scholarly journals Crooks Fluctuation Theorem for Single Polymer Dynamics in Time-Dependent Flows: Understanding Viscoelastic Hysteresis

Entropy ◽  
2021 ◽  
Vol 24 (1) ◽  
pp. 27
Author(s):  
Yuecheng Zhou ◽  
Folarin Latinwo ◽  
Charles M. Schroeder
Keyword(s):  
Single Molecule ◽  
Extensional Flow ◽  
Steady States ◽  
Fluctuation Theorem ◽  
Time Dependent ◽  
Polymer Dynamics ◽  
Nonequilibrium Steady States ◽  
Fluctuation Theorems ◽  
Wide Range ◽  
Crooks Fluctuation Theorem

Nonequilibrium work relations have fundamentally advanced our understanding of molecular processes. In recent years, fluctuation theorems have been extensively applied to understand transitions between equilibrium steady-states, commonly described by simple control parameters such as molecular extension of a protein or polymer chain stretched by an external force in a quiescent fluid. Despite recent progress, far less is understood regarding the application of fluctuation theorems to processes involving nonequilibrium steady-states such as those described by polymer stretching dynamics in nonequilibrium fluid flows. In this work, we apply the Crooks fluctuation theorem to understand the nonequilibrium thermodynamics of dilute polymer solutions in flow. We directly determine the nonequilibrium free energy for single polymer molecules in flow using a combination of single molecule experiments and Brownian dynamics simulations. We further develop a time-dependent extensional flow protocol that allows for probing viscoelastic hysteresis over a wide range of flow strengths. Using this framework, we define quantities that uniquely characterize the coil-stretch transition for polymer chains in flow. Overall, generalized fluctuation theorems provide a powerful framework to understand polymer dynamics under far-from-equilibrium conditions.

scholarly journals Proper effective temperature of nonequilibrium steady state

2020 ◽  
Vol 2020 (9) ◽  
Author(s):  
Hironori Hoshino ◽  
Shin Nakamura
Keyword(s):  
Steady State ◽  
Effective Temperature ◽  
Heat Bath ◽  
Steady States ◽  
Nonequilibrium Steady State ◽  
Nonequilibrium Steady States ◽  
Relativistic Systems ◽  
Wide Range

Abstract We define a proper effective temperature for relativistic nonequilibrium steady states (NESSs). A conventional effective temperature of NESSs is defined from the ratio of the fluctuation to the dissipation. However, NESSs have relative velocities to the heat bath in general, and hence the conventional effective temperature can be frame-dependent in relativistic systems. The proper effective temperature is introduced as a frame-independent (Lorentz-invariant) quantity that characterizes NESSs. We find that the proper effective temperature of NESSs is higher than the proper temperature of the heat bath in a wide range of holographic models even when the conventional effective temperature is lower than the temperature of the heat bath.

scholarly journals Vesicle dynamics in large amplitude oscillatory extensional flow

2021 ◽  
Vol 929 ◽  
Author(s):  
Charlie Lin ◽  
Dinesh Kumar ◽  
Channing M. Richter ◽  
Shiyan Wang ◽  
Charles M. Schroeder ◽  
...  
Keyword(s):  
Strain Rate ◽  
Time Scale ◽  
Large Amplitude ◽  
Extensional Flow ◽  
Boundary Integral ◽  
Time Dependent ◽  
Shape Transformation ◽  
Wide Range ◽  
Dynamical Regimes ◽  
Flow Frequency

Although the behaviour of fluid-filled vesicles in steady flows has been extensively studied, far less is understood regarding the shape dynamics of vesicles in time-dependent oscillatory flows. Here, we investigate the nonlinear dynamics of vesicles in large amplitude oscillatory extensional (LAOE) flows using both experiments and boundary integral (BI) simulations. Our results characterize the transient membrane deformations, dynamical regimes and stress response of vesicles in LAOE in terms of reduced volume (vesicle asphericity), capillary number ( ${Ca}$ , dimensionless flow strength) and Deborah number ( ${De}$ , dimensionless flow frequency). Results from single vesicle experiments are found to be in good agreement with BI simulations across a wide range of parameters. Our results reveal three distinct dynamical regimes based on vesicle deformation: pulsating, reorienting and symmetrical regimes. We construct phase diagrams characterizing the transition of vesicle shapes between pulsating, reorienting and symmetrical regimes within the two-dimensional Pipkin space defined by ${De}$ and ${Ca}$ . Contrary to observations on clean Newtonian droplets, vesicles do not reach a maximum length twice per strain rate cycle in the reorienting and pulsating regimes. The distinct dynamics observed in each regime result from a competition between the flow frequency, flow time scale and membrane deformation time scale. By calculating the particle stresslet, we quantify the nonlinear relationship between average vesicle stress and strain rate. Additionally, we present results on tubular vesicles that undergo shape transformation over several strain cycles. Broadly, our work provides new information regarding the transient dynamics of vesicles in time-dependent flows that directly informs bulk suspension rheology.

