In this article a novel model framework to simulate cells and their internal structure is described. The model is agent-based and suitable to simulate single cells with a detailed internal structure as well as multi-cellular compounds. Cells are simulated as a set of many interacting particles, with neighborhood relations defined via a Delaunay triangulation. The interacting sub-particles of a cell can assume specific roles – i.e., membrane sub-particle, internal sub-particle, organelles, etc –, distinguished by specific interaction potentials and, eventually, also by the use of modified interaction criteria. For example, membrane sub-particles may interact only on a two-dimensional surface embedded on three-dimensional space, described via a restricted Delaunay triangulation. The model can be used not only to study cell shape and movement, but also has the potential to investigate the coupling between internal space-resolved movement of molecules and determined cell behaviors.

Biological rhythms occur at different levels in the organism. In single cells, the celldivision cycle shows rhythmicity in the way its molecular regulators, the cyclin dependantkinases (CDKs), modulate their activity periodically to ensure a healthy progression. Intissues, cell proliferation is driven by the circadian clock, which modulates theprogression through the cell cycle along the day. The circadian clock shows endogenousrhythmicity through a robust network of transcription-translation feedback loops thatcreate sustained oscillations. Rhythmicity is preserved in cell populations by thecoordination of the clocks among cells, through rhythmic synchronization signals. Here wediscuss mechanisms for generating rhythmic activities in cell populations by reviewingsome of the mathematical models that deal with them. We discuss the implication ofbiological rhythms for tissue growth and the possible application to chronomodulatedcancer treatments.

Assuming the negative part of the potential is uniformly locallyL1, we prove a pointwiseLp estimate on derivatives ofeigenfunctions of one-dimensional Schrödinger operators. In particular, if aneigenfunction is in Lp, then so is itsderivative, for 1 ≤ p ≤ ∞.

The evolution of a force-free granular gas with a constant restitution coefficient isstudied by means of granular hydrodynamics. We numerically solve the hydrodynamicequations and analyze the mechanisms of cluster formation. According to our findings, thepresently accepted mode-enslaving mechanism may not be responsible for the latterphenomenon. On the contrary, we observe that the cluster formation is mainly driven byshock-waves, which spontaneously originate and develop in the system. This agrees with apreviously suggested mechanism of formation of density singularities in one-dimensionalgranular gases.

The matrix KdV equation with a negative dispersion term is considered in the right upperquarter–plane. The evolution law is derived for the Weyl function of a correspondingauxiliary linear system. Using the low energy asymptotics of the Weyl functions, theunboundedness of solutions is obtained for some classes of the initial–boundaryconditions.

Many cancer-associated genes and pathways remain to be identified in order to clarify themolecular mechanisms underlying cancer progression. In this area, genome-wideloss-of-function screens appear to be powerful biological tools, allowing the accumulationof large amounts of data. However, this approach currently lacks analytical tools toexploit the data with maximum efficiency, for which systems biology methods analyzingcomplex cellular networks may be extremely helpful. In this article we report such asystems biology strategy based on the construction of a Network for a biological processand specific for a given cell system (cell type). The networks are created fromgenome-wide loss-of-function screen datasets. We also propose tools to analyze networkproperties. As one of the tools, we suggest a mathematical model for discriminationbetween two distinct cell processes that may be affected by knocking down the activity ofa gene, i. e., a decreased cell number may be caused by arrested cell proliferation orenhanced cell death. Next we show how this discrimination between the two cell processeshelps to construct two corresponding subnetworks. Finally, we demonstrate an applicationof the proposed strategy to the identification and characterization of putative novelgenes and pathways significant for the control of lung cancer cell growth, based on theresults of a genome-wide proliferation/viability loss-of-function screen of human lungadenocarcinoma cells.

We study the role of interactions between habitats in rotifer dynamics. For this purpose we use a modified version of the Consensus model. The Consensus model has been shown to be realistic enough to reproduce distinguishing features of the rotifer species dynamics. Being uncoupled, intrinsically bistable rotifer populations, which inhabit the regions under different environmental conditions, do not impact each other. We show that migration of the rotifers between the habitats leads to the transformation of bistability to oscillatory dynamics. The coupling-induced oscillations of the rotifer biomass are shown to be either regular or irregular depending on the value of the model parameters, which describe environmental conditions and the biomass exchange between the habitats. We show that the irregular oscillations are characterized by positive values of the Lyapunov exponent, which means that they are chaotic.

The experimentally known phenomenon of oscillatory instability in convective burning ofporous explosives is discussed. A simple phenomenological model accounting for theejection of unburned particles from the consolidated charge is formulated and analyzed. Itis shown that the post-front hydraulic resistance induced by the ejected particlesprovides a mechanism for the oscillatory burning.

This work is devoted to analyze a numerical scheme for the approximation of the linear heat equation’s controls. It is known that, due to the regularizing effect, the efficient computation of the null controls for parabolic type equations is a difficult problem. A possible cure for the bad numerical behavior of the approximating controls consists of adding a singular perturbation depending on a small parameter ε which transforms the heat equation into a wave equation. A space discretization of step h leads us to a system of ordinary differential equations. The aim of this paper is to show that there exists a sequence of exact controls of the corresponding perturbed semi-discrete systems which converges to a control of the original heat equation when both h (the mesh size) and ε (the perturbation parameter) tend to zero.

