arXiv subjects

Kyogo Kawaguchi

Publications and source records attributed to Kyogo Kawaguchi.

27 records · Page 2Linked to original sources

arXiv2017

Dynamical Crossover in a Stochastic Model of Cell Fate Decision

We study the asymptotic behaviors of stochastic cell fate decision between proliferation and differentiation. We propose a model of a self-replicating Langevin system, where cells choose their fate (i.e. proliferation or differentiation) depending on local cell density. Based on this model, we propose a scenario for multi-cellular organisms to maintain the density of cells (i.e., homeostasis) through finite-ranged cell-cell interactions. Furthermore, we numerically show that the distribution of the number of descendant cells changes over time, thus unifying the previously proposed two models regarding homeostasis: the critical birth death process and the voter model. Our results provide a general platform for the study of stochastic cell fate decision in terms of nonequilibrium statistical mechanics.

cond-mat.stat-mech↗

arXiv2016

Nonequilibrium fluctuation response relation in a time scale separated system

We present a theoretical framework to analyze the violation of fluctuation-response relation (FRR) for any observable from a finite Markov system with two well-separated time scales. We find that, generally for both slow and fast observables, a broad plateau exists in the intermediate frequency region, which contributes to a finite hidden entropy production. Assuming that non-equilibrium behavior arises only from coupling of slow and fast processes, we find that, at large observation time scae, the effective temperature for a slow observable deviates only slightly from the bath temperature, accompanied by an emerging well-defined effective potential landscape, while the deviation is significant for a fast observable. Our study also identifies a wider range of applicability of the Harada-Sasa equality in Markov jumping systems.

cond-mat.stat-mech↗

arXiv2016

Entropy production of nano systems with timescale separation

Energy flow in bio-molecular motors and machines are vital to their function. Yet experimental observations are often limited to a small subset of variables that participate in energy transport and dissipation. Here we show, through a solvable Langevin model, that the seemingly hidden entropy production is measurable through the violation spectrum of the fluctuation-response relation of a slow observable. For general Markov systems with timescale separation, we prove that the violation spectrum exhibits a characteristic plateau in the intermediate frequency region. Despite its vanishing height, the plateau can account for energy dissipation over a broad timescale. Our findings suggest a general possibility to probe hidden entropy production in nano systems without direct observation of fast variables.

cond-mat.stat-mech↗

arXiv2016

Topological defect launches 3D mound in the active nematic sheet of neural progenitors

Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and macroscopic patterns resulting from cell-to-cell interactions remain largely qualitative, even though they are the simplest features observed in everyday experiments. Here we report that neural progenitor cells (NPCs), which are multipotent stem cells that give rise to cells in the central nervous system, rapidly glide and stochastically reverse its velocity while locally aligning with neighboring cells, thus showing features of an active nematic system. Within the two-dimensional nematic pattern, we find interspaced topological defects with +1/2 and -1/2 charges. Remarkably, we identified rapid cell accumulation leading to three-dimensional mounds at the +1/2 topological defects. Single-cell level imaging around the defects allowed quantification of the evolving cell density, clarifying that not only cells concentrate at +1/2 defects, but also escape from -1/2 defects. We propose the mechanism of instability around the defects as the interplay between the anisotropic friction and the active force field, thus addressing a novel universal mechanism for local cell density control.

cond-mat.soft↗

arXiv2015

Role of measurement-feedback separation in autonomous Maxwell's demons

We introduce an information heat engine that is autonomous (i.e., without any time-dependent parameter) but has separated measurement and feedback processes. This model serves as a bridge between the other types of information heat engines inspired by Maxwell's demon; from the original Szilard-engine type systems to the autonomous demonic setups. By analyzing our model on the basis of a general framework introduced in our previous paper [N. Shiraishi and T. Sagawa, Phys. Rev. E {\bf 91}, 012130 (2015).], we clarify the role of the separation of measurement and feedback in the integral fluctuation theorems.

cond-mat.stat-mech↗

arXiv2015

Invariance of Steady State Thermodynamics between Different Scales of Description

By considering general Markov stochastic dynamics and its coarse-graining, we study the framework of stochastic thermodynamics for the original and reduced descriptions corresponding to different scales. We are especially concerned with the case where the irreversible entropy production has a finite difference between the scales. We find that the sum of increment of nonequilibrium entropy and excess part of entropy production, which are key quantities in construction of steady state thermodynamics, is essentially kept invariant with respect to the change in the scales of description. This general result justifies experimental approaches toward steady state thermodynamics based on coarse-grained variables. We demonstrate our result in a mesoscopic heat engine system.

cond-mat.stat-mech↗

arXiv2014

Nonequilibrium dissipation-free transport in F1-ATPase and the thermodynamic role of asymmetric allosterism

F1-ATPase (or F1), the highly-efficient and reversible biochemical engine, has motivated physicists as well as biologists to imagine the design principles governing machines in the fluctuating world. Recent experiments have clarified yet another interesting property of F1; the dissipative heat inside the motor is very small, irrespective of the velocity of rotation and energy transport. Conceptual interest is devoted to the fact that the amount of internal dissipation is not simply determined by the sequence of equilibrium pictures, but also relies on the rotational-angular dependence of nucleotide affinity, which is a truly nonequilibrium aspect. We propose that the totally asymmetric allosteric model (TASAM), where adenosine triphosphate (ATP) binding to F1 is assumed to have low dependence on the angle of the rotating shaft, produces results that are most consistent with the experiment. Theoretical analysis proves the crucial role of two time scales in the model, which explains the universal mechanism to produce the internal dissipation-free feature. The model reproduces the characteristic torque dependence of the rotational velocity of F1, and predicts that the internal dissipation upon the ATP synthesis direction rotation becomes large at the low nucleotide condition.

cond-mat.stat-mech↗

arXiv2012

Fluctuation Theorem for Hidden Entropy Production

In the general process of eliminating dynamic variables in Markovian models, there exists a difference in the irreversible entropy production between the original and reduced dynamics. We call this difference the hidden entropy production, since it is an invisible quantity when only the reduced system's view is provided. We show that this hidden entropy production obeys a new integral fluctuation theorem for the generic case where all variables are time-reversal invariant, therefore supporting the intuition that entropy production should decrease by coarse graining. It is found, however, that in cases where the condition for our theorem does not hold, entropy production may also increase due to the reduction. The extended multibaker map is investigated as an example for this case.

cond-mat.stat-mech↗

arXiv2011

Efficiency of Free Energy Transduction in Autonomous Systems

We consider the thermodynamics of chemical coupling from the viewpoint of free energy transduction efficiency. In contrast to an external parameter-driven stochastic energetics setup, the dynamic change of the equilibrium distribution induced by chemical coupling, adopted, for example, in biological systems, is inevitably an autonomous process. We found that the efficiency is bounded by the ratio between the non-symmetric and the symmetrized Kullback-Leibler distance, which is significantly lower than unity. Consequences of this low efficiency are demonstrated in the simple two-state case, which serves as an important minimal model for studying the energetics of biomolecules.

cond-mat.stat-mech↗