Bifurcation, stability, and cluster formation of multi-strain infection models

Clustering behaviours have been found in numerous multi-strain transmission models. Numerical solutions of these models have shown that steady-states, periodic, or even chaotic motions can be self-organized into clusters. Such clustering behaviours are not a priori expected. It has been proposed that the cross-protection from multiple strains of pathogens is responsible for the clustering phenomenon. In this paper, we show that the steady-state clusterings in existing models can be analytically predicted. The clusterings occur via semi-simple double zero bifurcation from the quotient networks of the models and the patterns which follow can be predicted through the stability analysis of the bifurcation. We calculate the stability criteria for the clustering patterns and show that some patterns are inherently unstable. Finally, the biological implications of these results are discussed.     

Periodic metabolic systems: Oscillations in multiple-loop negative feedback biochemical control networks

Summary For a general multiple loop feedback inhibition system in which the end product can inhibit any or all of the intermediate reactions it is shown that biologically significant behaviour is always confined to a bounded region of reaction space containing a unique equilibrium. By explicit construction of a Liapunov function for the general n dimensional differential equation it is shown that some values of reaction parameters cause the concentration vector to approach the equilibrium asymptotically for all physically realizable initial conditions. As the parameter values change, periodic solutions can appear within the bounded region. Some information about these periodic solutions can be obtained from the Hopf bifurcation theorem. Alternatively, if specific parameter values are known a numerical method can be used to find periodic solutions and determine their stability by locating a zero of the displacement map. The single loop Goodwin oscillator is analysed in detail. The methods are then used to treat an oscillator with two feedback loops and it is found that oscillations are possible even if both Hill coefficients are equal to one.     

Effects of transients on pulsatile flow in arteries

Analytical solutions to the model problem of unsteady Newtonian fluid flow in straight, elastic-walled vessels can provide: theoretical insights into the flow of blood in arteries; a theoretical basis for clinical measurements in diagnoses of arterial flow rates; and guidance for boundary conditions in numerical simulations of flow in finite computational domains. However, while Womersley's analyses of blood flow assume solution forms that treat the flow as periodic and continuously unsteady, many flow variables in the smaller arteries are not continuously unsteady at all. They are characterized more accurately as rapid transient motions followed by a period of recovery to a stationary state, repeated in successive cycles. These flows are not continually unsteady ones described by Womersley's solutions but unsteady flows restarted from rest in each cycle, characterized as initial-boundary value problems. In this paper, we compare the Womersley and initial-boundary value solutions for model transients that stop then restart, explain these previously unreported limitations of Womersley's solutions, and demonstrate how the initial-boundary value solutions provide excellent agreement with measurements of blood flow in the anterior tibial and popliteal arteries of patients. Some consequences of these findings for understanding and interpreting measurements of blood flow, and for prescribing boundary conditions in computer simulations of arterial blood flow are discussed.     

An analysis of a dendritic neuron model with an active membrane site

We formulate and analyze a mathematical model that couples an idealized dendrite to an active boundary site to investigate the nonlinear interaction between these passive and active membrane patches. The active site is represented mathematically as a nonlinear boundary condition to a passive cable equation in the form of a space-clamped FitzHugh-Nagumo (FHN) equation. We perform a bifurcation analysis for both steady and periodic perturbation at the active site. We first investigate the uncoupled space-clamped FHN equation alone and find that for periodic perturbation a transition from phase locked (periodic) to phase pulling (quasiperiodic) solutions exist. For the model coupling a passive cable with a FHN active site at the boundary, we show for steady perturbation that the interval for repetitive firing is a subset of the interval for the space-clamped case and shrinks to zero for strong coupling. The firing rate at the active site decreases as the coupling strength increases. For periodic perturbation we show that the transition from phase locked to phase pulling solutions is also dependent on the coupling strength.This work was supported in part by NSF Grants MCS 83-00562 and MDS 85-01535     

Global ribosome motions revealed with elastic network model

The motions of large systems such as the ribosome are not fully accessible with conventional molecular simulations. A coarse-grained, less-than-atomic-detail model such as the anisotropic network model (ANM) is a convenient informative tool to study the cooperative motions of the ribosome. The motions of the small 30S subunit, the larger 50S subunit, and the entire 70S assembly of the two subunits have been analyzed using ANM. The lowest frequency collective modes predicted by ANM show that the 50S subunit and 30S subunit are strongly anti-correlated in the motion of the 70S assembly. A ratchet-like motion is observed that corresponds well to the experimentally reported ratchet motion. Other slow modes are also examined because of their potential links to the translocation steps in the ribosome. We identify several modes that may facilitate the E-tRNA exiting from the assembly. The A-site t-RNA and P-site t-RNA are found to be strongly coupled and positively correlated in these slow modes, suggesting that the translocations of these two t-RNAs occur simultaneously, while the motions of the E-site t-RNA are less correlated, and thus less likely to occur simultaneously. Overall the t-RNAs exhibit relatively large deformations. Animations of these slow modes of motion can be viewed at.     

