1,984 research outputs found
Quantum scale biomimicry of low dimensional growth: An unusual complex amorphous precursor route to TiO2 band confinement by shape adaptive biopolymer-like flexibility for energy applications
Crystallization via an amorphous pathway is often preferred by biologically driven processes enabling living species to better regulate activation energies to crystal formation that are intrinsically linked to shape and size of dynamically evolving morphologies. Templated ordering of 3-dimensional space around amorphous embedded non-equilibrium phases at heterogeneous polymer-metal interfaces signify important routes for the genesis of low-dimensional materials under stress-induced polymer confinement. We report the surface induced catalytic loss of P=O ligands to bond activated aromatization of C-C C=C and Ti=N resulting in confinement of porphyrin-TiO(2 )within polymer nanocages via particle attachment. Restricted growth nucleation of TiO2 to the quantum scale (˂= 2 nm) is synthetically assisted by nitrogen, phosphine and hydrocarbon polymer chemistry via self-assembly. Here, the amorphous arrest phase of TiO, is reminiscent of biogenic amorphous crystal growth patterns and polymer coordination has both a chemical and biomimetic significance arising from quantum scale confinement which is atomically challenging. The relative ease in adaptability of non-equilibrium phases renders host structures more shape compliant to congruent guests increasing the possibility of geometrical confinement. Here, we provide evidence for synthetic biomimicry akin to bio-polymerization mechanisms to steer disorder-to-order transitions via solvent plasticization-like behaviour. This challenges the rationale of quantum driven confinement processes by conventional processes. Further, we show the change in optoelectronic properties under quantum confinement is intrinsically related to size that affects their optical absorption band energy range in DSSC.This work was supported by the National Research Foundation of Korea (NRF) grant funded by Korea government (MEST) NRF-2012R1A1A2008196, NRF 2012R1A2A2A01047189, NRF 2017R1A2B4008801, 2016R1D1A1A02936936, (NRF-2018R1A4A1059976, NRF-2018R1A2A1A13078704) and NRF Basic Research Programme in Science and Engineering by the Ministry of Education (No. 2017R1D1A1B03036226) and by the INDO-KOREA JNC program of the National Research Foundation of Korea Grant No. 2017K1A3A1A68. We thank BMSI (A*STAR) and NSCC for support. SJF is funded by grant IAF25 PPH17/01/a0/009 funded by A* STAR/NRF/EDB. CSV is the founder of a spinoff biotech Sinopsee Therapeutics. The current work has no conflicting interests with the company. We would like to express our very great appreciation to Ms. Hyoseon Kim for her technical expertise during HRTEM imaging
Field-control, phase-transitions, and life's emergence
Instances of critical-like characteristics in living systems at each
organizational level as well as the spontaneous emergence of computation
(Langton), indicate the relevance of self-organized criticality (SOC). But
extrapolating complex bio-systems to life's origins, brings up a paradox: how
could simple organics--lacking the 'soft matter' response properties of today's
bio-molecules--have dissipated energy from primordial reactions in a controlled
manner for their 'ordering'? Nevertheless, a causal link of life's macroscopic
irreversible dynamics to the microscopic reversible laws of statistical
mechanics is indicated via the 'functional-takeover' of a soft magnetic
scaffold by organics (c.f. Cairns-Smith's 'crystal-scaffold'). A
field-controlled structure offers a mechanism for bootstrapping--bottom-up
assembly with top-down control: its super-paramagnetic components obey
reversible dynamics, but its dissipation of H-field energy for aggregation
breaks time-reversal symmetry. The responsive adjustments of the controlled
(host) mineral system to environmental changes would bring about mutual
coupling between random organic sets supported by it; here the generation of
long-range correlations within organic (guest) networks could include SOC-like
mechanisms. And, such cooperative adjustments enable the selection of the
functional configuration by altering the inorganic network's capacity to assist
a spontaneous process. A non-equilibrium dynamics could now drive the
kinetically-oriented system towards a series of phase-transitions with
appropriate organic replacements 'taking-over' its functions.Comment: 54 pages, pdf fil
Dynamic Combinatorial Libraries: From Exploring Molecular Recognition to Systems Chemistry
Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.
