Searcharxiv⌕ Search

arXiv subjects

Yoshihiko Hasegawa

Publications and source records attributed to Yoshihiko Hasegawa.

87 records · Page 5Linked to original sources

Augmented Variational Superposed Gaussian Approximation for Langevin Equations with Rational Polynomial Functions

Reliable methods for obtaining time-dependent solutions of Langevin equations are in high demand in the field of non-equilibrium theory. In this paper, we present a new method based on variational superposed Gaussian approximation (VSGA) and Padé approximant. The VSGA obtains time-dependent probability density functions as a superposition of multiple Gaussian distributions. However, a limitation of the VSGA is that the expectation of the drift term with respect to the Gaussian distribution should be calculated analytically, which is typically satisfied when the drift term is a polynomial function. When this condition is not met, the VSGA must rely on the numerical integration of the expectation at each step, resulting in huge computational cost. We propose an augmented VSGA (A-VSGA) method that effectively overcomes the limitation of the VSGA by approximating non-linear functions with the Padé approximant. We apply the A-VSGA to two systems driven by chaotic input signals, a stochastic genetic regulatory system and a soft bistable system, whose drift terms are a rational polynomial function and a hyperbolic tangent function, respectively. The numerical calculations show that the proposed method can provide accurate results with less temporal cost than that required for Monte Carlo simulation.

cond-mat.stat-mech↗

Thermodynamics of collective enhancement of precision

The circadian oscillator exhibits remarkably high temporal precision, despite its exposure to several fluctuations. The central mechanism that protects the oscillator from fluctuations is a collective enhancement of precision, where a population of coupled oscillators displays higher temporal precision than that achieved without coupling. Since coupling is essentially information exchange between oscillators, we herein investigate the relation between the temporal precision and the information flow between oscillators in the linearized Kuramoto model by using stochastic thermodynamics. For general coupling, we find that the temporal precision is bounded from below by the information flow. We generalize the model to incorporate a time-delayed coupling and demonstrate that the same relation also holds for the time-delayed case. Furthermore, the temporal precision is demonstrated to be improved in the presence of the time delay, and we show that the increased information flow is responsible for the time-delay-induced precision improvement.

physics.bio-ph↗

An algebraic method to calculate parameter regions for constrained steady-state distribution in stochastic reaction networks

Steady state is an essential concept in reaction networks. Its stability reflects fundamental characteristics of several biological phenomena such as cellular signal transduction and gene expression. Because biochemical reactions occur at the cellular level, they are affected by unavoidable fluctuations. Although several methods have been proposed to detect and analyze the stability of steady states for deterministic models, these methods cannot be applied to stochastic reaction networks. In this paper, we propose an algorithm based on algebraic computations to calculate parameter regions for constrained steady-state distribution of stochastic reaction networks, in which the means and variances satisfy some given inequality constraints. To evaluate our proposed method, we perform computer simulations for three typical chemical reactions and demonstrate that the results obtained with our method are consistent with the simulation results.

q-bio.MN↗

Approximate Vanishing Ideal via Data Knotting

The vanishing ideal is a set of polynomials that takes zero value on the given data points. Originally proposed in computer algebra, the vanishing ideal has been recently exploited for extracting the nonlinear structures of data in many applications. To avoid overfitting to noisy data, the polynomials are often designed to approximately rather than exactly equal zero on the designated data. Although such approximations empirically demonstrate high performance, the sound algebraic structure of the vanishing ideal is lost. The present paper proposes a vanishing ideal that is tolerant to noisy data and also pursued to have a better algebraic structure. As a new problem, we simultaneously find a set of polynomials and data points for which the polynomials approximately vanish on the input data points, and almost exactly vanish on the discovered data points. In experimental classification tests, our method discovered much fewer and lower-degree polynomials than an existing state-of-the-art method. Consequently, our method accelerated the runtime of the classification tasks without degrading the classification accuracy.

