A variational approach for continuous supply chain networks

We consider a continuous supply chain network consisting of buffering queues and processors first proposed by [D. Armbruster, P. Degond, and C. Ringhofer, SIAM J. Appl. Math., 66 (2006), pp. 896–920] and subsequently analyzed by [D. Armbruster, P. Degond, and C. Ringhofer, Bull. Inst. Math. Acad. Sin. (N.S.), 2 (2007), pp. 433–460] and [D. Armbruster, C. De Beer, M. Fre- itag, T. Jagalski, and C. Ringhofer, Phys. A, 363 (2006), pp. 104–114]. A model was proposed for such a network by [S. G ̈ottlich, M. Herty, and A. Klar, Commun. Math. Sci., 3 (2005), pp. 545–559] using a system of coupling ordinary differential equations and partial differential equations. In this article, we propose an alternative approach based on a variational method to formulate the network dynamics. We also derive, based on the variational method, a computational algorithm that guarantees numerical stability, allows for rigorous error estimates, and facilitates efficient computations. A class of network flow optimization problems are formulated as mixed integer programs (MIPs). The proposed numerical algorithm and the corresponding MIP are compared theoretically and numerically with existing ones [A. Fu ̈genschuh, S. Go ̈ttlich, M. Herty, A. Klar, and A. Martin, SIAM J. Sci. Comput., 30 (2008), pp. 1490–1507; S. Go ̈ttlich, M. Herty, and A. Klar, Commun. Math. Sci., 3 (2005), pp. 545–559], which demonstrates the modeling and computational advantages of the variational approach

Epigenetic Chromatin Silencing: Bistability and Front Propagation

The role of post-translational modification of histones in eukaryotic gene regulation is well recognized. Epigenetic silencing of genes via heritable chromatin modifications plays a major role in cell fate specification in higher organisms. We formulate a coarse-grained model of chromatin silencing in yeast and study the conditions under which the system becomes bistable, allowing for different epigenetic states. We also study the dynamics of the boundary between the two locally stable states of chromatin: silenced and unsilenced. The model could be of use in guiding the discussion on chromatin silencing in general. In the context of silencing in budding yeast, it helps us understand the phenotype of various mutants, some of which may be non-trivial to see without the help of a mathematical model. One such example is a mutation that reduces the rate of background acetylation of particular histone side-chains that competes with the deacetylation by Sir2p. The resulting negative feedback due to a Sir protein depletion effect gives rise to interesting counter-intuitive consequences. Our mathematical analysis brings forth the different dynamical behaviors possible within the same molecular model and guides the formulation of more refined hypotheses that could be addressed experimentally.Comment: 19 pages, 5 figure

Point queue models: a unified approach

In transportation and other types of facilities, various queues arise when the demands of service are higher than the supplies, and many point and fluid queue models have been proposed to study such queueing systems. However, there has been no unified approach to deriving such models, analyzing their relationships and properties, and extending them for networks. In this paper, we derive point queue models as limits of two link-based queueing model: the link transmission model and a link queue model. With two definitions for demand and supply of a point queue, we present four point queue models, four approximate models, and their discrete versions. We discuss the properties of these models, including equivalence, well-definedness, smoothness, and queue spillback, both analytically and with numerical examples. We then analytically solve Vickrey's point queue model and stationary states in various models. We demonstrate that all existing point and fluid queue models in the literature are special cases of those derived from the link-based queueing models. Such a unified approach leads to systematic methods for studying the queueing process at a point facility and will also be helpful for studies on stochastic queues as well as networks of queues.Comment: 25 pages, 6 figure

Continuum limit of self-driven particles with orientation interaction

We consider the discrete Couzin-Vicsek algorithm (CVA), which describes the interactions of individuals among animal societies such as fish schools. In this article, we propose a kinetic (mean-field) version of the CVA model and provide its formal macroscopic limit. The final macroscopic model involves a conservation equation for the density of the individuals and a non conservative equation for the director of the mean velocity and is proved to be hyperbolic. The derivation is based on the introduction of a non-conventional concept of a collisional invariant of a collision operator

Numerical schemes for the optimal input flow of a supply-chain

An innovative numerical technique is presented to adjust the inflow to a supply chain in order to achieve a desired outflow, reducing the costs of inventory, or the goods timing in warehouses. The supply chain is modelled by a conservation law for the density of processed parts coupled to an ODE for the queue buffer occupancy. The control problem is stated as the minimization of a cost functional J measuring the queue size and the quadratic difference between the outflow and the expected one. The main novelty is the extensive use of generalized tangent vectors to a piecewise constant control, which represent time shifts of discontinuity points. Such method allows convergence results and error estimates for an Upwind- Euler steepest descent algorithm, which is also tested by numerical simulations

Membrane penetration and trapping of an active particle

The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the particles can pass through cell membranes via passive endocytosis or by active penetration to reach a target cellular compartment or organelle. In this manuscript, we develop a simple model to describe the interaction of a self-driven spherical particle (moving through an effective constant active force) with a minimal membrane system, allowing for both penetration and trapping. We numerically calculate the state diagram of this system, the membrane shape, and its dynamics. In this context, we show that the active particle may either get trapped near the membrane or penetrates through it, where the membrane can either be permanently destroyed or recover its initial shape by self-healing. Additionally, we systematically derive a continuum description allowing to accurately predict most of our results analytically. This analytical theory helps identifying the generic aspects of our model, suggesting that most of its ingredients should apply to a broad range of membranes, from simple model systems composed of magnetic microparticles to lipid bilayers. Our results might be useful to predict mechanical properties of synthetic minimal membranes.Comment: 16 pages, 6 figures. Revised manuscript resubmitted to J. Chem. Phy