We study the statistical underpinnings of life, in particular its increase in order and complexity over evolutionary time. We question some common assumptions about the thermodynamics of life. We ...recall that contrary to widespread belief, even in a closed system entropy growth can accompany an increase in macroscopic order. We view metabolism in living things as microscopic variables directly driven by the second law of thermodynamics, while viewing the macroscopic variables of structure, complexity and homeostasis as mechanisms that are entropically favored because they open channels for entropy to grow via metabolism. This perspective reverses the conventional relation between structure and metabolism, by emphasizing the role of structure for metabolism rather than the converse. Structure extends in time, preserving information along generations, particularly in the genetic code, but also in human culture. We argue that increasing complexity is an inevitable tendency for systems with these dynamics and explain this with the notion of metastable states, which are enclosed regions of the phase-space that we call “bubbles,” and channels between these, which are discovered by random motion of the system. We consider that more complex systems inhabit larger bubbles (have more available states), and also that larger bubbles are more easily entered and less easily exited than small bubbles. The result is that the system entropically wanders into ever-larger bubbles in the foamy phase space, becoming more complex over time. This formulation makes intuitive why the increase in order/complexity over time is often stepwise and sometimes collapses catastrophically, as in biological extinction.
Heterogeneous materials: metastable and non-ergodic internal structures Alexandrov, Dmitri V; Zubarev, Andrey Yu
Philosophical transactions of the Royal Society of London. Series A: Mathematical, physical, and engineering sciences,
04/2019, Letnik:
377, Številka:
2143
Journal Article
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This issue is concerned with structural and phase transitions in heterogeneous and composite materials, the effects of external magnetic fields on these phenomena and the macroscopic properties and ...behaviour of materials with isotropic and anisotropic internal structures. Using experimental, theoretical and computer methods, these transitions are studied at the atomic and mesoscopic levels. The fundamental specific feature of structural transitions in many heterogeneous media consists of the fact that these transitions are stacked for a long time in non-equilibrium states that appear due to either macroscopic dissipative processes (an alternating magnetic field or hydrodynamic flow, for instance) or system lifetime in a metastable state. It is important to explain and describe these transitional states using the general approach of non-equilibrium physical mechanics. The review and research articles in the issue will cover the whole spectrum of scales (from nano to macro) and materials (from metastable liquids to biological polymers) in order to exhibit recently developed trends in the field of heterogeneous materials. Atomistic modelling, structuring induced by external magnetic fields and hydrodynamic flows, metastable and non-ergodic states, mechanical properties and phenomena in heterogeneous materials-all these are covered. This article is part of the theme issue 'Heterogeneous materials: metastable and non-ergodic internal structures'.
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•Revealing the independent correlation of photochromism and PersL in the same material.•Achieving the largest coloration contrast and multicolor photochromism in ...inorganics.•Demonstrating application of the light-responsive materials in flexible electronics.
Photochromism and persistent luminescence (PersL) are two fascinating light-responsive effects in phosphors, both of which have found widespread applications in optical switching, optical anticounterfeiting and information storage. However, the relationship between photochromism and PersL has not been clarified, thus greatly limiting the use and design of the light-responsive materials in multifunctional applications. Herein, taking BaMgSiO4:Eu2+, TM (TM = transition metal: Fe, Co and Cr) as model materials, we first reveal that photochromism and PersL could be two independent photophysical effects, although they are both related to the charge carrier trapping/detrapping processes. Notably, photochromism and PersL show have different responses to light wavelengths, and the depth of traps involved in the two effects is also quite different. Moreover, by codoping different transition metal elements, we obtain the largest reflectance difference of ∼71 % among inorganic photochromic materials reported thus far, and demonstrate interesting multicolor photochromism, including magenta, golden and pink. Based on their distinct response to light and temperature, a multi-functionalized optical anticounterfeiting technology is proposed, which may open up a new avenue for applying the light-responsive materials in flexible electronics and wearable devices.
Computer simulations based on simplified representations are routinely used to explore the early steps of amyloid aggregation. However, when protein models with implicit solvent are employed, these ...simulations miss the effect of solvent induced correlations on the aggregation kinetics and lifetimes of metastable states. In this work, we apply the multi-scale Lattice Boltzmann Molecular Dynamics technique (LBMD) to investigate the initial aggregation phases of the amyloid Aβ16-22 peptide. LBMD includes naturally hydrodynamic interactions (HIs) via a kinetic on-lattice representation of the fluid kinetics. The peptides are represented by the flexible OPEP coarse-grained force field. First, we have tuned the essential parameters that control the coupling between the molecular and fluid evolutions in order to reproduce the experimental diffusivity of elementary species. The method is then deployed to investigate the effect of HIs on the aggregation of 100 and 1000 Aβ16-22 peptides. We show that HIs clearly impact the aggregation process and the fluctuations of the oligomer sizes by favouring the fusion and exchange dynamics of oligomers between aggregates. HIs also guide the growth of the leading largest cluster. For the 100 Aβ16-22 peptide system, the simulation of ∼300 ns allowed us to observe the transition from ellipsoidal assemblies to an elongated and slightly twisted aggregate involving almost the totality of the peptides. For the 1000 Aβ16-22 peptides, a system of unprecedented size at quasi-atomistic resolution, we were able to explore a branched disordered fibril-like structure that has never been described by other computer simulations, but has been observed experimentally.
