated preconditions for the evolution of parasitism in this lineage. The ancestor could apparently form chitinous cysts, possessed proteolytic enzyme machinery, compartmentalized the sulfate activation pathway in mitochondrion-related organelles, and possessed the components for anaerobic energy metabolism. After the split of Entamoebidae, this lineage gained genes encoding surface membrane proteins that are involved in host–parasite interactions. In contrast, gene gains identified in the M. balamuthi lineage were predominantly associated with polysaccharide catabolic processes. A phylogenetic analysis of acquired genes suggested an essential role of lateral gene transfer in parasite evolution (Entamoeba) and in adaptation to anaerobic aquatic sediments (Mastigamoeba).
Journal Article
Revealing Pathway Complexity and Helical Inversion in Supramolecular Assemblies Through Solvent‐Induced Radical Disparities
2024
New insights are raised to interpret pathway complexity in the supramolecular assembly of chiral triarylamine tris‐amide (TATA) monomer. In cosolvent systems, the monomer undergoes entirely different assembly processes depending on the chemical feature of the two solvents. Specifically, 1,2‐dichloroethane (DCE) and methylcyclohexane (MCH) cosolvent trigger the cooperative growth of monomers with M helical arrangement, and hierarchical thin nanobelts are further formed. But in DCE and hexane (HE) combination, a different pathway occurs where monomers go through isodesmic growth to generate twisted nanofibers with P helical arrangement. Moreover, the two distinct assemblies exhibit opposite excited‐state chirality. The driving force for both assemblies is the formation of intermolecular hydrogen bonds between amide moieties. However, the mechanistic investigation indicates that radical and neutral triarylamine species go through distinct assembly phases by changing solvent structures. The neutralization of radicals in MCH plays a critical role in pathway complexity, which significantly impacts the overall supramolecular assembly process, giving rise to inversed supramolecular helicity and distinct morphologies. This differentiation in pathways affected by radicals provides a new approach to manipulate chiral supramolecular assembly process by facile solvent–solute interactions.
Pathway complexity and helical inversion of chiral triarylamine assembly is investigated. In different solvents, monomer undergoes isodesmic and cooperative growth separately, and 1D supramolecular assemblies with opposite helicity are constructed. Mechanistic study reveals that compared with radical form in linear alkanes, monomers are neutralized by cycloalkanes, thus triggering a distinct pathway.
Journal Article
Pathway Complexity in Supramolecular Polymerization of Porphyrin Dyads for Kinetic Control of Helicity
by
Lee, Hosoowi
,
Kim, Jiwon
,
Kim, Dong Ha
in
circular dichroism
,
circularly polarized luminescence
,
Cooling
2025
ABSTRACT
The supramolecular polymerization of porphyrin dyad (PD) shows the pathway complexity leading to the formation of kinetically metastable nanoparticles (PDParticle) through rapid cooling and thermodynamically stable fibrous supramolecular polymers (PDFiber) through slow cooling. The kinetically metastable PDParticle is gradually transformed to the thermodynamically stable PDFiber. Due to the inherent achirality of PD, AFM images exhibited a random distribution of both M and P helices. Introducing chiral alkyl chains achieved a predominant helicity in PDFiber, with (S)‐PD favoring M helices and (R)‐PD favoring P helices. The addition of chiral 2‐methyl pyrrolidine (MePy) further influences this transformation by retarding the transition from PDParticle to PDFiber through axial coordination with the zinc porphyrin units, affecting the helicity of the resulting supramolecular polymer. By manipulating the cooling rates and environmental conditions, we demonstrate the reversible control over circular dichroism (CD) and circularly polarized luminescence (CPL), providing insight into the relationship between structural chirality and optical activity.
Supramolecular polymerization of porphyrin dyads (PDs) forms kinetically stable nanoparticles (PDParticle) via rapid cooling and thermodynamically stable fibrous polymers (PDFiber) via slow cooling. PDParticle gradually transforms into PDFiber. Introducing chiral alkyl chains induces helicity, with (S)‐PD favoring M helices and (R)‐PD favoring P helices. Chiral 2‐methyl pyrrolidine (MePy) retards this transition via axial coordination. Cooling rates and conditions enable reversible control of CD and CPL.
Journal Article
Controlled Supramolecular Polymerization of d8 Metal Complexes through Pathway Complexity and Seeded Growth
by
Fernández, Gustavo
,
Ghosh, Goutam
,
Ghosh, Tanwistha
in
d8 metal complexes
,
pathway complexity
,
self-assembly
2020
In recent years, pathway complexity has been studied in detail for a large variety of organic and π‐conjugated molecules. However, such investigations on their metal‐containing analogues have received only little attention to date, despite the well‐known potential of metal complexes in various fields. In this Minireview, we have collected recent examples of d8 metal complexes (Pt(II), Pd(II) and Au(III) complexes) exhibiting controlled supramolecular polymerization through pathway complexity and seeded‐growth approaches. Controlling the competing thermodynamic vs. kinetic pathways in these systems should help develop advanced metallosupramolecular functional materials with excellent photophysical, electronic, magnetic, catalytic, and biomedical applications.
In this Minireview, recent examples are presented of d8 metal complexes that exhibit competing kinetic and thermodynamic pathways, a property that has been exploited to control the length of supramolecular polymers via the seed‐induced living approach. Kinetically controlled products in these systems can be achieved by modulation of various experimental conditions (solvent composition, temperature, concentration, etc.) as well as by molecular design. The understanding gained from these studies may pave the way to sophisticated metallosupramolecular assemblies with tunable size and shape and exciting optical and electronic properties.
