### Concept: Differential equation

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##### Perspective: Stochastic algorithms for chemical kinetics

- The Journal of chemical physics
- Published over 6 years ago
- Discuss

We outline our perspective on stochastic chemical kinetics, paying particular attention to numerical simulation algorithms. We first focus on dilute, well-mixed systems, whose description using ordinary differential equations has served as the basis for traditional chemical kinetics for the past 150 years. For such systems, we review the physical and mathematical rationale for a discrete-stochastic approach, and for the approximations that need to be made in order to regain the traditional continuous-deterministic description. We next take note of some of the more promising strategies for dealing stochastically with stiff systems, rare events, and sensitivity analysis. Finally, we review some recent efforts to adapt and extend the discrete-stochastic approach to systems that are not well-mixed. In that currently developing area, we focus mainly on the strategy of subdividing the system into well-mixed subvolumes, and then simulating diffusional transfers of reactant molecules between adjacent subvolumes together with chemical reactions inside the subvolumes.

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##### Modeling extracellular electrical stimulation: I. Derivation and interpretation of neurite equations.

- Journal of neural engineering
- Published almost 7 years ago
- Discuss

Neuroprosthetic devices, such as cochlear and retinal implants, work by directly stimulating neurons with extracellular electrodes. This is commonly modeled using the cable equation with an applied extracellular voltage. In this paper a framework for modeling extracellular electrical stimulation is presented. To this end, a cylindrical neurite with confined extracellular space in the subthreshold regime is modeled in three-dimensional space. Through cylindrical harmonic expansion of Laplace’s equation, we derive the spatio-temporal equations governing different modes of stimulation, referred to as longitudinal and transverse modes, under types of boundary conditions. The longitudinal mode is described by the well-known cable equation, however, the transverse modes are described by a novel ordinary differential equation. For the longitudinal mode, we find that different electrotonic length constants apply under the two different boundary conditions. Equations connecting current density to voltage boundary conditions are derived that are used to calculate the trans-impedance of the neurite-plus-thin-extracellular-sheath. A detailed explanation on depolarization mechanisms and the dominant current pathway under different modes of stimulation is provided. The analytic results derived here enable the estimation of a neurite’s membrane potential under extracellular stimulation, hence bypassing the heavy computational cost of using numerical methods.

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##### Continuous time Boolean modeling for biological signaling: application of Gillespie algorithm.

- BMC systems biology
- Published about 7 years ago
- Discuss

Mathematical modeling is used as a Systems Biology tool to answer biological questions, and more precisely, to validate a network that describes biological observations and predict the effect of perturbations. This article presents an algorithm for modeling biological networks in a discrete framework with continuous time. BACKGROUND: There exist two major types of mathematical modeling approaches: (1) quantitative modeling, representing various chemical species concentrations by real numbers, mainly based on differential equations and chemical kinetics formalism; (2) and qualitative modeling, representing chemical species concentrations or activities by a finite set of discrete values. Both approaches answer particular (and often different) biological questions. Qualitative modeling approach permits a simple and less detailed description of the biological systems, efficiently describes stable state identification but remains inconvenient in describing the transient kinetics leading to these states. In this context, time is represented by discrete steps. Quantitative modeling, on the other hand, can describe more accurately the dynamical behavior of biological processes as it follows the evolution of concentration or activities of chemical species as a function of time, but requires an important amount of information on the parameters difficult to find in the literature. RESULTS: Here, we propose a modeling framework based on a qualitative approach that is intrinsically continuous in time. The algorithm presented in this article fills the gap between qualitative and quantitative modeling. It is based on continuous time Markov process applied on a Boolean state space. In order to describe the temporal evolution of the biological process we wish to model, we explicitly specify the transition rates for each node. For that purpose, we built a language that can be seen as a generalization of Boolean equations. Mathematically, this approach can be translated in a set of ordinary differential equations on probability distributions. We developed a C++ software, MaBoSS, that is able to simulate such a system by applying Kinetic Monte-Carlo (or Gillespie algorithm) on the Boolean state space. This software, parallelized and optimized, computes the temporal evolution of probability distributions and estimates stationary distributions. CONCLUSIONS: Applications of the Boolean Kinetic Monte-Carlo are demonstrated for three qualitative models: a toy model, a published model of p53/Mdm2 interaction and a published model of the mammalian cell cycle. Our approach allows to describe kinetic phenomena which were difficult to handle in the original models. In particular, transient effects are represented by time dependent probability distributions, interpretable in terms of cell populations.

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##### The Reservoir Model: A Differential Equation Model of Psychological Regulation

- Psychological methods
- Published over 6 years ago
- Discuss

Differential equation models can be used to describe the relationships between the current state of a system of constructs (e.g., stress) and how those constructs are changing (e.g., based on variable-like experiences). The following article describes a differential equation model based on the concept of a reservoir. With a physical reservoir, such as one for water, the level of the liquid in the reservoir at any time depends on the contributions to the reservoir (inputs) and the amount of liquid removed from the reservoir (outputs). This reservoir model might be useful for constructs such as stress, where events might “add up” over time (e.g., life stressors, inputs), but individuals simultaneously take action to “blow off steam” (e.g., engage coping resources, outputs). The reservoir model can provide descriptive statistics of the inputs that contribute to the “height” (level) of a construct and a parameter that describes a person’s ability to dissipate the construct. After discussing the model, we describe a method of fitting the model as a structural equation model using latent differential equation modeling and latent distribution modeling. A simulation study is presented to examine recovery of the input distribution and output parameter. The model is then applied to the daily self-reports of negative affect and stress from a sample of older adults from the Notre Dame Longitudinal Study on Aging. (PsycINFO Database Record © 2013 APA, all rights reserved).

