scholarly journals Dissipation-driven selection of states in non-equilibrium chemical networks

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Daniel Maria Busiello ◽  
Shiling Liang ◽  
Francesco Piazza ◽  
Paolo De Los Rios
Keyword(s):  
Deep Sea ◽  
Thermal Gradient ◽  
Dissipation Rate ◽  
Reaction Path ◽  
Individual State ◽  
Equilibrium Conditions ◽  
Simple Chemical ◽  
Equilibrium Chemical ◽  
Selection Of ◽  
Non Equilibrium

AbstractLife has most likely originated as a consequence of processes taking place in non-equilibrium conditions (e.g. in the proximity of deep-sea thermal vents) selecting states of matter that would have been otherwise unfavorable at equilibrium. Here we present a simple chemical network in which the selection of states is driven by the thermodynamic necessity of dissipating heat as rapidly as possible in the presence of a thermal gradient: states participating to faster reactions contribute the most to the dissipation rate, and are the most populated ones in non-equilibrium steady-state conditions. Building upon these results, we show that, as the complexity of the chemical network increases, the velocity of the reaction path leading to a given state determines its selection, giving rise to non-trivial localization phenomena in state space. A byproduct of our studies is that, in the presence of a temperature gradient, thermophoresis-like behavior inevitably appears depending on the transport properties of each individual state, thus hinting at a possible microscopic explanation of this intriguing yet still not fully understood phenomenon.

scholarly journals Non-equilibrium conditions inside rock pores drive fission, maintenance and selection of coacervate protocells

2021 ◽  
Author(s):  
Alan Ianeselli ◽  
Damla Tetiker ◽  
Julian Stein ◽  
Alexandra Kuehnlein ◽  
Christof Mast ◽  
...  
Keyword(s):  
Gas Bubbles ◽  
Early Evolution ◽  
Early Earth ◽  
Biochemical Reactions ◽  
Equilibrium Conditions ◽  
Daughter Cells ◽  
Complex Coacervate ◽  
Selection Of ◽  
Non Equilibrium

Key requirements for the first cells on Earth include the ability to compartmentalize and evolve. Compartmentalization spatially localizes biomolecules from a dilute pool and an evolving cell which grows and divides permits mixing and propagation of information to daughter cells. Complex coacervate micro-droplets are excellent candidates as primordial cells with the ability to partition and concentrate molecules into their core and support primitive and complex biochemical reactions. However, the evolution of coacervate protocells by fusion, growth and fission has not yet been demonstrated. In this work, a primordial environment initiated the evolution of coacervate-based protocells. Gas bubbles inside heated rock pores perturb the coacervate protocell distribution and drive the growth, fusion, division and selection of coacervate microdroplets. This setting provides a primordial non-equilibrium environment. Our findings describe how common gas bubbles within heated rock pores induce the early evolution processes of coacervate-based protocells, providing a compelling scenario for the evolution of membrane-free coacervate microdroplets on the early Earth.

scholarly journals Non-equilibrium conditions inside rock pores drive fission, maintenance and selection of coacervate protocells

2021 ◽  
Author(s):  
Alan Ianeselli ◽  
Damla Tetiker ◽  
Julian Stein ◽  
Alexandra Kühnlein ◽  
Christof B. Mast ◽  
...  
Keyword(s):  
Gas Bubbles ◽  
Early Earth ◽  
Biochemical Reactions ◽  
Equilibrium Conditions ◽  
Daughter Cells ◽  
Complex Coacervate ◽  
Selection Of ◽  
Non Equilibrium

AbstractKey requirements for the first cells on Earth include the ability to compartmentalize and evolve. Compartmentalization spatially localizes biomolecules from a dilute pool and an evolving cell, which, as it grows and divides, permits mixing and propagation of information to daughter cells. Complex coacervate microdroplets are excellent candidates as primordial cells with the ability to partition and concentrate molecules into their core and support primitive and complex biochemical reactions. However, the evolution of coacervate protocells by fusion, growth and fission has not yet been demonstrated. In this work, a primordial environment initiated the evolution of coacervate-based protocells. Gas bubbles inside heated rock pores perturb the coacervate protocell distribution and drive the growth, fusion, division and selection of coacervate microdroplets. Our findings provide a compelling scenario for the evolution of membrane-free coacervate microdroplets on the early Earth, induced by common gas bubbles within heated rock pores.