Global analysis of an SAIS model

This paper is concerned with global analysis of an SAIS epidemiological model in a population of varying size introduced by Busenberg and van den Driessche. In this model the population is divided into three subgroups of susceptible, asymptomatic and infective individuals. It has been shown that this system has no periodic solutions and all its trajectories tend to the equilibria of the system. We use the Poincaré Index theorem to determine the number of the equilibria and their stability properties. We have shown that bistability occurs for suitable values of parameters and found a set of examples of all possible dynamics of the system.     

Global analysis of an SAIS model

This paper is concerned with global analysis of an SAIS epidemiological model in a population of varying size introduced by Busenberg and van den Driessche. In this model the population is divided into three subgroups of susceptible, asymptomatic and infective individuals. It has been shown that this system has no periodic solutions and all its trajectories tend to the equilibria of the system. We use the Poincaré Index theorem to determine the number of the equilibria and their stability properties. We have shown that bistability occurs for suitable values of parameters and found a set of examples of all possible dynamics of the system.     

On the behavior of solutions in viral dynamical models

We consider simple mathematical models for the early population dynamics of the human immunodefficiency type 1 virus (HIV-1). Although these systems of differential equations may be solved by numerical methods, few general theoretical results are available due to nonlinearities. We analyze a model whose components are plasma densities of uninfected CD4+ T-cells and infected cells (assumed in this model to be proportional to virion density). In addition to analyzing the nature of the equilibrium points, we show that there are no periodic or limit-cycle solutions. Depending on the values of the parameters, solutions either tend without oscillation to an equilibrium point with zero virion density or to an equilibrium point in which there are a nonzero number of virions. In the latter case the approach to equilibrium may be through damped oscillations or without oscillation.     

State-dependent impulsive models of integrated pest management (IPM) strategies and their dynamic consequences

A state-dependent impulsive model is proposed for integrated pest management (IPM). IPM involves combining biological, mechanical, and chemical tactics to reduce pest numbers to tolerable levels after a pest population has reached its economic threshold (ET). The complete expression of an orbitally asymptotically stable periodic solution to the model with a maximum value no larger than the given ET is presented, the existence of which implies that pests can be controlled at or below their ET levels. We also prove that there is no periodic solution with order larger than or equal to three, except for one special case, by using the properties of the LambertW function and Poincare map. Moreover, we show that the existence of an order two periodic solution implies the existence of an order one periodic solution. Various positive invariant sets and attractors of this impulsive semi-dynamical system are described and discussed. In particular, several horseshoe-like attractors, whose interiors can simultaneously contain stable order 1 periodic solutions and order 2 periodic solutions, are found and the interior structure of the horseshoe-like attractors is discussed. Finally, the largest invariant set and the sufficient conditions which guarantee the global orbital and asymptotic stability of the order 1 periodic solution in the meaningful domain for the system are given using the Lyapunov function. Our results show that, in theory, a pest can be controlled such that its population size is no larger than its ET by applying effects impulsively once, twice, or at most, a finite number of times, or according to a periodic regime. Moreover, our theoretical work suggests how IPM strategies could be used to alter the levels of the ET in the farmers' favour.     

Disaccharide conformational flexibility. II. Molecular dynamics simulations of sucrose

Molecular dynamics simulations have been used to study the motions in vacuum of the disaccharide sucrose. Ensembles of trajectories were calculated for each of the five local minimum energy conformations identified in the adiabatic conformational energy mapping of this molecule. The model sucrose molecules were found to exhibit a variety of motions, although the global minimum energy conformation was found to be dynamically stable, and no transitions away from this structure were observed to occur spontaneously. In all but one of these vacuum trajectories, the intramolecular hydrogen bond between residues was maintained, in accord with recent nmr studies of this molecule in aqueous solution. Considerable flexibility of the furanoid ring was found in the trajectories. No "flips" to the opposite puckering for this ring were found in the simulations starting from the global minimum, although such a transition was observed for a trajectory initiated with one of the higher local minimum energy conformations. Overall, the observed structural fluctuations were consistent with the experimental picture of sucrose as a relatively rigid molecule.     

The relationship between periodic dinucleotides and the nucleosomal DNA deformation revealed by normal mode analysis

Nucleosomes, which contain DNA and proteins, are the basic unit of eukaryotic chromatins. Polymers such as DNA and proteins are dynamic, and their conformational changes can lead to functional changes. Periodic dinucleotide patterns exist in nucleosomal DNA chains and play an important role in the nucleosome structure. In this paper, we use normal mode analysis to detect significant structural deformations of nucleosomal DNA and investigate the relationship between periodic dinucleotides and DNA motions. We have found that periodic dinucleotides are usually located at the peaks or valleys of DNA and protein motions, revealing that they dominate the nucleosome dynamics. Also, a specific dinucleotide pattern CA/TG appears most frequently.     

