Thermodynamics and Statistical Mechanics of Small Systems

Puglisi, Andrea; Sarracino, Alessandro; Vulpiani, Angelo

doi:10.3390/e20060392

Cited by 12 publications

(9 citation statements)

References 24 publications

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“…Further challenges in defining mechanisms of condensate formation in vivo arise from the thermodynamics of small-number systems (containing only tens to hundreds of individual molecular species), where stochastic assembly state fluctuations become significant, as described elsewhere in this roadmap (see below in subsection The question of size) 154,155 . experimental findings such as rapid recovery of fluorescent signal after photobleaching are not sufficient to conclude a condensate forms via llPS, and single-molecule imaging can provide more detailed information 141 .…”

Section: Enhancing Activity Through Concentrating Enzymes and Substramentioning

confidence: 99%

“…Rather, transitions are broader, and intermediate states with intermediate compositions and densities exist. Stochastic fluctuations in assem bly, existence and size are also significant for small assemblies [155][156][157] . Thus, very small condensates need not be longlived and homogeneous, or form in switchlike fashion with changes in molecular concentration or environment.…”

Section: The Question Of Sizementioning

confidence: 99%

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A framework for understanding the functions of biomolecular condensates across scales

Lyon

Peeples

Rosen

2020

Nat Rev Mol Cell Biol

626

492

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Biomolecular condensates are found throughout eukaryotic cells, including in the nucleus, in the cytoplasm and on membranes. They are also implicated in a wide range of cellular functions, organizing molecules that act in processes ranging from RNA metabolism to signalling to gene regulation. Early work in the field focused on identifying condensates and understanding how their physical properties and regulation arise from molecular constituents. Recent years have brought a focus on understanding condensate functions. Studies have revealed functions that span different length scales: from molecular (modulating the rates of chemical reactions) to mesoscale (organizing large structures within cells) to cellular (facilitating localization of cellular materials and homeostatic responses). In this Roadmap, we discuss representative examples of biochemical and cellular functions of biomolecular condensates from the recent literature and organize these functions into a series of non-exclusive classes across the different length scales. We conclude with a discussion of areas of current interest and challenges in the field, and thoughts about how progress may be made to further our understanding of the widespread roles of condensates in cell biology.

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Section: Enhancing Activity Through Concentrating Enzymes and Substramentioning

confidence: 99%

Section: The Question Of Sizementioning

confidence: 99%

A framework for understanding the functions of biomolecular condensates across scales

Lyon

Peeples

Rosen

2020

Nat Rev Mol Cell Biol

626

492

View full text Add to dashboard Cite

show abstract

“…Moreover, even in moderate system size, say N = 64 for the Ehrenfest's model, the recurrence time becomes of the order of 2 64 , i.e., essentially infinity. Therefore, although irreversibility appears to be a consequence of thermodynamic limit, N → ∞, in practice even in moderate system size a thermodynamic statistical description appears to be the adequate one [4].…”

Section: Introductionmentioning

confidence: 99%

“…The node (3,2) has null neighborhood (its neighbors are marked by boxes), while the neighborhood of the node located at (1,4) is not null (its neighbors are marked by double boxes accordingly, to the toroidal lattice). So, the state φ(x) will have a -1 value at position (3,2) and a 1 value at position (1,4) that are also marked, with a box and a double box, respectively, in φ(x). In a similar way, all other values of φ(x) are obtained.…”

Section: Introductionmentioning

confidence: 99%

Phase space classification of an Ising cellular automaton: The Q2R model

Montalva-Medel

Rica

Urbina

2020

Chaos, Solitons & Fractals

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An exact characterization of the different dynamical behavior that exhibit the space phase of a reversible and conservative cellular automaton, the so called Q2R model, is shown in this paper. Q2R is a cellular automaton which is a dynamical variation of the Ising model in statistical physics and whose space of configurations grows exponentially with the system size. As a consequence of the intrinsic reversibility of the model, the phase space is composed only by configurations that belong to a fixed point or a limit cycle. In this work we classify them in four types accordingly to well differentiated topological characteristics. Three of them -which we call of type S-I, S-II and S-III-share a symmetry property, while the fourth, which we call of type AS, does not. Specifically, we prove that any configuration of Q2R belongs to one of the four previous limit cycles. Moreover, at a combinatorial level, we are able to determine the number of limit cycles for some small periods which are almost always present in the Q2R. Finally, we provide a general overview of the resulting decomposition of the arbitrary size Q2R phase space, in addition, we realize an exhaustive study of a small Ising system (4 × 4) which is fully analyzed under this new framework.

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“…In addition, small open systems display many special properties with respect to their macroscopic counterparts due to finite-size fluctuations, reduced dimensionality, boundary effects, disorder, etc. [ 2 , 3 ]. Among countless examples of applications, we may mention heat transfer in nanoscale systems and nanophononics [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

Dephasing-Assisted Macrospin Transport

Iubini

Borlenghi

Delin

et al. 2020

Entropy

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Transport phenomena are ubiquitous in physics, and it is generally understood that the environmental disorder and noise deteriorates the transfer of excitations. There are, however, cases in which transport can be enhanced by fluctuations. In the present work, we show, by means of micromagnetics simulations, that transport efficiency in a chain of classical macrospins can be greatly increased by an optimal level of dephasing noise. We also demonstrate the same effect in a simplified model, the dissipative Discrete Nonlinear Schrödinger equation, subject to phase noise. Our results point towards the realization of a large class of magnonics and spintronics devices, where disorder and noise can be used to enhance spin-dependent transport efficiency.

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Thermodynamics and Statistical Mechanics of Small Systems

Abstract: A challenging frontier in modern statistical physics is concerned with systems with a small number of degrees of freedom, far from the thermodynamic limit.[...]

Cited by 12 publications

References 24 publications

A framework for understanding the functions of biomolecular condensates across scales

A framework for understanding the functions of biomolecular condensates across scales

Phase space classification of an Ising cellular automaton: The Q2R model

Dephasing-Assisted Macrospin Transport

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