scholarly journals Reaction Networks as Systems for Resource Allocation: A Variational Principle for Their Non-Equilibrium Steady States

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e39849 ◽  
Author(s):  
Andrea De Martino ◽  
Daniele De Martino ◽  
Roberto Mulet ◽  
Guido Uguzzoni
2003 ◽  
Vol 15 (08) ◽  
pp. 905-923 ◽  
Author(s):  
TAKU MATSUI ◽  
YOSHIKO OGATA

We show that non-equilibrium steady states of the one-dimensional exactly-solved XX model can be characterized by the variational principle of free energy of a long range interaction and that they cannot be a KMS state for any C*-dynamical system of the UHF algebra.


Entropy ◽  
2021 ◽  
Vol 23 (1) ◽  
pp. 77
Author(s):  
Angus J. Dunnett ◽  
Alex W. Chin

Simulating the non-perturbative and non-Markovian dynamics of open quantum systems is a very challenging many body problem, due to the need to evolve both the system and its environments on an equal footing. Tensor network and matrix product states (MPS) have emerged as powerful tools for open system models, but the numerical resources required to treat finite-temperature environments grow extremely rapidly and limit their applications. In this study we use time-dependent variational evolution of MPS to explore the striking theory of Tamascelli et al. (Phys. Rev. Lett. 2019, 123, 090402.) that shows how finite-temperature open dynamics can be obtained from zero temperature, i.e., pure wave function, simulations. Using this approach, we produce a benchmark dataset for the dynamics of the Ohmic spin-boson model across a wide range of coupling strengths and temperatures, and also present a detailed analysis of the numerical costs of simulating non-equilibrium steady states, such as those emerging from the non-perturbative coupling of a qubit to baths at different temperatures. Despite ever-growing resource requirements, we find that converged non-perturbative results can be obtained, and we discuss a number of recent ideas and numerical techniques that should allow wide application of MPS to complex open quantum systems.


2021 ◽  
Author(s):  
Patrick S. Schwarz ◽  
Sudarshana Laha ◽  
Jacqueline Janssen ◽  
Tabea Huss ◽  
Job Boekhoven ◽  
...  

Non-equilibrium, fuel-driven reaction cycles serve as model systems of the intricate reaction networks of life. Rich and dynamic behavior is observed when reaction cycles regulate assembly processes, such as phase...


2018 ◽  
Vol 54 (5) ◽  
pp. 427-444 ◽  
Author(s):  
R. D. Astumian

Fluctuations favour state B = (B,B′) based on kinetic asymmetry combined with moderate dissipation rather than state A = (A,A′) in which the absolute amount of dissipation is greater but where there is no kinetic asymmetry.


2020 ◽  
Vol 58 (9) ◽  
pp. 2061-2093
Author(s):  
Michael F. Adamer ◽  
Martin Helmer

Abstract We study families of chemical reaction networks whose positive steady states are toric, and therefore can be parameterized by monomials. Families are constructed algorithmically from a core network; we show that if a family member is multistationary, then so are all subsequent networks in the family. Further, we address the questions of model selection and experimental design for families by investigating the algebraic dependencies of the chemical concentrations using matroids. Given a family with toric steady states and a constant number of conservation relations, we construct a matroid that encodes important information regarding the steady state behaviour of the entire family. Among other things, this gives necessary conditions for the distinguishability of families of reaction networks with respect to a data set of measured chemical concentrations. We illustrate our results using multi-site phosphorylation networks.


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