scholarly journals Thermodynamics of structure-forming systems

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jan Korbel ◽  
Simon David Lindner ◽  
Rudolf Hanel ◽  
Stefan Thurner
Keyword(s):  
Self Assembly ◽  
Fluctuation Theorem ◽  
Physical Systems ◽  
Patchy Particles ◽  
First Order Phase Transition ◽  
Low Concentrations ◽  
Gibbs Entropy ◽  
Large Systems ◽  
First Order Phase ◽  
Grand Canonical

AbstractStructure-forming systems are ubiquitous in nature, ranging from atoms building molecules to self-assembly of colloidal amphibolic particles. The understanding of the underlying thermodynamics of such systems remains an important problem. Here, we derive the entropy for structure-forming systems that differs from Boltzmann-Gibbs entropy by a term that explicitly captures clustered states. For large systems and low concentrations the approach is equivalent to the grand-canonical ensemble; for small systems we find significant deviations. We derive the detailed fluctuation theorem and Crooks’ work fluctuation theorem for structure-forming systems. The connection to the theory of particle self-assembly is discussed. We apply the results to several physical systems. We present the phase diagram for patchy particles described by the Kern-Frenkel potential. We show that the Curie-Weiss model with molecule structures exhibits a first-order phase transition.

scholarly journals Force generation by protein–DNA co-condensation

2021 ◽  
Author(s):  
Thomas Quail ◽  
Stefan Golfier ◽  
Maria Elsner ◽  
Keisuke Ishihara ◽  
Vasanthanarayan Murugesan ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Self Assembly ◽  
Spider Silk ◽  
Regulatory Elements ◽  
Heterochromatin Formation ◽  
First Order Phase Transition ◽  
Dna Strand ◽  
First Order Phase

AbstractInteractions between liquids and surfaces generate forces1,2 that are crucial for many processes in biology, physics and engineering, including the motion of insects on the surface of water3, modulation of the material properties of spider silk4 and self-assembly of microstructures5. Recent studies have shown that cells assemble biomolecular condensates via phase separation6. In the nucleus, these condensates are thought to drive transcription7, heterochromatin formation8, nucleolus assembly9 and DNA repair10. Here we show that the interaction between liquid-like condensates and DNA generates forces that might play a role in bringing distant regulatory elements of DNA together, a key step in transcriptional regulation. We combine quantitative microscopy, in vitro reconstitution, optical tweezers and theory to show that the transcription factor FoxA1 mediates the condensation of a protein–DNA phase via a mesoscopic first-order phase transition. After nucleation, co-condensation forces drive growth of this phase by pulling non-condensed DNA. Altering the tension on the DNA strand enlarges or dissolves the condensates, revealing their mechanosensitive nature. These findings show that DNA condensation mediated by transcription factors could bring distant regions of DNA into close proximity, suggesting that this physical mechanism is a possible general regulatory principle for chromatin organization that may be relevant in vivo.

Molecular Simulation of Adsorption of Simple Gases in Aluminophosphates and Pillared Clays

1992 ◽  
Vol 290 ◽  
Author(s):  
Roger Cracknell ◽  
Carolyn A Koh ◽  
Stephen M Thompson ◽  
Keith E Gubbins
Keyword(s):  
Qualitative Agreement ◽  
Pillared Clays ◽  
Inert Gases ◽  
Simulation Studies ◽  
Lennard Jones ◽  
First Order Phase Transition ◽  
Gcmc Simulation ◽  
Pillar Density ◽  
First Order Phase ◽  
Grand Canonical

AbstractWe report Grand Canonical Monte Carlo (GCMC) simulation studies of the adsorption and heat of adsorption of simple inert gases in two model microporous materials: aluminophosphates (AℓPO4-5, AℓPO4-8 and VPI-5) and alumina-pillared clays. The intermolecular potentials are spherical Lennard-Jones for both the fluid-fluid and fluid-solid interactions; both structured and structureless walls are considered. For argon in VPI-5 and AℓPO4-5 we find qualitative agreement with experiment, but the predicted maximum adsorption is about 20% higher than that obtained experimentally; possible reasons for this discrepancy are discussed. For the pillared clays we find a first order phase transition below some critical pillar density. This finding seems to be in qualitative agreement with existing experimental data.

Morphological studies of linear (AB)n multiblock copolymers and their blends

1992 ◽  
Vol 50 (1) ◽  
pp. 384-385
Author(s):  
Richard J. Spontak ◽  
Steven D. Smith ◽  
Arman Ashraf
Keyword(s):  
Electron Microscopy ◽  
Microphase Separation ◽  
Multiblock Copolymers ◽  
First Order ◽  
Morphological Studies ◽  
Transmission Electron ◽  
First Order Phase Transition ◽  
Covalently Bonded ◽  
Total Molecular Weight ◽  
First Order Phase

