Proliferating coacervate droplets as the missing link between chemistry and biology in the origins of life

The hypothesis that prebiotic molecules were transformed into polymers that evolved into proliferating molecular assemblages and eventually a primitive cell was first proposed about 100 years ago. To the best of our knowledge, however, no model of a proliferating prebiotic system has yet been realised because different conditions are required for polymer generation and self-assembly. In this study, we identify conditions suitable for concurrent peptide generation and self-assembly, and we show how a proliferating peptide-based droplet could be created by using synthesised amino acid thioesters as prebiotic monomers. Oligopeptides generated from the monomers spontaneously formed droplets through liquid–liquid phase separation in water. The droplets underwent a steady growth–division cycle by periodic addition of monomers through autocatalytic self-reproduction. Heterogeneous enrichment of RNA and lipids within droplets enabled RNA to protect the droplet from dissolution by lipids. These results provide experimental constructs for origins-of-life research and open up directions in the development of peptide-based materials.

UnitCell Tools, a package to determine unit-cell parameters from a single electron diffraction pattern

Electron diffraction techniques in transmission electron microscopy (TEM) have been successfully employed for determining the unit-cell parameters of crystal phases, albeit they exhibit a limited accuracy compared with X-ray or neutron diffraction, and they often involve a tedious measurement procedure. Here, a new package for determining unit-cell parameters from a single electron diffraction pattern has been developed. The essence of the package is to reconstruct a 3D reciprocal primitive cell from a single electron diffraction pattern containing both zero-order Laue zone and high-order Laue zone reflections. Subsequently, the primitive cell can be reduced to the Niggli cell which, in turn, can be converted into the unit cell. Using both simulated and experimental patterns, we detail the working procedure and address some effects of experimental conditions (diffraction distortions, misorientation of the zone axis and the use of high-index zone axis) on the robustness and accuracy of the software developed. The feasibility of unit-cell determination of the TiO2 nanorod using this package is also demonstrated. Should the parallel-beam, nano-beam and convergent-beam modes of the TEM be used flexibly, the software can determine unit-cell parameters of unknown-structure crystallites (typically >50 nm).

Crystal Structure Prediction of the Novel Cr2SiN4 Compound via Global Optimization, Data Mining, and the PCAE Method

A number of studies have indicated that the implementation of Si in CrN can significantly improve its performance as a protective coating. As has been shown, the Cr-Si-N coating is comprised of two phases, where nanocrystalline CrN is embedded in a Si3N4 amorphous matrix. However, these earlier experimental studies reported only Cr-Si-N in thin films. Here, we present the first investigation of possible bulk Cr-Si-N phases of composition Cr2SiN4. To identify the possible modifications, we performed global explorations of the energy landscape combined with data mining and the Primitive Cell approach for Atom Exchange (PCAE) method. After ab initio structural refinement, several promising low energy structure candidates were confirmed on both the GGA-PBE and the LDA-PZ levels of calculation. Global optimization yielded six energetically favorable structures and five modifications possible to be observed in extreme conditions. Data mining based searches produced nine candidates selected as the most relevant ones, with one of them representing the global minimum in the Cr2SiN4. Additionally, employing the Primitive Cell approach for Atom Exchange (PCAE) method, we found three more promising candidates in this system, two of which are monoclinic structures, which is in good agreement with results from the closely related Si3N4 system, where some novel monoclinic phases have been predicted in the past.

Gauge-dependent topology in non-reciprocal hopping systems with pseudo-Hermitian symmetry

Energy conservation is not valid in non-Hermitian systems with gain/loss or non-reciprocity, which leads to various extraordinary resonant characteristics. Compared with Hermitian systems, the intersection of non-Hermitian physics and topology generates new phases that have not been observed in condensed-matter systems before. Here, utilizing the designed two-dimensional periodical model with non-reciprocal hopping terms, we show how to obtain both the ellipse-like or hyperbolic-like spectral degeneracy, the topological boundary modes and the bulk-boundary correspondence by the protection of time-reversal symmetry and pseudo-Hermitian symmetry. Notably, the boundary modes and bulk-boundary correspondence can simultaneously appear only for specific selection of the primitive cell, and we explored the analytical solution to verify such gauge-dependent topological behaviors. Our topolectrical circuit simulation provides a flexible approach to confirm the designed properties and clarify the crucial role of pseudo-Hermiticity on the stability of a practical system. In a broader view, our findings can be compared to other platforms such as meta-surface or photonic crystals, for the purpose on the control of resonant frequency and localization properties.

