Translocation is a nonequilibrium process at all stages: Simulating the capture and translocation of a polymer by a nanopore

2016 ◽  
Vol 145 (15) ◽  
pp. 154902 ◽  
Author(s):  
Sarah C. Vollmer ◽  
Hendrick W. de Haan
Keyword(s):  
Nonequilibrium Process

Organization and Self-Assembly Away from Equilibrium: Toward Thermodynamic Design Principles

2021 ◽  
Vol 12 (1) ◽  
pp. 273-290
Author(s):  
Michael Nguyen ◽  
Yuqing Qiu ◽  
Suriyanarayanan Vaikuntanathan
Keyword(s):  
Energy Dissipation ◽  
Self Assembly ◽  
Biological Systems ◽  
Design Principles ◽  
Nonequilibrium Process ◽  
Nanoscale Materials ◽  
Stochastic Thermodynamics ◽  
Synthetic Materials ◽  
Starting Point

Studies of biological systems and materials, together with recent experimental and theoretical advances in colloidal and nanoscale materials, have shown how nonequilibrium forcing can be used to modulate organization in many novel ways. In this review, we focus on how an accounting of energy dissipation, using the tools of stochastic thermodynamics, can constrain and provide intuition for the correlations and configurations that emerge in a nonequilibrium process. We anticipate that the frameworks reviewed here can provide a starting point to address some of the unique phenomenology seen in biophysical systems and potentially replicate them in synthetic materials.

DYNAMICAL MODES OF POLYMER TRANSLOCATING THROUGH INTERACTING PORE UNDER CHEMICAL POTENTIAL DIFFERENCE

2011 ◽  
Vol 25 (25) ◽  
pp. 3345-3351 ◽  
Author(s):  
WEI-PING CAO ◽  
LI-ZHEN SUN ◽  
CHAO WANG ◽  
MENG-BO LUO
Keyword(s):  
Monte Carlo ◽  
Polymer Chain ◽  
Power Law ◽  
Chemical Potential ◽  
Monte Carlo Technique ◽  
Potential Difference ◽  
Nonequilibrium Process ◽  
Chemical Potential Difference ◽  
Translocation Time

The translocation of polymer chain through an interacting pore under chemical potential difference Δμ is simulated using Monte Carlo technique. Three translocation modes, dependent on the polymer–pore interaction ε and Δμ, are discovered. The translocation process is found to be an nonequilibrium process, which influences the dependence of translocation time τ on ε and Δμ. It is found that τ decreases in a power law relation with the increase of Δμ, and the exponent is dependent on the interaction.

Nonequilibrium process of magnetization switching influenced by thermal spin fluctuations

2007 ◽  
Vol 244 (12) ◽  
pp. 4486-4490 ◽  
Author(s):  
B. C. Choi ◽  
Y. K. Hong ◽  
J. Rudge ◽  
E. Girgis ◽  
J. Kolthammer ◽  
...  
Keyword(s):  
Spin Fluctuations ◽  
Nonequilibrium Process ◽  
Magnetization Switching

scholarly journals Study of Nonequilibrium Size and Concentration Effects on the Heat and Mass Diffusion of Indistinguishable Particles Using Steepest-Entropy-Ascent Quantum Thermodynamics

2017 ◽  
Vol 139 (12) ◽  
Author(s):  
Guanchen Li ◽  
Michael R. von Spakovsky
Keyword(s):  
Spatial Scales ◽  
Local Equilibrium ◽  
Phenomenological Approach ◽  
Mass Diffusion ◽  
Nonequilibrium Process ◽  
First Principle ◽  
Quantum Thermodynamics ◽  
Concentration Effects ◽  
Nonequilibrium Processes ◽  
Far From Equilibrium

Conventional first-principle approaches for studying nonequilibrium processes depend on the mechanics of individual particles or quantum states and as a result require many details of the mechanical features of the system to arrive at a macroscopic property. In contrast, thermodynamics, which has been successful in the stable equilibrium realm, provides an approach for determining macroscopic properties without the mechanical details. Nonetheless, this phenomenological approach is not generally applicable to a nonequilibrium process except in the near-equilibrium realm and under the local equilibrium and continuum assumptions, both of which limit its ability to describe nonequilibrium phenomena. Furthermore, predicting the thermodynamic features of a nonequilibrium process (of entropy generation) across all scales is difficult. To address these drawbacks, steepest-entropy-ascent quantum thermodynamics (SEAQT) can be used. It provides a first-principle thermodynamic-ensemble based approach applicable to the entire nonequilibrium realm even that far-from-equilibrium and does so with a single kinematics and dynamics, which crosses all temporal and spatial scales. Based on prior developments by the authors, SEAQT is used here to study the heat and mass diffusion of indistinguishable particles. The study focuses on the thermodynamic features of far-from-equilibrium state evolution, which is separated from the specific mechanics of individual particle interactions. Results for nonequilibrium size (volume) and concentration effects on the evolutionary state trajectory are presented for the case of high temperature and low particle concentration, which, however, do not impact the generality of the theory and will in future studies be relaxed.

Sign in / Sign up

Export Citation Format

Share Document