The origins and physical roots of life’s dual – metabolic and genetic – nature
This review paper aims at a better understanding of the origin and physical foundation of life’s dual – metabolic and genetic – nature. First, I give a concise ‘top-down’ survey of the origin of life, i.e., backwards in time from extant DNA/RNA/protein-based life over the RNA world to the earliest, pre-RNA stages of life’s origin, with special emphasis on the metabolism-first versus gene/replicator-first controversy. Secondly, I critically assess the role of minerals in the earliest origins of bothmetabolism and genetics. And thirdly, relying on the work of Erwin Schrödinger, Carl Woese and Stuart Kauffman, I sketch and reframe the origin of metabolism and genetics from a physics, i.e., thermodynamics, perspective. I conclude that life’s dual nature runs all the way back to the very dawn and physical constitution of life on Earth. Relying on the current state of research, I argue that life’s origin stems from the congregation of two kinds of sources of negentropy – thermodynamic and statistical negentropy. While thermodynamic negentropy (which could have been provided by solar radiation and/or geochemical and thermochemical sources), led to life’s combustive and/or metabolic aspect, the abundant presence of mineral surfaces on the prebiotic Earth – with their selectively adsorbing and catalysing (thus ‘organizing’) micro-crystalline structure or order – arguably provided for statistical negentropy for life to originate, eventually leading to life’s crystalline and/or genetic aspect. However, the transition from a prebiotic world of relatively simple chemical compounds including periodically structured mineral surfaces towards the complex aperiodic and/or informational structure, specificity and organization of biopolymers and biochemical reaction sequences remains a ‘hard problem’ to solve
Peptide-Based Supramolecular Systems Chemistry
Peptide-based supramolecular systems chemistry seeks to mimic the ability of life forms to use conserved sets of building blocks and chemical reactions to achieve a bewildering array of functions. Building on the design principles for short peptide-based nanomaterials with properties, such as self-assembly, recognition, catalysis, and actuation, are increasingly available. Peptide-based supramolecular systems chemistry is starting to address the far greater challenge of systems-level design to access complex functions that emerge when multiple reactions and interactions are coordinated and integrated. We discuss key features relevant to systems-level design, including regulating supramolecular order and disorder, development of active and adaptive systems by considering kinetic and thermodynamic design aspects and combinatorial dynamic covalent and noncovalent interactions. Finally, we discuss how structural and dynamic design concepts, including preorganization and induced fit, are critical to the ability to develop adaptive materials with adaptive and tunable photonic, electronic, and catalytic properties. Finally, we highlight examples where multiple features are combined, resulting in chemical systems and materials that display adaptive properties that cannot be achieved without this level of integration
Remnants of an ancient metabolism without phosphate
Phosphate is essential for all living systems, serving as a building block of genetic and metabolic machinery. However, it is unclear how phosphate could have assumed these central roles on primordial Earth, given its poor geochemical accessibility. We used systems biology approaches to explore the alternative hypothesis that a protometabolism could have emerged prior to the incorporation of phosphate. Surprisingly, we identified a cryptic phosphate-independent core metabolism producible from simple prebiotic compounds. This network is predicted to support the biosynthesis of a broad category of key biomolecules. Its enrichment for enzymes utilizing iron-sulfur clusters, and the fact that thermodynamic bottlenecks are more readily overcome by thioester rather than phosphate couplings, suggest that this network may constitute a "metabolic fossil" of an early phosphate-free nonenzymatic biochemistry. Our results corroborate and expand previous proposals that a putative thioester-based metabolism could have predated the incorporation of phosphate and an RNA-based genetic system. PAPERCLIP
The Algorithmic Origins of Life
Although it has been notoriously difficult to pin down precisely what it is
that makes life so distinctive and remarkable, there is general agreement that
its informational aspect is one key property, perhaps the key property. The
unique informational narrative of living systems suggests that life may be
characterized by context-dependent causal influences, and in particular, that
top-down (or downward) causation -- where higher-levels influence and constrain
the dynamics of lower-levels in organizational hierarchies -- may be a major
contributor to the hierarchal structure of living systems. Here we propose that
the origin of life may correspond to a physical transition associated with a
shift in causal structure, where information gains direct, and
context-dependent causal efficacy over the matter it is instantiated in. Such a
transition may be akin to more traditional physical transitions (e.g.
thermodynamic phase transitions), with the crucial distinction that determining
which phase (non-life or life) a given system is in requires dynamical
information and therefore can only be inferred by identifying causal
architecture. We discuss some potential novel research directions based on this
hypothesis, including potential measures of such a transition that may be
amenable to laboratory study, and how the proposed mechanism corresponds to the
onset of the unique mode of (algorithmic) information processing characteristic
of living systems.Comment: 13 pages, 1 tabl
Insight into the esterase like activity demonstrated by an imidazole appended self-assembling hydrogelator
A low molecular weight hydrogelator with a covalently appended imidazole moiety is reported. Capable of percolating water in the pH range of 6 to 8, it proves to be an efficient catalyst upon self-assembly, showing Michaelis-Menten type kinetics. Activities at different pH values correlated with dramatic structural changes were observed. It can hydrolyse p-nitrophenyl acetate (pNPA) as well as inactivated esters, and l and d-phenylalanine methyl esters. The enhanced activity can be related to the conglomeration of catalytic groups upon aggregation resulting in their close proximity and the formation of hydrophobic pockets
Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks
Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed syn-ergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assembliesThe research was supported by the H2020 FET-Open (A.d.l.E and G.A.; CLASSY project, Grant Agreement Nº 862081), an NSF-BSF grant (GA; BSF-2015671), and the Spanish Ministry of Economy and Competitivity (A.d.l.E; MINECO: CTQ-2014-53673-P, CTQ-2017-89539-P, and EUIN2017-87022). The European COST Action CM1304 funded a Short-Term Scientific Mission of S.M.R. to BGU. A.K.B. received support from the BGU Kreitmann fellowships progra
Amyloid and the origin of life : self-replicating catalytic amyloids as prebiotic informational and protometabolic entities
A crucial stage in the origin of life was the emergence of the first molecular entity that was able to replicate, transmit information, and evolve on the early Earth. The amyloid world hypothesis posits that in the pre-RNA era, information processing was based on catalytic amyloids. The self-assembly of short peptides into beta-sheet amyloid conformers leads to extraordinary structural stability and novel multifunctionality that cannot be achieved by the corresponding nonaggregated peptides. The new functions include self-replication, catalytic activities, and information transfer. The environmentally sensitive template-assisted replication cycles generate a variety of amyloid polymorphs on which evolutive forces can act, and the fibrillar assemblies can serve as scaffolds for the amyloids themselves and for ribonucleotides proteins and lipids. The role of amyloid in the putative transition process from an amyloid world to an amyloid-RNA-protein world is not limited to scaffolding and protection: the interactions between amyloid, RNA, and protein are both complex and cooperative, and the amyloid assemblages can function as protometabolic entities catalyzing the formation of simple metabolite precursors. The emergence of a pristine amyloid-based in-put sensitive, chiroselective, and error correcting information-processing system, and the evolvement of mutualistic networks were, arguably, of essential importance in the dynamic processes that led to increased complexity, organization, compartmentalization, and, eventually, the origin of life.Peer reviewe
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