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Integer linear programming (ILP) encompasses a very important class of optimization problems that are of great interest to both academia and industry. Several algorithms are available that attempt to explore the solution space of this class…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
We describe a parallel solver for the discretized weakly singular space-time boundary integral equation of the spatially two-dimensional heat equation. The global space-time nature of the system matrices leads to improved parallel…
Interactions mediated by the cell membrane between inclusions, such as membrane proteins or antimicrobial peptides, play important roles in their biological activity. They also constitute a fascinating challenge for physicists, since they…
Previous devices to separate cells by the characteristic force they experience due to dielectrophoresis, which depends on the size and electric properties of the particle, were limited by the flow rates and particle concentrations…
Symmetry in mathematical optimisation is of broad and current interest. In problem classes such as mixed-integer linear programming (MILP), equivalent solutions created by symmetric variables and constraints may combinatorially increase the…
The Canham-Helfrich-Evans models of biomembranes consist of a family of geometric constrained variational problems. In this article, we compare two classes of numerical methods for these variational problems based on piecewise linear (PL)…
We introduce the percolation with plasticity (PWP) systems that exhibit neuromorphic functionalities including multi-valued memory, random number generation, matrix-vector multiplication, and associative learning. PWP systems have multiple…
In this paper, we develop high-order splitting methods for linear port-Hamiltonian systems, focusing on preserving their intrinsic structure, particularly the dissipation inequality. Port-Hamiltonian systems are characterized by their…
When it is polarised, a cell develops an asymmetric distribution of specific molecular markers, cytoskeleton and cell membrane shape. Polarisation can occur spontaneously or be triggered by external signals, like gradients of signalling…
Current algorithms for large-scale industrial optimization problems typically face a trade-off: they either require exponential time to reach optimal solutions, or employ problem-specific heuristics. To overcome these limitations, we…
Previous work has shown that there are two major complexity barriers in the synthesis of fault-tolerant distributed programs: (1) generation of fault-span, the set of states reachable in the presence of faults, and (2) resolving deadlock…
Port-based network modeling of multi-physics problems leads naturally to a formulation as port-Hamiltonian differential-algebraic system. In this way, the physical properties are directly encoded in the structure of the model. Since the…
We study the computational complexity of the recently proposed nubot model of molecular-scale self-assembly. The model generalises asynchronous cellular automata to have non-local movement where large assemblies of molecules can be pushed…
We develop a formal framework for the behavioral comparison of linear systems across different time domains. We accomplish this by introducing the notion of system interpolation, which determines whether the input-state trajectories of a…
Membranes are of great technological and biological as well as theoretical interest. Two main classes of membranes can be distinguished: Fluid membranes and polymerized, tethered membranes. Here, we review progress in the theoretical…
Solving partial differential equations (PDEs) by numerical methods meet computational cost challenge for getting the accurate solution since fine grids and small time steps are required. Machine learning can accelerate this process, but…
The cellular cytoplasm is organized into compartments. Phase separation is a simple manner to create membrane-less compartments in order to confine and localize particles like proteins. In many cases these particles are bound to fluctuating…
We consider asynchronous multiprocessor systems where processes communicate by accessing shared memory. Exchange of information among processes in such a multiprocessor necessitates costly memory accesses called \emph{remote memory…
Cell membranes separate the cell interior from the external environment. They are constituted by a variety of lipids; their composition determines the dynamics of membrane proteins and affects the ability of the cells to adapt. Even though…