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This paper is about partitioning in parallel and distributed simulation. That means decomposing the simulation model into a numberof components and to properly allocate them on the execution units. An adaptive solution based on…
Introducing flexibility in the time-discretisation mesh can improve convergence and computational time when solving differential equations numerically, particularly when the solutions are discontinuous, as commonly found in control problems…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
Tailoring many-body interactions among a proper quantum system endows it with computing ability by means of static quantum computation in the sense that some of the physical degrees of freedom can be used to store binary information and the…
All cells must keep time to consistently perform vital biological functions. To that end, the coupling and interrelatedness of diverse subsecond events in the complex cellular environment, such as protein folding or translation rates,…
In this paper, we design, analyze, and numerically validate positive and energy-dissipating schemes for solving the time-dependent multi-dimensional system of Poisson-Nernst-Planck (PNP) equations, which has found much use in the modeling…
Living systems are capable of locomotion, reconfiguration, and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, "active" molecules that create and manipulate non-equilibrium…
We present the living application, a method to autonomously manage applications on the grid. During its execution on the grid, the living application makes choices on the resources to use in order to complete its tasks. These choices can be…
The observation and modeling of natural Complex Systems (CSs) like the human nervous system, the evolution or the weather, allows the definition of special abilities and models reusable to solve other problems. For instance, Genetic…
Stem cells, through their ability to produce daughter stem cells and differentiate into specialized cells, are essential in the growth, maintenance, and repair of biological tissues. Understanding the dynamics of cell populations in the…
Inactive constraints do not contribute to the solution of an optimal control problem, but increase the problem size and burden the numerical computations. We present a novel strategy for handling inactive constraints efficiently by…
Large classes of materials systems in physics and engineering are governed by magnetic and electrostatic interactions. Continuum or mesoscale descriptions of such systems can be cast in terms of integral equations, whose direct…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
Replication time is among the most important components of a bacterial cell's reproductive fitness. Paradoxically, larger cells replicate in less time than smaller cells despite the fact that building a larger cell requires increased…
Memoryless computation is a novel means of computing any function of a set of registers by updating one register at a time while using no memory. We aim to emulate how computations are performed on modern cores, since they typically involve…
Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to…
A Boolean network is a discrete dynamical system operating on vectors of Boolean variables. The action of a Boolean network can be conveniently expressed as a system of Boolean update functions, computing the new values for each component…
Many claims of computational advantages have been made for quantum computing over classical, but they have not been demonstrated for practical problems. Here, we present algorithms for solving time-dependent PDEs, with particular reference…
The biological immune system is a robust, complex, adaptive system that defends the body from foreign pathogens. It is able to categorize all cells (or molecules) within the body as self-cells or non-self cells. It does this with the help…
The active-time scheduling problem considers the problem of scheduling preemptible jobs with windows (release times and deadlines) on a parallel machine that can schedule up to $g$ jobs during each timestep. The goal in the active-time…