stat.ML↗

Multi-dimensional biochemical information processing of dynamical patterns

Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multi-dimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multi-dimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

physics.bio-ph↗

Optimal temporal patterns for dynamical cellular signaling

Cells use temporal dynamical patterns to transmit information via signaling pathways. As optimality with respect to the environment plays a fundamental role in biological systems, organisms have evolved optimal ways to transmit information. Here, we use optimal control theory to obtain the dynamical signal patterns for the optimal transmission of information, in terms of efficiency (low energy) and reliability (low uncertainty). Adopting an activation-deactivation decoding network, we reproduce several dynamical patterns found in actual signals, such as steep, gradual, and overshooting dynamics. Notably, when minimizing the energy of the input signal, the optimal signals exhibit overshooting, which is a biphasic pattern with transient and steady phases; this pattern is prevalent in actual dynamical patterns. We also identify conditions in which these three patterns (steep, gradual, and overshooting) confer advantages. Our study shows that cellular signal transduction is governed by the principle of minimizing free energy dissipation and uncertainty; these constraints serve as selective pressures when designing dynamical signaling patterns.

physics.bio-ph↗

Variational superposed Gaussian approximation for time-dependent solutions of Langevin equations

We propose a variational superposed Gaussian approximation (VSGA) for dynamical solutions of Langevin equations subject to applied signals, determining time-dependent parameters of superposed Gaussian distributions by the variational principle. We apply the proposed VSGA to systems driven by a chaotic signal, where the conventional Fourier method cannot be adopted, and calculate the time evolution of probability density functions (PDFs) and moments. Both white and colored Gaussian noises terms are included to describe fluctuations. Our calculations show that time-dependent PDFs obtained by VSGA agree excellently with those obtained by Monte Carlo simulations. The correlation between the chaotic input signal and the mean response are also calculated as a function of the noise intensity, which confirms the occurrence of aperiodic stochastic resonance with both white and colored noises.

cond-mat.stat-mech↗

Temperature compensation via cooperative stability in protein degradation

Temperature compensation is a notable property of circadian oscillators that indicates the insensitivity of the oscillator system's period to temperature changes; the underlying mechanism, however, is still unclear. We investigated the influence of protein dimerization and cooperative stability in protein degradation on the temperature compensation ability of two oscillators. Here, cooperative stability means that high-order oligomers are more stable than their monomeric counterparts. The period of an oscillator is affected by the parameters of the dynamic system, which in turn are influenced by temperature. We adopted the Repressilator and the Atkinson oscillator to analyze the temperature sensitivity of their periods. Phase sensitivity analysis was employed to evaluate the period variations of different models induced by perturbations to the parameters. Furthermore, we used experimental data provided by other studies to determine the reasonable range of parameter temperature sensitivity. We then applied the linear programming method to the oscillatory systems to analyze the effects of protein dimerization and cooperative stability on the temperature sensitivity of their periods, which reflects the ability of temperature compensation in circadian rhythms. Our study explains the temperature compensation mechanism for circadian clocks. Compared with the no-dimer mathematical model and linear model for protein degradation, our theoretical results show that the nonlinear protein degradation caused by cooperative stability is more beneficial for realizing temperature compensation of the circadian clock.

physics.bio-ph↗

Optimal implementations for reliable circadian clocks

Circadian rhythms are acquired through evolution to increase the chances for survival through synchronizing with the daylight cycle. Reliable synchronization is realized through two trade-off properties: regularity to keep time precisely, and entrainability to synchronize the internal time with daylight. We found by using a phase model with multiple inputs that achieving the maximal limit of regularity and entrainability entails many inherent features of the circadian mechanism. At the molecular level, we demonstrate the role sharing of two light inputs, phase advance and delay, as is well observed in mammals. At the behavioral level, the optimal phase-response curve inevitably contains a dead zone, a time during which light pulses neither advance nor delay the clock. We reproduce the results of phase-controlling experiments entrained by two types of periodic light pulses. Our results indicate that circadian clocks are designed optimally for reliable clockwork through evolution.

physics.bio-ph↗

Circadian clocks optimally adapt to sunlight for reliable synchronization

Circadian oscillation provides selection advantages through synchronization to the daylight cycle. However, a reliable clock must be designed through two conflicting properties: entrainability to synchronize internal time with periodic stimuli such as sunlight, and regularity to oscillate with a precise period. These two aspects do not easily coexist because better entrainability favors higher sensitivity, which may sacrifice the regularity. To investigate conditions for satisfying the two properties, we analytically calculated the optimal phase-response curve with a variational method. Our result indicates an existence of a dead zone, i.e., a time period during which input stimuli neither advance nor delay the clock. A dead zone appears only when input stimuli obey the time course of actual solar radiation but a simple sine curve cannot yield a dead zone. Our calculation demonstrates that every circadian clock with a dead zone is optimally adapted to the daylight cycle.