Journal Article
Continuous- versus Segmented-Flow Microfluidic Synthesis in Materials Science
by
Gonidec, Mathieu
,
Puigmartí-Luis, Josep
in
Chemical Sciences
,
Composite materials
,
Continuous flow
2019
Materials science is a fast-evolving area that aims to uncover functional materials with ever more sophisticated properties and functions. For this to happen, new methodologies for materials synthesis, optimization, and preparation are desired. In this context, microfluidic technologies have emerged as a key enabling tool for a low-cost and fast prototyping of materials. Their ability to screen multiple reaction conditions rapidly with a small amount of reagent, together with their unique physico-chemical characteristics, have made microfluidic devices a cornerstone technology in this research field. Among the different microfluidic approaches to materials synthesis, the main contenders can be classified in two categories: continuous-flow and segmented-flow microfluidic devices. These two families of devices present very distinct characteristics, but they are often pooled together in general discussions about the field with seemingly little awareness of the major divide between them. In this perspective, we outline the parallel evolution of those two sub-fields by highlighting the key differences between both approaches, via a discussion of their main achievements. We show how continuous-flow microfluidic approaches, mimicking nature, provide very finely-tuned chemical gradients that yield highly-controlled reaction–diffusion (RD) areas, while segmented-flow microfluidic systems provide, on the contrary, very fast homogenization methods, and therefore well-defined super-saturation regimes inside arrays of micro-droplets that can be manipulated and controlled at the milliseconds scale. Those two classes of microfluidic reactors thus provide unique and complementary advantages over classical batch synthesis, with a drive towards the rational synthesis of out-of-equilibrium states for the former, and the preparation of high-quality and complex nanoparticles with narrow size distributions for the latter.
Journal Article
Transient Supramolecular Hydrogels Formed by Aging‐Induced Seeded Self‐Assembly of Molecular Hydrogelators
2020
Here, transient supramolecular hydrogels that are formed through simple aging‐induced seeded self‐assembly of molecular gelators are reported. In the involved molecular self‐assembly system, multicomponent gelators are formed from a mixture of precursor molecules and, typically, can spontaneously self‐assemble into thermodynamically more stable hydrogels through a multilevel self‐sorting process. In the present work, it is surprisingly found that one of the precursor molecules is capable of self‐assembling into nano‐sized aggregates upon a gentle aging treatment. Importantly, these tiny aggregates can serve as seeds to force the self‐assembly of gelators along a kinetically controlled pathway, leading to transient hydrogels that eventually spontaneously convert into thermodynamically more stable hydrogels over time. Such an aging‐induced seeded self‐assembly process is not only a new route toward synthetic out‐of‐equilibrium supramolecular systems, but also suggests the necessity of reporting the age of self‐assembling building block solutions in other self‐assembly systems.
A simple aging‐induced seeded self‐assembly resulting in transient supramolecular hydrogels is reported. The obtained transient hydrogels can convert into the thermodynamically more stable state over time. The findings demonstrate a new route toward out‐of‐equilibrium self‐assembly system, and suggest the necessity of stating the ages of self‐assembling building blocks in some other supramolecular systems.
Journal Article
Long-Term Regional Landscape Change in the Northern Tequila Region of Jalisco, Mexico
by
Heredia Espinoza, Verenice Y.
in
Alternate pathways to complexity
,
diachronic change
,
full-coverage survey
2017
The Tequila Valleys, in Jalisco, Mexico, are well-known in archaeology for an early complex society known as the Teuchitlán tradition (350 b.c.-a.d. 450/500), but later developments have received little attention. Here I report on the first systematic, full-coverage survey of the Tequila region north of the Tequila volcano. I explore the ways in which the societies that occupied this territory experienced sociopolitical change diachronically by investigating settlement scale, integration, complexity, and boundedness. Through the use of these core features, I analyze how each changed in varying ways, resulting in patterns that do not conform to static societal categories. Interestingly, there is no evidence that a large polity controlled the entire region at any point in the sequence. Results indicate a dynamic sociopolitical landscape that did not develop along any predetermined pathway.
Journal Article
Complexities of health and care worker migration pathways and corresponding international reporting requirements
by
Bourgeault, Ivy L.
,
Walton-Roberts, Margaret
,
Spitzer, Denise L.
in
Agreements
,
Caregivers
,
Codes
2023
The increasing complexity of the migration pathways of health and care workers is a critical consideration in the reporting requirements of international agreements designed to address their impacts. There are inherent challenges across these different agreements including reporting functions that are misaligned across different data collection tools, variable capacity of country respondents, and a lack of transparency or accountability in the reporting process. Moreover, reporting processes often neglect to recognize the broader intersectional gendered and racialized political economy of health and care worker migration. We argue for a more coordinated approach to the various international reporting requirements and processes that involve building capacity within countries to report on their domestic situation in response to these codes and conventions, and internationally to make such reporting result in more than simply the sum of their responses, but to reflect cross-national and transnational interactions and relationships. These strategies would better enable policy interventions along migration pathways that would more accurately recognize the growing complexity of health worker migration leading to more effective responses to mitigate its negative effects for migrants, source, destination, and transit countries. While recognizing the multiple layers of complexity, we nevertheless reaffirm the fact that countries still have an ethical responsibility to undertake health workforce planning in their countries that does not overly rely on the recruitment of migrant health and care workers.
Journal Article