Cryptic surface-associated multicellularity emerges through cell adhesion and its regulation

The repeated evolution of multicellularity leads to a wide diversity of organisms, many of which are sessile, including land plants, many fungi, and colonial animals. Sessile organisms adhere to a surface for most of their lives, where they grow and compete for space. Despite the prevalence of surface-associated multicellularity, little is known about its evolutionary origin. Here, we introduce a novel theoretical approach, based on spatial lineage tracking of cells, to study this origin. We show that multicellularity can rapidly evolve from 2 widespread cellular properties: cell adhesion and the regulatory control of adhesion. By evolving adhesion, cells attach to a surface, where they spontaneously give rise to primitive cell collectives that differ in size, life span, and mode of propagation. Selection in favor of large collectives increases the fraction of adhesive cells until a surface becomes fully occupied. Through kin recognition, collectives then evolve a central-peripheral polarity in cell adhesion that supports a division of labor between cells and profoundly impacts growth. Despite this spatial organization, nascent collectives remain cryptic, lack well-defined boundaries, and would require experimental lineage tracking technologies for their identification. Our results suggest that cryptic multicellularity could readily evolve and originate well before multicellular individuals become morphologically evident.

Thermal oscillations enable reshuffling of genetic material in a primitive cell cycle

Self-assembling single-chain amphiphiles available in the prebiotic environment likely played a fundamental role in the advent of primitive cell cycles. However, the instability of prebiotic fatty acid-based membranes to temperature and pH seems to suggest that primitive cells could only host prebiotically-relevant processes in a narrow range of non-fluctuating environmental conditions. Here we propose a novel primitive cell cycle driven by environmental fluctuations, which enable the generation of daughter protocells with reshuffled content. A reversible membrane-to-oil phase transition accounts for the dissolution of fatty acid-based vesicles at high temperatures, and the concomitant release of genetic content. At low temperatures, fatty acid bilayers reassemble and encapsulate reshuffled genetic material in a new cohort of protocells. Notably, we find that our disassembly/reassembly cycle drives the emergence of functional RNA-containing primitive cells from parent non-functional compartments. Thus, by exploiting the intrinsic instability of prebiotic fatty acid vesicles, our results point at an environmentally-driven tunable primitive cell cycle, which supports the release and reshuffle of protocellular genetic and membrane components, potentially leading to a new generation of protocells with superior traits. In the absence of protocellular transport machinery, the environmentally-driven disassembly/assembly cycle proposed herein would have supported genetic content reshuffling transmitted to primitive cell progeny, hinting at a potential mechanism important to initiate Darwinian evolution of early lifeforms.

Rapid computation of effective conductivity of 2D composites by equivalent circuit and spectral methods

<abstract><p>This work presents models for homogenizing or finding the effective transport or mechanical properties of microscale composites formed from highly contrasting phases described on a grid. The methods developed here are intended for engineering applications where speed and geometrical flexibility are a premium. A canonical case that is mathematically challenging and yet can be applied to many realistic materials is a 4-phase 2-dimensional periodic checkerboard or tiling. While analytic solutions for calculating effective properties exist for some cases, versatile methods are needed to handle anisotropic and non-square grids. A reinterpretation and extension of an existing analytic solution that utilizes equivalent circuits is developed. The resulting closed-form expressions for effective conductivity are shown to be accurate within a few percent or better for multiple cases of interest. Secondly a versatile and efficient spectral method is presented as a solution to the 4-phase primitive cell with a variety of external boundaries. The spectral method expresses the solution to effective conductivity in terms of analytically derived eigenfunctions and numerically determined spectral coefficients. The method is validated by comparing to known solutions and can allow extensions to cases with no current analytic solution.</p></abstract>

Proliferating droplets formed via prebiotic polymerisation: the missing link between chemistry and biology on the origin of life

The hypothesis that prebiotic molecules were transformed into polymers that evolved into proliferating molecular assemblages and eventually a primitive cell was first proposed about a hundred years ago. However, no proliferating model prebiotic system has yet been realised because different conditions are required for polymer generation and self-assembly of polymers. In this study, we identified conditions suitable for concurrent peptide generation and self-assembly, and we showed how a proliferating peptide-based droplet could be created by using synthesised amino acid thioesters as prebiotic monomers. Oligopeptides generated from the monomers spontaneously formed droplets through liquid–liquid phase separation in water. The droplets underwent a steady growth–division cycle by periodic addition of monomers through autocatalytic self-reproduction. Heterogeneous enrichment of RNA and lipids within droplets enabled RNA to protect the droplet from dissolution by lipids. These results provide experimental platforms for origin-of-life research and open up novel directions in peptide-based material development.