physics.bio-ph↗

Enhanced entrainability of genetic oscillators by period mismatch

Biological oscillators coordinate individual cellular components so that they function coherently and collectively. They are typically composed of multiple feedback loops, and period mismatch is unavoidable in biological implementations. We investigated the advantageous effect of this period mismatch in terms of a synchronization response to external stimuli. Specifically, we considered two fundamental models of genetic circuits: smooth- and relaxation oscillators. Using phase reduction and Floquet multipliers, we numerically analyzed their entrainability under different coupling strengths and period ratios. We found that a period mismatch induces better entrainment in both types of oscillator; the enhancement occurs in the vicinity of the bifurcation on their limit cycles. In the smooth oscillator, the optimal period ratio for the enhancement coincides with the experimentally observed ratio, which suggests biological exploitation of the period mismatch. Although the origin of multiple feedback loops is often explained as a passive mechanism to ensure robustness against perturbation, we study the active benefits of the period mismatch, which include increasing the efficiency of the genetic oscillators. Our findings show a qualitatively different perspective for both the inherent advantages of multiple loops and their essentiality.

physics.bio-ph↗

Fluctuating noise drives Brownian transport

The transport properties of Brownian ratchet was studied in the presence of stochastic intensity noise (SIN) in both overdamped and underdamped regimes. In the overdamped case, analytical solution using the matrix continued fraction method revealed the existence of a maximum current when the noise intensity fluctuates on intermediate time scale regions. Similar effects were observed for the underdamped case by Monte Carlo simulations. The optimal time-correlation for the Brownian transport coincided with the experimentally observed time-correlation of the extrinsic noise in Esherichia coli gene expression and implied the importance of environmental noise for molecular mechanisms.

cond-mat.stat-mech↗

Escape process and stochastic resonance under noise-intensity fluctuation

We study the effects of noise-intensity fluctuations on the stationary and dynamical properties of an overdamped Langevin model with a bistable potential and external periodical driving force. We calculated the stationary distributions, mean-first passage time (MFPT) and the spectral amplification factor using a complete set expansion (CSE) technique. We found resonant activation (RA) and stochastic resonance (SR) phenomena in the system under investigation. Moreover, the strength of RA and SR phenomena exhibit non-monotonic behavior and their trade-off relation as a function of the squared variation coefficient of the noise-intensity process. The reliability of CSE is verified with Monte Carlo simulations.

cond-mat.stat-mech↗

Noise-intensity fluctuation in Langevin model and its higher-order Fokker-Planck equation

In this paper, we investigate a Langevin model subjected to stochastic intensity noise (SIN), which incorporates temporal fluctuations in noise-intensity. We derive a higher-order Fokker-Planck equation (HFPE) of the system, taking into account the effect of SIN by the adiabatic elimination technique. Stationary distributions of the HFPE are calculated by using the perturbation expansion. We investigate the effect of SIN in three cases: (a) parabolic and quartic bistable potentials with additive noise, (b) a quartic potential with multiplicative noise, and (c) a stochastic gene expression model. We find that the existence of noise intensity fluctuations induces an intriguing phenomenon of a bimodal-to-trimodal transition in probability distributions. These results are validated with Monte Carlo simulations.

cond-mat.stat-mech↗

Bistable stochastic processes in the q-exponential family

Stochastic bistable systems whose stationary distributions belong to the q-exponential family are investigated using two approaches: (i) the Langevin model subjected to additive and quadratic multiplicative noise, and (ii) the superstatistical model. Previously, the bistable Langevin model has been analyzed under linear multiplicative noise, whereas this paper reports on quadratic multiplicative noise, which is more physically meaningful. The stationary distribution of the Langevin model under quadratic multiplicative noise, which agrees with that derived by the maximum Tsallis entropy method, is found to be qualitatively different from its counterpart under linear multiplicative noise. We also show that the stationary distribution of the superstatistical model is the same as that of the Langevin model, whereas their transient properties, described in terms of mean first passage times (MFPTs), are qualitatively different.

cond-mat.stat-mech↗