scholarly journals A time-domain phase diagram of metastable states in a charge ordered quantum material

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jan Ravnik ◽  
Michele Diego ◽  
Yaroslav Gerasimenko ◽  
Yevhenii Vaskivskyi ◽  
Igor Vaskivskyi ◽  
...  
Keyword(s):  
Phase Diagram ◽  
Time Domain ◽  
Metastable States ◽  
Scanning Tunneling ◽  
Photon Density ◽  
Tunneling Microscopy ◽  
Equilibrium Conditions ◽  
Time Resolved ◽  
A Charge ◽  
Non Equilibrium

AbstractMetastable self-organized electronic states in quantum materials are of fundamental importance, displaying emergent dynamical properties that may be used in new generations of sensors and memory devices. Such states are typically formed through phase transitions under non-equilibrium conditions and the final state is reached through processes that span a large range of timescales. Conventionally, phase diagrams of materials are thought of as static, without temporal evolution. However, many functional properties of materials arise as a result of complex temporal changes in the material occurring on different timescales. Hitherto, such properties were not considered within the context of a temporally-evolving phase diagram, even though, under non-equilibrium conditions, different phases typically evolve on different timescales. Here, by using time-resolved optical techniques and femtosecond-pulse-excited scanning tunneling microscopy (STM), we track the evolution of the metastable states in a material that has been of wide recent interest, the quasi-two-dimensional dichalcogenide 1T-TaS2. We map out its temporal phase diagram using the photon density and temperature as control parameters on timescales ranging from 10−12 to 103 s. The introduction of a time-domain axis in the phase diagram enables us to follow the evolution of metastable emergent states created by different phase transition mechanisms on different timescales, thus enabling comparison with theoretical predictions of the phase diagram, and opening the way to understanding of the complex ordering processes in metastable materials.

scholarly journals Deep-sea amphipods around cobalt-rich ferromanganese crusts: Taxonomic diversity and selection of candidate species for connectivity analysis

PLoS ONE ◽  
2020 ◽  
Vol 15 (2) ◽  
pp. e0228483
Author(s):  
Akira Iguchi ◽  
Miyuki Nishijima ◽  
Yuki Yoshioka ◽  
Aika Miyagi ◽  
Ryuichi Miwa ◽  
...  
Keyword(s):  
Deep Sea ◽  
Taxonomic Diversity ◽  
Connectivity Analysis ◽  
Ferromanganese Crusts ◽  
Candidate Species ◽  
Selection Of

A Theoretical Study of the Temperature Gradient Effect on the Soret Coefficient in n-Pentane/n-Decane Mixtures Using Non-Equilibrium Molecular Dynamics

2020 ◽  
Vol 45 (4) ◽  
pp. 319-332
Author(s):  
Xiaoyu Chen ◽  
Ruquan Liang ◽  
Yong Wang ◽  
Ziqi Xia ◽  
Lichun Wu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Temperature Gradient ◽  
Thermal Gradient ◽  
Linear Response ◽  
Theoretical Study ◽  
Soret Coefficient ◽  
Thermal Gradients ◽  
Gradient Effect ◽  
Non Equilibrium Molecular Dynamics ◽  
Non Equilibrium

AbstractThe effect of the temperature gradient on the Soret coefficient in n-pentane/n-decane (n-C5/n-C10) mixtures was investigated using non-equilibrium molecular dynamics (NEMD) with the heat exchange (eHEX) algorithm. n-Pentane/n-decane mixtures with three different compositions (0.25, 0.5, and 0.75 mole fractions, respectively) and the TraPPE-UA force field were used in computing the Soret coefficient ({S_{T}}) at 300 K and 1 atm. Added/removed heat quantities (ΔQ) of 0.002, 0.004, 0.006, 0.008, and 0.01 kcal/mol were employed in eHEX processes in order to study the effect of different thermal gradients on the Soret coefficient. Moreover, a phenomenological description was applied to discuss the mechanism of this effect. Present results show that the Soret coefficient values firstly fluctuate violently and then become increasingly stable with increasing ΔQ (especially in the mixture with a mole fraction of 0.75), which means that ΔQ has a smaller effect on the Soret coefficient when the temperature gradient is higher than a certain thermal gradient. Thus, a high temperature gradient is recommended for calculating the Soret coefficient under the conditions that a linear response and constant phase are ensured in the system. In addition, the simulated Soret coefficient obtained at the highest ΔQ within three different compositions is in great agreement with experimental data.