Transient oscillations induced by delayed growth response in the chemostat

In this paper, in order to try to account for the transient oscillations observed in chemostat experiments, we consider a model of single species growth in a chemostat that involves delayed growth response. The time delay models the lag involved in the nutrient conversion process. Both monotone response functions and nonmonotone response functions are considered. The nonmonotone response function models the inhibitory effects of growth response of certain nutrients when concentrations are too high. By applying local and global Hopf bifurcation theorems, we prove that the model has unstable periodic solutions that bifurcate from unstable nonnegative equilibria as the parameter measuring the delay passes through certain critical values and that these local periodic solutions can persist, even if the delay parameter moves far from the critical (local) bifurcation values.When there are two positive equilibria, then positive periodic solutions can exist. When there is a unique positive equilibrium, the model does not have positive periodic oscillations and the unique positive equilibrium is globally asymptotically stable. However, the model can have periodic solutions that change sign. Although these solutions are not biologically meaningful, provided the initial data starts close enough to the unstable manifold of one of these periodic solutions they may still help to account for the transient oscillations that have been frequently observed in chemostat experiments. Numerical simulations are provided to illustrate that the model has varying degrees of transient oscillatory behaviour that can be controlled by the choice of the initial data.Mathematics Subject Classification: 34D20, 34K20, 92D25Research was partially supported by NSERC of Canada.This work was partly done while this author was a postdoc at McMaster.     

On periodic solutions of a delay integral equation modelling epidemics

Summary A delay-integral equation, proposed by Cooke and Kaplan in [1] as a model of epidemics, is studied. The focus of this work is on the qualitative behavior of solutions as a certain parameter is allowed to vary. It is shown that if a certain threshold is not exceeded then solutions tend to zero exponentially while if this threshold is exceeded, periodic solutions exist. Many features of the numerical studies in [1] are explained.     

General equilibrium of an ecosystem

Ecosystems and economies are inextricably linked: ecosystem models and economic models are not linked. Consequently, using either type of model to design policies for preserving ecosystems or improving economic performance omits important information. Improved policies would follow from a model that links the systems and accounts for the mutual feedbacks by recognizing how key ecosystem variables influence key economic variables, and vice versa. Because general equilibrium economic models already are widely used for policy making, the approach used here is to develop a general equilibrium ecosystem model which captures salient biological functions and which can be integrated with extant economic models. In the ecosystem model, each organism is assumed to be a net energy maximizer that must exert energy to capture biomass from other organisms. The exerted energies are the "prices" that are paid to biomass, and each organism takes the prices as signals over which it has no control. The maximization problem yields the organism's demand for and supply of biomass to other organisms as functions of the prices. The demands and supplies for each biomass are aggregated over all organisms in each species which establishes biomass markets wherein biomass prices are determined. A short-run equilibrium is established when all organisms are maximizing and demand equals supply in every biomass market. If a species exhibits positive (negative) net energy in equilibrium, its population increases (decreases) and a new equilibrium follows. The demand and supply forces in the biomass markets drive each species toward zero stored energy and a long-run equilibrium. Population adjustments are not based on typical Lotka-Volterra differential equations in which one entire population adjusts to another entire population thereby masking organism behavior; instead, individual organism behavior is central to population adjustments. Numerical simulations use a marine food web in Alaska to illustrate the model and to show several simultaneous predator/prey relationships, prey switching by the top predator, and energy flows through the web.     

Effects of quarantine in six endemic models for infectious diseases

Thresholds, equilibria, and their stability are found for SIQS and SIQR epidemiology models with three forms of the incidence. For most of these models, the endemic equilibrium is asymptotically stable, but for the SIQR model with the quarantine-adjusted incidence, the endemic equilibrium is an unstable spiral for some parameter values and periodic solutions arise by Hopf bifurcation. The Hopf bifurcation surface and stable periodic solutions are found numerically.     

Spatial stability of traveling wave solutions of a nerve conduction equation.

A simplified FitzHugh-Nagumo nerve conduction equation with known traveling wave solutions is considered. The spatial stability of these solutions is analyzed to determine which solutions should occur in signal transmission along such a nerve model. It is found that the slower of the two pulse solutions is unstable while the faster one is stable, so the faster one should occur. This agrees with conjectures which have been made about the solutions of other nerve conduction equations. Furthermore for certain parameter values the equation has two periodic wave solutions, each representing a train of impulses, at each frequency less than a maximum frequency wmax. The slower one is found to be unstable and the faster one to be stable, while that at wmax is found to be neutrally stable. These spatial stability results complement the previous results of Rinzel and Keller (1973. Biophys. J. 13: 1313) on temporal stability, which are applicable to the solutions of initial value problems.     