We derive the conserved vectors for the nonlinear two-dimensional Euler equationsdescribing nonviscous incompressible fluid flows on a three-dimensional rotating sphericalsurface superimposed by a particular stationary latitude dependent flow. Under theassumption of no friction and a distribution of temperature dependent only upon latitude,the equations in question can be used to model zonal west-to-east flows in the upperatmosphere between the Ferrel and Polar cells. As a particualr example, the conserveddensities are analyzed by visualizing the exact invariant solutions associated with thegiven model for the particular form of finite disturbances for which the invariantsolutions are also exact solutions of Navier-Stokes equations.

In this paper we are interested in a mathematical model of migration of grass eels in an estuary. We first revisit a previous model proposed by O. Arino and based on a degenerate convection-diffusion equation of parabolic-hyperbolic type with time-varying subdomains. Then, we propose an adapted mathematical framework for this model, we prove a result of existence of a weak solution and we propose some numerical simulations.

The paper presents theoretical and numerical results on the identifiability, i.e. theunique identification for the one-dimensional sine-Gordon equation. The identifiabilityfor nonlinear sine-Gordon equation remains an open question. In this paper we establishthe identifiability for a linearized sine-Gordon problem. Our method consists of a carefulanalysis of the Laplace and Fourier transforms of the observation of the system, conductedat a single point. Numerical results based on the best fit to data method confirm that theidentification is unique for a wide choice of initial approximations for the sought testparameters. Numerical results compare the identification for the nonlinear and thelinearized problems.

We prove that the minimal operator and the maximal operator of the Hermite operator arethe same on Lp(ℝn), 4 / 3<p< 4. Thedomain and the spectrum of the minimal operator (=maximal operator) of the Hermiteoperator on Lp(ℝn),4/3 <p<4, are computed. In addition, we can give anestimate for the Lp-norm of thesolution to the initial value problem for the heat equation governed by the minimal(maximal) operator for 4/3<p<4.

Multifractal analysis is known as a useful tool in signal analysis. However, themethods are often used without methodological validation. In this study, wepresent multidimensional models in order to validate multifractal analysismethods.

Inverse scattering problem is discussed for the Maxwell’s equations. A reduction of theMaxwell’s system to a new Fredholm second-kind integral equation with a scalarweakly singular kernel is given for electromagnetic (EM) wave scattering. Thisequation allows one to derive a formula for the scattering amplitude in which only ascalar function is present. If this function is small (an assumption that validates aBorn-type approximation), then formulas for the solution to the inverse problem areobtained from the scattering data: the complex permittivityϵ′(x) in a bounded regionD ⊂ R3 is found from the scattering amplitudeA(β,α,k) known for a fixed k = ω √ϵ0μ0 >0 and allβ,α ∈ S2, whereS2 is the unit sphere in R3,ϵ0 and μ0 are constantpermittivity and magnetic permeability in the exterior regionD′ = R3\D. The novel pointsin this paper include: i) A reduction of the inverse problem for vectorEM waves to a vector integral equation with scalar kernelwithout any symmetry assumptions on the scatterer, ii) A derivation of thescalar integral equation of the first kind for solving the inversescattering problem, and iii) Presenting formulas for solving this scalar integralequation. The problem of solving this integral equation is an ill-posed one. A method fora stable solution of this problem is given.

We have developed a chemical kinetics simulation that can be used as both an educationaland research tool. The simulator is designed as an accessible, open-source project thatcan be run on a laptop with a student-friendly interface. The application can potentiallybe scaled to run in parallel for large simulations. The simulation has been successfullyused in a classroom setting for teaching basic electrochemical properties. We have shownthat this can be used for simulating fundamental molecular and chemical processes and evensimplified models of predator–prey interactions. By giving the simulated entities spatialextent in the lattice, the particles do not interpenetrate, and clusters of particles canspatially exclude one another. Our simulation demonstrates that spatial inhomogeneityleads to different results than those that are obtained by using standard ordinarydifferential equation models, as previously reported.

A simple model of biological evolution of community food webs is introduced. This modelis based on the niche model, which is known to generate model food webs that are verysimilar to empirical food webs. The networks evolve by speciation and extinction.Co-extinctions due to the loss of all prey species are found to play a major role indetermining the longterm shape of the food webs. The central aim is to design the modelsuch that the characteristic parameters of the niche model food webs remain in realisticintervals. When the mutation rule is chosen accordingly, it is found that food webs with acomplex, biologically meaningful structure emerge and that the statistics of extinctionevents agrees well with that observed in the paleontological data.

Nothing is more fundamental to life than the ability to reproduce and duplicate theinformation cells store in their genomes. The mechanism of duplication of DNA has beenconserved from prokaryotes to eukaryotes. The aim of the study was to quantify whichevolutionary forces could produce the pattern of genome replication architecture observedin present-day organisms. This was achieved using an evolutionary simulation, combiningrandom genome sequence shuffling, mutation, selection and the mathematical modeling of DNAreplication. We have found parameter values which explained evolutionary pressures of DNAreplication in E.coli, P.calidifontis and S.cerevisae. Surprisingly, the results of the evolutionary simulation suggeststhat for a fixed cost per replication origin it is more advantageous for genomes to reducethe number of replication origins under increasing uncertainty in origin activationtiming.