Related papers: Finding Optimal Pathways in Chemical Reaction Netw…
This work considers the method of uniformisation for continuous-time Markov chains in the context of chemical reaction networks. Previous work in the literature has shown that uniformisation can be beneficial in the context of…
Dynamical Ising machines achieve accelerated solving of complex combinatorial optimization problems by remapping the convergence to the ground state of the classical spin networks to the evolution of specially constructed continuous…
Combinatorial optimization problems can be mapped onto Ising models, and their ground state is generally difficult to find. A lot of heuristics for these problems have been proposed, and one promising approach is to use continuous…
Quantum error correction is an essential ingredient for reliable quantum computation for theoretically provable quantum speedup. Topological color codes, one of the quantum error correction codes, have an advantage against the surface codes…
An introduction to the application of combinatorial optimization methods to ground state calculations of frustrated, disordered systems is given. We discuss the interface problem in the random bond Ising ferromagnet, the random field Ising…
Spatio-temporal biochemical signaling in a large class of protein-protein interaction networks is well modeled by a reaction-diffusion system. The global existence of the solution to the reaction-diffusion system is determined by the…
Disentangling the mechanistic details of a chemical reaction pathway is a hard problem that often requires a considerable amount of chemical intuition and a component of luck. Experiments struggle in observing short-life metastable…
One of the main challenges in diffusion-based molecular communication is dealing with the non-linearity of reaction-diffusion chemical equations. While numerical methods can be used to solve these equations, a change in the input signals or…
Modelling and predicting protein configurations is crucial for advancing drug discovery, enabling the design of treatments for life-threatening diseases. A critical aspect of this challenge is rotamer optimisation - the determination of…
Combinatorial optimization problems are computationally hard in general, but they are ubiquitous in our modern life. A coherent Ising machine (CIM) based on a multiple-pulse degenerate optical parametric oscillator (DOPO) is an alternative…
Ising machines are a form of quantum-inspired processing-in-memory computer which has shown great promise for overcoming the limitations of traditional computing paradigms while operating at a fraction of the energy use. The process of…
Quality control in industrial processes is increasingly making use of prior scientific knowledge, often encoded in physical models that require numerical approximation. Statistical prediction, and subsequent optimization, is key to ensuring…
The commercial and industrial demand for the solution of hard combinatorial optimization problems push forward the development of efficient solvers. One of them is the Ising machine which can solve combinatorial problems mapped to Ising…
Quantum computers use quantum resources to carry out computational tasks and may outperform classical computers in solving certain computational problems. Special-purpose quantum computers such as quantum annealers employ quantum adiabatic…
The transport of conserved quantities like spin and charge is fundamental to characterizing the behavior of quantum many-body systems. Numerically simulating such dynamics is generically challenging, which motivates the consideration of…
High-energy particle collisions can convert energy into matter through the inelastic production of new particles. Quantum computers are an ideal platform for simulating the out-of-equilibrium dynamics of collisions and the formation of…
We present a new way to make Ising machines, i.e., using networks of coupled self-sustaining nonlinear oscillators. Our scheme is theoretically rooted in a novel result that establishes that the phase dynamics of coupled oscillator systems,…
Motivation: Identifying the molecular pathways more prone to disruption during a pathological process is a key task in network medicine and, more in general, in systems biology. Results: In this work we propose a pipeline that couples a…
Effective therapy of complex diseases requires control of highly non-linear complex networks that remain incompletely characterized. In particular, drug intervention can be seen as control of signaling in cellular networks. Identification…
Real-world optimization problems must undergo a series of transformations before becoming solvable on current quantum hardware. Even for a fixed problem, the number of possible transformation paths -- from industry-relevant formulations…