arXiv subjects

Koji Yonekura

Publications and source records attributed to Koji Yonekura.

3 recordsLinked to original sources

arXiv2026

Vesicle-surface-templated catalytic polymers drive differential growth in synthetic minimal cell variants

Understanding how life-like behaviors can emerge from simple molecular assemblies and primitive compartments remains a central challenge in origins-of-life research. Synthetic minimal cells provide a bottom-up platform for investigating, from scratch, the minimal physicochemical principles underlying compartment growth, reproduction, and evolution. Previously, we developed a vesicle/polymer-based compartment system in which the vesicle membranes template the formation of a catalytic polymer. This polymer promotes selective incorporation of amphiphiles into the vesicle membrane, driving vesicle growth while maintaining the compositional identity and enabling spontaneous deformation and division over several generations. Here, we report about experiments in which we advanced this system beyond reproduction by systematically constructing eight synthetic minimal cell variants from combinations of two template vesicles, two catalytic polymers, and two supplied amphiphiles. The variants exhibited distinct, composition-dependent vesicle growth responses, ranging from pronounced growth to suppressed growth or vesicle shrinkage. These growth responses were described by the Hill kinetics and characterized by three parameters, revealing a multi-dimensional fitness landscape shaped by environmental conditions, in which the relative advantage of each variant depends on both composition and amphiphile availability. This framework links molecular recognition, compositional inheritance, and differential growth, providing a physicochemical route toward evolvable synthetic minimal cells.

cond-mat.soft↗

arXiv2025

New metastable ice phases via supercooled water

Water exhibits rich polymorphism, where more than 20 crystalline phases have been experimentally reported. Five of them are metastable and form at low temperatures by either heating amorphous ice or degassing clathrate hydrates. However, such metastable phases rarely crystallise directly from liquid water, making it challenging to study metastable phase relations at relatively high temperatures. Here, we report that high-pressure metastable phases of ice, including two unknown phases named ices XXI and XXII, crystallise directly from liquid water in a deeply supercooled region around the homogeneous nucleation temperature. The key is to use emulsified water to stabilise supercooled water in laboratory timescales. Ices XXI and XXII are obtained by isothermal compression of emulsified water at 295 K and 250 K, respectively. Our powder x-ray and neutron diffraction analyses combined with molecular dynamics (MD) simulations revealed the surprisingly complex structures of these new phases with Z = 152 (ice XXI) and 304 (ice XXII). Ice XXI is topologically identical to 'ice T2' previously predicted by MD simulations, and our experimental structural model can be used as a benchmark for its structures in simulations, which depend on the force fields. On cooling, ice XXI transforms into an orientationally ordered counterpart named ice XXIII. Our results revealed the "hidden" structural complexity of water underlying the phase diagram, as implied by previous computational works. Further efforts at unveiling such metastable phase relations will bridge the large gaps between computational and experimental phase diagrams of water.

cond-mat.mtrl-sci↗

arXiv2013

Single-shot 3D structure determination of nanocrystals with femtosecond X-ray free electron laser pulses

Coherent diffraction imaging (CDI) using synchrotron radiation, X-ray free electron lasers (X-FELs), high harmonic generation, soft X-ray lasers, and optical lasers has found broad applications across several disciplines. An active research direction in CDI is to determine the structure of single particles with intense, femtosecond X-FEL pulses based on diffraction-before-destruction scheme. However, single-shot 3D structure determination has not been experimentally realized yet. Here we report the first experimental demonstration of single-shot 3D structure determination of individual nanocrystals using ~10 femtosecond X-FEL pulses. Coherent diffraction patterns are collected from high-index-faceted nanocrystals, each struck by a single X-FEL pulse. Taking advantage of the symmetry of the nanocrystal, we reconstruct the 3D structure of each nanocrystal from a single-shot diffraction pattern at ~5.5 nm resolution. As symmetry exists in many nanocrystals and virus particles, this method can be applied to 3D structure studies of such particles at nanometer resolution on femtosecond time scales.

physics.optics↗