Emergence of a Promiscuous Peroxidase Under Non‐Equilibrium Conditions

2021 ◽  
Author(s):  
Sumit Pal ◽  
Antara Reja ◽  
Subhajit Bal ◽  
Baishakhi Tikader ◽  
Dibyendu Das
Keyword(s):  
Equilibrium Conditions ◽  
Non Equilibrium

scholarly journals Quantification of fast molecular adhesion by fluorescence footprinting

2021 ◽  
Author(s):  
Adam B. Yasunaga ◽  
Isaac T.S. Li
Keyword(s):  
Shear Stress ◽  
Dynamic Range ◽  
Force Distribution ◽  
Equilibrium Conditions ◽  
Ligand Dissociation ◽  
Molecular Adhesion ◽  
Molecular Force ◽  
Adhesion Complex ◽  
Non Equilibrium

AbstractRolling adhesion is a unique process in which the adhesion events are short-lived and operate under highly non-equilibrium conditions. These characteristics pose a challenge in molecular force quantification, where in situ measurement of such forces cannot be achieved with most molecular force sensors that probe near equilibrium. In this report, we demonstrated a quantitative adhesion footprint assay combining DNA-based non-equilibrium force probes and modelling to measure the molecular force involved in fast rolling adhesion. We were able to directly profile the ensemble molecular force distribution during rolling adhesion with a dynamic range between 0 – 18 pN. Our results showed that the shear stress driving bead rolling motility directly controls the molecular tension on the probe-conjugated adhesion complex. Furthermore, the shear stress can steer the dissociation bias of components within the molecular force probe complex, favouring either DNA probe dissociation or receptor-ligand dissociation.

scholarly journals Dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis revealed by its hologenome

2020 ◽  
Author(s):  
Yi Lan ◽  
Jin Sun ◽  
Chong Chen ◽  
Yanan Sun ◽  
Yadong Zhou ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Snail Host ◽  
Bacterial Symbionts ◽  
Mutualistic Relationship ◽  
Genomic Studies ◽  
Similar Depth ◽  
Selection Of ◽  
Chromosome Level

AbstractAnimals endemic to deep-sea hydrothermal vents often form obligatory relationships with bacterial symbionts, maintained by intricate host-symbiont interactions. Endosymbiosis with more than one symbiont is uncommon, and most genomic studies focusing on such ‘dual symbiosis’ systems have not investigated the host and the symbionts to a similar depth simultaneously. Here, we report a novel dual symbiosis among the peltospirid snail Gigantopelta aegis and its two Gammaproteobacteria endosymbionts – one being a sulphur oxidiser and the other a methane oxidiser. We assembled high-quality genomes for all three parties of this holobiont, with a chromosome-level assembly for the snail host (1.15 Gb, N50 = 82 Mb, 15 pseudo-chromosomes). In-depth analyses of these genomes reveal an intimate mutualistic relationship with complementarity in nutrition and metabolic codependency, resulting in a system highly versatile in transportation and utilisation of chemical energy. Moreover, G. aegis has an enhanced immune capability that likely facilitates the possession of more than one type of symbiont. Comparisons with Chrysomallon squamiferum, another chemosymbiotic snail in the same family but only with one sulphur-oxidising endosymbiont, show that the two snails’ sulphur-oxidising endosymbionts are phylogenetically distant, agreeing with previous results that the two snails have evolved endosymbiosis independently and convergently. Notably, the same capabilities of biosynthesis of specific nutrition lacking in the host genome are shared by the two sulphur-oxidising endosymbionts of the two snail genera, which may be a key criterion in the selection of symbionts by the hosts.

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