Fluctuation theorems from non-equilibrium Onsager-Machlup theory for a Brownian particle in a time-dependent harmonic potential

Open Physics ◽  
2009 ◽  
Vol 7 (3) ◽  
Author(s):  
Roberto Deza ◽  
Gonzalo Izús ◽  
Horacio Wio
Keyword(s):  
Probability Distribution ◽  
Brownian Particle ◽  
Functional Integral ◽  
Equilibrium States ◽  
Fluctuation Theorem ◽  
Time Dependent ◽  
Harmonic Potential ◽  
Fluctuation Theorems ◽  
Non Equilibrium

AbstractWe discuss the case of a Brownian particle which is harmonically bound and multiplicatively forced-namely bound by V(x,t)=1/2 a(t)x 2 where a(t)is externally controlled-as another instance that provides a generalization of Onsager-Machlup’s theory to non-equilibrium states, thus allowing establishment of several fluctuation theorems. In particular, we outline the derivation of a fluctuation theorem for work, through the calculation of the work probability distribution as a functional integral over stochastic trajectories.

Synthesis and Biological Evaluation of Novel 4,5,6,7-Tetrahydrobenzo[D]-Thiazol-2- Yl Derivatives Derived from Dimedone with Anti-Tumor, C-Met, Tyrosine Kinase and Pim-1 Inhibitions

2019 ◽  
Vol 19 (12) ◽  
pp. 1438-1453 ◽  
Author(s):  
Rafat M. Mohareb ◽  
Amr S. Abouzied ◽  
Nermeen S. Abbas
Keyword(s):  
Tyrosine Kinase ◽  
Tumor Cell ◽  
Cell Lines ◽  
Single Molecule ◽  
Anticancer Agents ◽  
Biological Evaluation ◽  
New Drugs ◽  
Tumor Cell Lines ◽  
Thiazole Derivatives ◽  
Wide Range

Background: Dimedone and thiazole moieties are privileged scaffolds (acting as primary pharmacophores) in many compounds that are useful to treat several diseases, mainly tropical infectious diseases. Thiazole derivatives are a very important class of compounds due to their wide range of pharmaceutical and therapeutic activities. On the other hand, dimedone is used to synthesize many therapeutically active compounds. Therefore, the combination of both moieties through a single molecule to produce heterocyclic compounds will produce excellent anticancer agents. Objective: The present work reports the synthesis of 47 new substances belonging to two classes of compounds: Dimedone and thiazoles, with the purpose of developing new drugs that present high specificity for tumor cells and low toxicity to the organism. To achieve this goal, our strategy was to synthesize a series of 4,5,6,7-tetrahydrobenzo[d]-thiazol-2-yl derivatives using the reaction of the 2-bromodimedone with cyanothioacetamide. Methods: The reaction of 2-bromodimedone with cyanothioacetamide gave the 4,5,6,7-tetrahydrobenzo[d]- thiazol-2-yl derivative 4. The reactivity of compound 4 towards some chemical reagents was observed to produce different heterocyclic derivatives. Results: A cytotoxic screening was performed to evaluate the performance of the new derivatives in six tumor cell lines. Thirteen compounds were shown to be promising toward the tumor cell lines which were further evaluated toward five tyrosine kinases. Conclusion: The results of antitumor screening showed that many of the tested compounds were of high inhibition towards the tested cell lines. Compounds 6c, 8c, 11b, 11d, 13b, 14b, 15c, 15g, 21b, 21c, 20d and 21d were the most potent compounds toward c-Met kinase and PC-3 cell line. The most promising compounds 6c, 8c, 11b, 11d, 13b, 14b, 15c, 15g, 20c, 20d, 21b, 21c and 21d were further investigated against tyrosine kinase (c-Kit, Flt-3, VEGFR-2, EGFR, and PDGFR). Compounds 6c, 11b, 11d, 14b, 15c, and 20d were selected to examine their Pim-1 kinase inhibition activity the results revealed that compounds 11b, 11d and 15c had high activities.

scholarly journals Matrix Product State Simulations of Non-Equilibrium Steady States and Transient Heat Flows in the Two-Bath Spin-Boson Model at Finite Temperatures

Entropy ◽  
2021 ◽  
Vol 23 (1) ◽  
pp. 77
Author(s):  
Angus J. Dunnett ◽  
Alex W. Chin
Keyword(s):  
Finite Temperature ◽  
Open Quantum Systems ◽  
Quantum Systems ◽  
Steady States ◽  
Matrix Product ◽  
Open Quantum ◽  
Matrix Product State ◽  
Wide Range ◽  
Boson Model ◽  
Non Equilibrium

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.

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