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Ken Sekimoto

Publications and source records attributed to Ken Sekimoto.

35 records · Page 2Linked to original sources

Compatibility between itinerant synaptic receptors and stable postsynaptic structure

The density of synaptic receptors in front of presynaptic release sites is stabilized in the presence of scaffold proteins, but the receptors and scaffold molecules have local exchanges with characteristic times shorter than that of the receptor-scaffold assembly. We propose a mesoscopic model to account for the regulation of the local density of receptors as quasiequilibrium. It is based on two zones (synaptic and extrasynaptic) and multi-layer (membrane, sub-membrane and cytoplasmic) topological organization. The model includes the balance of chemical potentials associated with the receptor and scaffold protein concentrations in the various compartments. The model shows highly cooperative behavior including a "phase change" resulting in the formation of well-defined post-synaptic domains. This study provides theoretical tools to approach the complex issue of synaptic stability at the synapse, where receptors are transiently trapped yet rapidly diffuse laterally on the plasma membrane.

physics.bio-ph↗

Internal stress as a link between macroscale and mesoscale mechanics

The internal (or residual) stress is among the key notions to describe the state of the systems far from equilibrium. Such stress is invisible on the macroscopic scale where the system is regarded as a blackbox. Yet nonequilibrium macroscopic operations allow to create and observe the internal stress. We present in this lecture some examples of the internal stress and its operations. We describe the memory effect in some detail, the process in which the history of past operations is recalled through the relaxation of internal stress.

cond-mat.soft↗

Microscopic heat from the energetics of stochastic phenomena

The energetics of the stochastic process has shown the balance of energy on the mesoscopic level. The heat and the energy defined there are, however, generally different from their macroscopic counterpart. We show that this discrepancy can be removed by adding to these quantities the reversible heat associated with the mesoscopic free energy.

cond-mat.stat-mech↗

General up to next-nearest neighbour elasticity of triangular lattices in three dimensions

We establish the most general form of the discrete elasticity of a 2D triangular lattice embedded in three dimensions, taking into account up to next-nearest neighbour interactions. Besides crystalline system, this is relevant to biological physics (e.g., red blood cell cytoskeleton) and soft matter (e.g., percolating gels, etc.). In order to correctly impose the rotational invariance of the bulk terms, it turns out to be necessary to take into account explicitly the elasticity associated with the vertices located at the edges of the lattice. We find that some terms that were suspected in the litterature to violate rotational symmetry are in fact admissible

cond-mat.soft↗

Internal Stress in a Model Elasto-Plastic Fluid

Plastic materials can carry memory of past mechanical treatment in the form of internal stress. We introduce a natural definition of the vorticity of internal stress in a simple two-dimensional model of elasto-plastic fluids, which generates the internal stress. We demonstrate how the internal stress is induced under external loading, and how the presence of the internal stress modifies the plastic behavior.

cond-mat.soft↗

Autonomous free-energy transducer working under thermal fluctuations

By a modular combination of mesoscopic detectors and gates, we present a thoughtful pump that transports gas particles against the difference of their density at the expense of the diffusion of another species of gas particles. We also discuss briefly the relevance of the model to the study of structure-function relationship of the biomolecular machines.

physics.bio-ph↗

Generic theory of active polar gels: a paradigm for cytoskeletal dynamics

We develop a general theory for active viscoelastic materials made of polar filaments. This theory is motivated by the dynamics of the cytoskeleton. The continuous consumption of a fuel generates a non equilibrium state characterized by the generation of flows and stresses. Our theory can be applied to experiments in which cytoskeletal patterns are set in motion by active processes such as those which are at work in cells.

physics.bio-ph↗

Mechano-chemical coupling in growth process of actin gels and a symmetry breaking instability

It has been observed experimentally that the actin gel grown from spherical beads coated with polymerization enzymes spontaneously breaks the symmetry of its spherical shape, and yields a ``comet'' pushing the bead forward. We propose a mechano-chemical coupling mechanism for the initialization of this symmetry breaking. Key assumptions are that the dissociation of the gel takes place mostly in the region of the external surface, and that the rates of the dissociation depends on the tensile stress in the gel. We analyze a simplified two-dimensional model with a circular substrate. Our analysis shows that the symmetric steady state is always unstable against the inhomogeneous modulation of the thickness of the gel layer, for any radius of the circular substrate. We argue that this model represents the essential feature of the three-dimensional systems for a certain range of characteristic lengths of the modulation. The characteristic time of the symmetry breaking process in our model depends linearly on the radius of curvature of the substrate surface, which is consistent with experimental results, using spherical latex beads as substrate. Our analysis of the symmetry breaking phenomenon demonstrates aspects of mechano-chemical couplings that should be working in vivo as well as in vitro.