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##### Boundary layer flow and heat transfer over a nonlinearly permeable stretching/shrinking sheet in a nanofluid

- Scientific reports
- Published over 5 years ago
- Discuss

The steady boundary layer flow and heat transfer of a nanofluid past a nonlinearly permeable stretching/shrinking sheet is numerically studied. The governing partial differential equations are reduced into a system of ordinary differential equations using a similarity transformation, which are then solved numerically using a shooting method. The local Nusselt number and the local Sherwood number and some samples of velocity, temperature and nanoparticle concentration profiles are graphically presented and discussed. Effects of the suction parameter, thermophoresis parameter, Brownian motion parameter and the stretching/shrinking parameter on the flow, concentration and heat transfer characteristics are thoroughly investigated. Dual solutions are found to exist in a certain range of the stretching/shrinking parameter for both shrinking and stretching cases. Results indicate that suction widens the range of the stretching/shrinking parameter for which the solution exists.

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##### Analysis of Coupled Reaction-Diffusion Equations for RNA Interactions

- Journal of mathematical analysis and applications
- Published almost 5 years ago
- Discuss

We consider a system of coupled reaction-diffusion equations that models the interaction between multiple types of chemical species, particularly the interaction between one messenger RNA and different types of non-coding microRNAs in biological cells. We construct various modeling systems with different levels of complexity for the reaction, nonlinear diffusion, and coupled reaction and diffusion of the RNA interactions, respectively, with the most complex one being the full coupled reaction-diffusion equations. The simplest system consists of ordinary differential equations (ODE) modeling the chemical reaction. We present a derivation of this system using the chemical master equation and the mean-field approximation, and prove the existence, uniqueness, and linear stability of equilibrium solution of the ODE system. Next, we consider a single, nonlinear diffusion equation for one species that results from the slow diffusion of the others. Using variational techniques, we prove the existence and uniqueness of solution to a boundary-value problem of this nonlinear diffusion equation. Finally, we consider the full system of reaction-diffusion equations, both steady-state and time-dependent. We use the monotone method to construct iteratively upper and lower solutions and show that their respective limits are solutions to the reaction-diffusion system. For the time-dependent system of reaction-diffusion equations, we obtain the existence and uniqueness of global solutions. We also obtain some asymptotic properties of such solutions.

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This article addresses the effects of homogeneous-heterogeneous reactions in peristaltic transport of Carreau fluid in a channel with wall properties. Mathematical modelling and analysis have been carried out in the presence of Hall current. The channel walls satisfy the more realistic convective conditions. The governing partial differential equations along with long wavelength and low Reynolds number considerations are solved. The results of temperature and heat transfer coefficient are analyzed for various parameters of interest.

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We have developed a mathematical framework for describing a bispecific monoclonal antibody interaction with two independent membrane-bound targets that are expressed on the same cell surface. The bispecific antibody in solution binds either of the two targets first, and then cross-links with the second one whilst on the cell surface, subject to rate-limiting lateral diffusion step within the lifetime of the monovalently engaged antibody-antigen complex. At experimental densities, only a small fraction of the free targets is expected to lie within the reach of the antibody binding sites at any time. Using ordinary differential equation and Monte Carlo simulation-based models, we validated this approach against an independently published anti-CD4/CD70 DuetMab experimental data set. As a result of dimensional reduction, the cell surface reaction is expected to be so rapid that, in agreement with the experimental data, no monovalently bound bispecific antibody binary complexes accumulate until cross-linking is complete. The dissociation of the bispecific antibody from the ternary cross-linked complex is expected to be significantly slower than that from either of the monovalently bound variants. We estimate that the effective affinity of the bivalently bound bispecific antibody is enhanced for about four orders of magnitude over that of the monovalently bound species. This avidity enhancement allows for the highly specific binding of anti-CD4/CD70 DuetMab to the cells that are positive for both target antigens over those that express only one or the other We suggest that the lateral diffusion of target antigens in the cell membrane also plays a key role in the avidity effect of natural antibodies and other bivalent ligands in their interactions with their respective cell surface receptors.

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##### DSP-based adaptive backstepping using the tracking errors for high-performance sensorless speed control of induction motor drive

- ISA transactions
- Published almost 4 years ago
- Discuss

This paper presents a modified structure of the backstepping nonlinear control of the induction motor (IM) fitted with an adaptive backstepping speed observer. The control design is based on the backstepping technique complemented by the introduction of integral tracking errors action to improve its robustness. Unlike other research performed on backstepping control with integral action, the control law developed in this paper does not propose the increase of the number of system state so as not increase the complexity of differential equations resolution. The digital simulation and experimental results show the effectiveness of the proposed control compared to the conventional PI control. The results analysis shows the characteristic robustness of the adaptive control to disturbances of the load, the speed variation and low speed.

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##### Modeling Intraindividual Dynamics Using Stochastic Differential Equations: Age Differences in Affect Regulation

- The journals of gerontology. Series B, Psychological sciences and social sciences
- Published over 2 years ago
- Discuss

Life-span theories of aging suggest improvements and decrements in individuals' ability to regulate affect. Dynamic process models, with intensive longitudinal data, provide new opportunities to articulate specific theories about individual differences in intraindividual dynamics. This paper illustrates a method for operationalizing affect dynamics using a multilevel stochastic differential equation (SDE) model, and examines how those dynamics differ with age and trait-level tendencies to deploy emotion regulation strategies (reappraisal and suppression).