Block copolymers are composed of sequences of dissimilar chemical moieties covalently bonded together. If the block lengths of each component are sufficiently long and the blocks are thermodynamically incompatible, these materials are capable of undergoing microphase separation, a weak first-order phase transition which results in the formation of an ordered microstructural network. Most efforts designed to elucidate the phase and configurational behavior in these copolymers have focused on the simple AB and ABA designs. Few studies have thus far targeted the perfectly-alternating multiblock (AB)n architecture. In this work, two series of neat (AB)n copolymers have been synthesized from styrene and isoprene monomers at a composition of 50 wt% polystyrene (PS). In Set I, the total molecular weight is held constant while the number of AB block pairs (n) is increased from one to four (which results in shorter blocks). Set II consists of materials in which the block lengths are held constant and n is varied again from one to four (which results in longer chains). Transmission electron microscopy (TEM) has been employed here to investigate the morphologies and phase behavior of these materials and their blends.

scholarly journals Gravitational wave signals of dark matter freeze-out

2021 ◽  
Vol 2021 (2) ◽  
Author(s):  
Danny Marfatia ◽  
Po-Yan Tseng
Keyword(s):  
Phase Transition ◽  
Dark Matter ◽  
Gravitational Waves ◽  
Order Phase Transition ◽  
First Order ◽  
Stochastic Background ◽  
First Order Phase Transition ◽  
Relic Abundance ◽  
First Order Phase ◽  
Freeze Out

Abstract We study the stochastic background of gravitational waves which accompany the sudden freeze-out of dark matter triggered by a cosmological first order phase transition that endows dark matter with mass. We consider models that produce the measured dark matter relic abundance via (1) bubble filtering, and (2) inflation and reheating, and show that gravitational waves from these mechanisms are detectable at future interferometers.

scholarly journals Dark Matter production from relativistic bubble walls

2021 ◽  
Vol 2021 (3) ◽  
Author(s):  
Aleksandr Azatov ◽  
Miguel Vanvlasselaer ◽  
Wen Yin
Keyword(s):  
Phase Transition ◽  
Dark Matter ◽  
Electroweak Phase Transition ◽  
First Order ◽  
Matter Production ◽  
First Order Phase Transition ◽  
Relic Abundance ◽  
Higgs Portal ◽  
First Order Phase ◽  
Gravitational Background

Abstract In this paper we present a novel mechanism for producing the observed Dark Matter (DM) relic abundance during the First Order Phase Transition (FOPT) in the early universe. We show that the bubble expansion with ultra-relativistic velocities can lead to the abundance of DM particles with masses much larger than the scale of the transition. We study this non-thermal production mechanism in the context of a generic phase transition and the electroweak phase transition. The application of the mechanism to the Higgs portal DM as well as the signal in the Stochastic Gravitational Background are discussed.

scholarly journals Self-replication of a quantum artificial organism driven by single-photon pulses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daniel Valente
Keyword(s):  
Self Assembly ◽  
Artificial Life ◽  
Single Photon ◽  
Self Organization ◽  
Physical Systems ◽  
Self Organized ◽  
Living Organisms ◽  
A Chain ◽  
Thermodynamic Mechanism ◽  
Self Replication

AbstractImitating the transition from inanimate to living matter is a longstanding challenge. Artificial life has achieved computer programs that self-replicate, mutate, compete and evolve, but lacks self-organized hardwares akin to the self-assembly of the first living cells. Nonequilibrium thermodynamics has achieved lifelike self-organization in diverse physical systems, but has not yet met the open-ended evolution of living organisms. Here, I look for the emergence of an artificial-life code in a nonequilibrium physical system undergoing self-organization. I devise a toy model where the onset of self-replication of a quantum artificial organism (a chain of lambda systems) is owing to single-photon pulses added to a zero-temperature environment. I find that spontaneous mutations during self-replication are unavoidable in this model, due to rare but finite absorption of off-resonant photons. I also show that the replication probability is proportional to the absorbed work from the photon, thereby fulfilling a dissipative adaptation (a thermodynamic mechanism underlying lifelike self-organization). These results hint at self-replication as the scenario where dissipative adaptation (pointing towards convergence) coexists with open-ended evolution (pointing towards divergence).

scholarly journals Solving puzzles in deformed JT gravity: phase transitions and non-perturbative effects

2021 ◽  
Vol 2021 (4) ◽  
Author(s):  
Clifford V. Johnson ◽  
Felipe Rosso
Keyword(s):  
Phase Structure ◽  
Scalar Potential ◽  
String Equation ◽  
Two Dimensional ◽  
Leading Order ◽  
Classical Analysis ◽  
First Order ◽  
First Order Phase Transition ◽  
Definition Of ◽  
First Order Phase

Abstract Recent work has shown that certain deformations of the scalar potential in Jackiw-Teitelboim gravity can be written as double-scaled matrix models. However, some of the deformations exhibit an apparent breakdown of unitarity in the form of a negative spectral density at disc order. We show here that the source of the problem is the presence of a multi-valued solution of the leading order matrix model string equation. While for a class of deformations we fix the problem by identifying a first order phase transition, for others we show that the theory is both perturbatively and non-perturbatively inconsistent. Aspects of the phase structure of the deformations are mapped out, using methods known to supply a non-perturbative definition of undeformed JT gravity. Some features are in qualitative agreement with a semi-classical analysis of the phase structure of two-dimensional black holes in these deformed theories.

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