相关论文: A bond swap algorithm for simulating dynamically c…
Link prediction in multilayer networks is a key challenge in applications such as recommendation systems and protein-protein interaction prediction. While many techniques have been developed, most rely on assumptions about shared structures…
Discrete modelling frameworks of Biological networks can be divided in two distinct categories: Boolean and Multi-valued. Although Multi-valued networks are more expressive for qualifying the regulatory behaviours modelled by more than two…
Machine learning and deep learning have revolutionized computational physics, particularly the simulation of complex systems. Equivariance is essential for simulating physical systems because it imposes a strong inductive bias on the…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
Many physical systems can be described in terms of matrix models that we often cannot solve analytically. Fortunately, they can be studied numerically in a straightforward way. Many commonly used algorithms follow the Monte Carlo method,…
The investigation of freezing transitions of single polymers is computationally demanding, since surface effects dominate the nucleation process. In recent studies we have systematically shown that the freezing properties of flexible,…
We present a lattice Monte Carlo algorithm based on the one originally proposed by Maggs and Rossetto for simulating electrostatic interactions in inhomogeneous dielectric media. The original algorithm is known to produce attractive…
We propose a coarse-grained model to investigate stress relaxation in star-polymer networks induced by dynamic bond exchange processes. We show how the swapping mechanism, once activated, allows the network to reconfigure, exploring…
This paper describes a new Monte Carlo method based on a novel stochastic potential switching algorithm. This algorithm enables the equilibrium properties of a system with potential $V$ to be computed using a Monte Carlo simulation for a…
A recent reformulation [1] of the problem of Coulomb gases in the presence of a dynamical dielectric medium showed that finite temperature simulations of such systems can be accomplished on the basis of completely local Hamiltonians on a…
Automated Market Makers (AMMs) are decentralized exchange protocols that provide continuous access to token liquidity without the need for order books or traditional market makers. However, this innovation has failed to scale when it comes…
We propose a new Monte Carlo method for efficiently sampling trajectories with fixed initial and final conditions in a system with discrete degrees of freedom. The method can be applied to any stochastic process with local interactions,…
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…
A boundary-based net-exchange Monte Carlo method was introduced in [1] that allows to bypass the difficulties encountered by standard Monte Carlo algorithms in the limit of optically thick absorption (and/or for quasi-isothermal…
Recent experiments have demonstrated that the nonlinear elasticity of in vitro networks of the biopolymer actin is dramatically altered in the presence of a flexible cross-linker such as the abundant cytoskeletal protein filamin. The basic…
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature/energy range around the critical point. By combining the replica-exchange algorithm with cluster updates…
Flexible manipulation of quantum correlation resources enables the implementation of diverse quantum tasks based on hybrid quantum networks, where atom-magnon and optomagnonic entanglements and steerings play important roles. In this work,…
We show how a Monte Carlo method for generating self-avoiding walks on lattice geometries which employs a binary-tree data structure can be adapted for hard-sphere polymers with continuous degrees of freedom. Data suggests that the time per…
This article presents an algorithm that allows modeling of biological networks in a qualitative framework with continuous time. Mathematical modeling is used as a systems biology tool to answer biological questions, and more precisely, to…
The probability of accepting a candidate move in the hybrid Monte Carlo algorithm can be increased by considering a transition to be between windows of several states at the beginning and end of the trajectory, with a state within the…