We report on the direct observation of a nanostructural transformation from a twisted ribbon to a helical ribbon in supramolecular assemblies of peptide amphiphiles. Using cryogenic electron ...microscopy, a peptide amphiphile molecule containing aromatic residues was found to first assemble into short twisted ribbons in the time range of seconds, which then elongate in the time scale of minutes, and finally transform into helical ribbons over the course of weeks. By synthesizing an analogous molecule without the aromatic side groups, it was found that a cylindrical nanostructure is formed that does not undergo any transitions during the same time period. The study of metastable states in peptide aggregation can contribute to our understanding of amyloid-related diseases, such as Alzheimer’s disease.
The origin of water's anomalous properties has been debated for decades. Resolution of the problem is hindered by a lack of experimental data in a crucial region of temperatures,
, and pressures ...where supercooled water rapidly crystallizes-a region often referred to as "no man's land." A recently developed technique where water is heated and cooled at rates greater than 10
K/s now enables experiments in this region. Here, it is used to investigate the structural relaxation and crystallization of deeply supercooled water for 170 K <
< 260 K. Water's relaxation toward a new equilibrium structure depends on its initial structure with hyperquenched glassy water (HQW) typically relaxing more quickly than low-density amorphous solid water (LDA). For HQW and
> 230 K, simple exponential relaxation kinetics is observed. For HQW at lower temperatures, increasingly nonexponential relaxation is observed, which is consistent with the dynamics expected on a rough potential energy landscape. For LDA, approximately exponential relaxation is observed for
> 230 K and
< 200 K, with nonexponential relaxation only at intermediate temperatures. At all temperatures, water's structure can be reproduced by a linear combination of two, local structural motifs, and we show that a simple model accounts for the complex kinetics within this context. The relaxation time,
, is always shorter than the crystallization time,
For HQW, the ratio,
/
, goes through a minimum at ∼198 K where the ratio is about 60.
•Tungsten is an important metal as it is under consideration as a plasma-facing material in the thermonuclear experiment such as ITER.•Electron-impact ionization data is required to model tungsten ...impurities that may sputter into the fusion plasma.•This work present the new and the only theoretical electron-impact ionization data for W7+.•We demonstrated the importance of the metastable states, their contribution also should be considered for adjacent ions of tungsten.
In this paper, we present the electron-impact single ionization cross sections for W7+. The level-to-level distorted-wave method implemented in the flexible atomic code (FAC) was used for calculation. Contributions from direct ionization (DI) and excitation-autoionization (EA) processes are taken into account. Comparison between the results of previous experimental measurements and the present calculations show a prominent contribution from metastable states in the W7+ ion. We extended the theoretical analysis including level-to-level calculations from long-lived levels of the Cd4f135p6 ground configuration and excited, metastable Cd4f145p5, Cd4f135p55d and Cd4f145p45d configurations. Calculated results are in good agreement with experimental data when, within a statistical model, a 56% fraction of parent ions in the ground configuration is assumed.
•Relevant, robust and reliable benchmarks for viscous free-surface flows are proposed.•They include cases with steady, periodic and metastable responses.•Solved with meshfree and mesh-based schemes. ...Qualitative & quantitative agreement.•Metastable states on cylinder wake are investigated and found for the 3 solvers.•Deltaplus SPH variant is demonstrated necessary to model metastable states.
The question of whether it is possible to set relevant, robust and reliable benchmarks for viscous free-surface flows with complex free-surface dynamics is investigated in this work. The proposed method for finding an answer to this question consists of selecting three conditions leading to increasing flow complexity and to simulate them using three well established solvers based on diverse numerical techniques. In the three conditions, a submerged horizontal cylinder in an uniform current perpendicular to its axis is considered, the Reynolds number is fixed to 180, and the analysis is limited to a 2D framework. While the unbounded solution for such flow is well established, adding a free surface and setting the submergence ratio and the Froude number in certain ranges, challenging free-surface dynamics takes place. In the specific conditions selected, phenomena of increasing complexity are identified and studied with: (i) δ+-SPH, an enhanced version of the Smoothed Particle Hydrodynamics method, (ii) a single-phase Finite Volume scheme with a Level Set function for tracking the free-surface (LS-FVM), and (iii) a two-phase Finite Volume with a Volume-of-Fluid algorithm to treat the gas/liquid interface (VOF-FVM). It is shown that the test-cases, even being geometrically simple, present intricate complexities, such as alternate metastable states in the wake, linked to the strong non-linearities induced by the interactions between the wake’s vorticity and the free surface. It is also shown that the solvers considered are able to depict a consistent representation of these complex flows, useful as benchmarks for other solvers and methods. An additional research question, investigating whether the improvements of the δ+ variant of the SPH method are necessary for simulating specific aspects of the flows treated in the paper, is also posed and discussed.
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