physics.bio-ph↗

The Carnot Cycle for Small Systems: Irreversibility and the Cost of Operations

We employ the recently developed framework of the energetics of stochastic processes (called `stochastic energetics'), to re-analyze the Carnot cycle in detail, taking account of fluctuations, without taking the thermodynamic limit. We find that both processes of connection to and disconnection from heat baths and adiabatic processes that cause distortion of the energy distribution are sources of inevitable irreversibility within the cycle. Also, the so-called null-recurrence property of the cumulative efficiency of energy conversion over many cycles and the irreversible property of isolated, purely mechanical processes under external `macroscopic' operations are discussed in relation to the impossibility of a perpetual machine, or Maxwell's demon.

cond-mat.stat-mech↗

Inattainability of Carnot efficiency in the Brownian heat engine

We discuss the reversibility of Brownian heat engine. We perform asymptotic analysis of Kramers equation on Büttiker-Landauer system and show quantitatively that Carnot efficiency is inattainable even in a fully overdamping limit. The inattainability is attributed to the inevitable irreversible heat flow over the temperature boundary.

cond-mat.stat-mech↗

Contraction of a Bundle of Actin Filaments: 50 years after Szent-Gyorgyi

Biological systems are among the most challenging subjects for theoretical physicists, as well as experimentalists or simulationists. Physical principles should have been both constraints and guide-lines for the evolution of living systems over billions of years. One generally aims at clarifying what physical principles, possibly new ones, are behind the phenomena of biological interest and at understanding how they work within the entire biological world. In the present talk we describe an example of such an effort. Since the discovery of `superprecipitation' by Szent-Gyorgyi's group in 1940's, it has been a long puzzle how an assemblage of actin filaments with random orientation can contract in the presence of the two-headed myosin molecules undergoing actin-activated ATP-hydrolysis reaction. It is widely accepted that during the contraction the two-headed myosin mediates the relative sliding of two actin filaments whose polarity directions are not parallel but rather anti-parallel. But this fact solely does not account for the shortening. We propose a dynamical model which, upon numerical simulation, exhibits the shortening of an bundle of the actin filaments which are initially dirstributed randomly both in space along a line and in polarity direction. In the course of shortening several clusters of actins appears along the bundle. The model also shows the sorting of the actin filaments according to their polarity in the late stage. These findings are in accordance with the recent experiment by Takiguchi.

physics.bio-ph↗

Energetics of Open Systems and Chemical Potential From Micro-Dynamics Viewpoints

We present the energetic aspect of open systems which may exchange particles with their environments. Our attention shall be paid to the scale that the motion of the particles is described by the classical Langevin dynamics. Along a particular realization of the stochastic process, we study the energy transfer into the open system from the environments. We are able to clarify how much energy each particle carries when it enters or leaves the system. On the other hand, the chemical potential should be considered as the concept in macro scale, which is relevant to the free energy potential with respect to the number of particles. Keywords: open systems, stochastic energetics, chemical potential

cond-mat.stat-mech↗

Logarithmically Slow Expansion of Hot Bubbles in Gases

We report logarithmically slow expansion of hot bubbles in gases in the process of cooling. A model problem first solved, when the temperature has compact support. Then temperature profile decaying exponentially at large distances is considered. The periphery of the bubble is shown to remain essentially static ("glassy") in the process of cooling until it is taken over by a logarithmically slowly expanding "core". An analytical solution to the problem is obtained by matched asymptotic expansion. This problem gives an example of how logarithmic corrections enter dynamic scaling.

patt-sol↗

Discontinuous Crack Fronts of Three-Dimensional Fractures

The relation between fracture surface morphology and the three-dimensional structure of crack fronts is investigated through direct observation of brittle cracks in gels. A key notion in this investigation is the discontinuity of the crack front, whose advancement creates the fracture surface. We discuss the significance of our findings in the studies of general three-dimensional brittle fractures.

cond-mat.soft↗

Complementarity relation for irreversible process derived from stochastic energetics

When the process of a system in contact with a heat bath is described by classical Langevin equation, the method of stochastic energetics [K. Sekimoto, J. Phys. Soc. Jpn. vol. 66 (1997) p.1234] enables to derive the form of Helmholtz free energy and the dissipation function of the system. We prove that the irreversible heat Q_irr and the time lapse $Delta t} of an isothermal process obey the complementarity relation, Q_irr {Delta t} >= k_B T S_min, where S_min depends on the initial and the final values of the control parameters, but it does not depend on the pathway between these values.

cond-mat.stat-mech↗

Energetics of thermal ratchet models

Several stochastic models called thermal ratchet models have been recently proposed to analyze the motor proteins such as myosin and kinesin,etc. We propose a method to study the energetics of those models, and show how the rate of energy consumption and the energy dissipation are evaluated. As a demonstration we consider "Feynman's ratchet", a typical fluctuating heat engine.

cond-mat.stat-mech↗

Oscillatory instability of crack propagations in quasi-static fracture

Crack propagations in quasi-static fracture are studied theoretically. The Griffith theory is applied to discuss a crack extension condition and motion of crack tips in straight propagations. Stability of the straight propagations is investigated based on the simple assumption that a curvature near the crack tip is determined by a singular shear stress. It is shown that straight propagations become unstable under ceatain conditions. Combined with boundary effects, this instability leads to an oscillatory propagation of cracks. The critical conditions are calculated quantitatively.

patt-sol↗