Neural fields with fast learning dynamic kernel

We introduce a modified-firing-rate model based on Hebbian-type changing synaptic connections. The existence and stability of solutions such as rest state, bumps, and traveling waves are shown for this type of model. Three types of kernels, namely exponential, Mexican hat, and periodic synaptic connections, are considered. In the former two cases, the existence of a rest state solution is proved and the conditions for their stability are found. Bump solutions are shown for two kinds of synaptic kernels, and their stability is investigated by constructing a corresponding Evans function that holds for a specific range of values of the kernel coefficient strength (KCS). Applying a similar method, we consider exponential synaptic connections, where traveling wave solutions are shown to exist. Simulation and numerical analysis are presented for all these cases to illustrate the resulting solutions and their stability.     

Natural selection of life history attributes: An analytical approach

The life history attributes which maximize fitness can be established analytically through Fisher's equation for reproductive value. Maximizing the reproductive value at age zero is equivalent to maximizing the ultimate rate of increase. As an example of the usefulness of this equality it is shown that when survivorship is uniformly reduced, the corresponding optimal maternal frequency is unaltered, even though the ultimate rate of increase is lowered by a known amount. A general life history model is proposed which links these demographic determinants of rate of increase with the energy utilization alternatives (as among maintenance, growth, and reproduction) characterizing an individual organism's development. Since the energy partitioning alternatives at any age may depend on previous allocations, an organism state variable is introduced to describe the domain over which the maximization of reproductive value may take place. Further, if the reproductive value is to be a maximum at age zero, it must be maximized at every age. An optimal life history, then, is characterized by the energy allocations which maximize sequential reproductive values. Further examples of the utility of the model focus on growth vs reproduction decisions under biomass specific life history attributes. It is shown that if births per unit energy is a linear or convex function, then an organism will not simultaneously grow and reproduce. Determinant growth, biomass at first reproduction, and explicit calculation of the maximum ultimate rate of increase are also illustrated.     

Periodic and traveling wave solutions to Volterra-Lotka equations with diffusion

Analytic and numerical solutions to two coupled nonlinear diffusion equations are studied. They are the modified equations of Volterra and Lotka for the spatially stratified predatorprey population model. In a bounded domain with the reflecting boundary, equilibrium, stability, and transition to time-periodic solutions are analyzed. For a wide class of initial states, the solutions to the initial boundary-value problem evolve into their corresponding stable, space-homogeneous, periodic oscillations. In an unbounded domain, a family of traveling wave solutions is found for certain exponential, initial distributions in the limit as the diffusion coefficientv ₁ of the prey tends to zero. In the presence of both diffusions, the results of a numerical simulation to an initial-value problem showed the rapid formation of the Pursuit-Evasion Waves whose speed of propagation and amplitudes increase with the diffusion coefficientv ₁. Presented at the 1974 SIAM Fall Meeting.     

Heat capacities and a snapshot of the energy landscape in protein GB1 from the pre-denaturation temperature dependence of backbone NH nanosecond fluctuations

Protein stability is usually characterized calorimetrically by a melting temperature and related thermodynamic parameters. Despite its importance, the microscopic origin of the melting transition and the relationship between thermodynamic stability and dynamics remains a mystery. Here, NMR relaxation parameters were acquired for backbone 15NH groups of the 56 residue immunoglobulin-binding domain of streptococcal protein G over a pre-denaturation temperature range of 5-50 degrees C. Relaxation data were analyzed using three methods: the standard three-Lorentzian model free approach; the F(omega)=2omegaJ(omega) spectral density approach that yields motional correlation time distributions, and a new approach that determines frequency-dependent order parameters. Regardless of the method of analysis, the temperature dependence of internal motional correlation times and order parameters is essentially the same. Nanosecond time-scale internal motions are found for all NHs in the protein, and their temperature dependence yields activation energies ranging up to about 33kJ/mol residue. NH motional barrier heights are structurally correlated, with the largest energy barriers being found for residues in the most "rigid" segments of the fold: beta-strands 1 and 4 and the alpha-helix. Trends in this landscape also parallel the free energy of folding-unfolding derived from hydrogen-deuterium (H-D) exchange measurements, indicating that the energetics for internal motions occurring on the nanosecond time-scale mirror those occurring on the much slower time-scale of H-D exchange. Residual heat capacities, derived from the temperature dependence of order parameters, range from near zero to near 100J/mol K residue and correlate with this energy landscape. These results provide a unique picture of this protein's energy landscape and a relationship between thermodynamic stability and dynamics that suggests thermosensitive regions in the fold that could initiate the melting process.