Related papers: Scaffolding Generation using a 3D Physarum Polycep…
The structure of a polystyrene matrix filled with tightly cross-linked polystyrene nanoparticles, forming an athermal nanocomposite system, is investigated by means of a Monte Carlo sampling formalism. The polymer chains are represented as…
We introduce an efficient, scalable Monte Carlo algorithm to simulate cross-linked architectures of freely-jointed and discrete worm-like chains. Bond movement is based on the discrete tractrix construction, which effects conformational…
Population Monte Carlo simulations in the form commonly referred to as population annealing can serve as a useful meta-algorithm for simulating systems with complex free-energy landscapes. In the present paper we provide an easily…
In this study we address existing deficiencies in the literature on applications of Particle Swarm Optimization to generate optimal designs. We present the results of a large computer study in which we bench-mark both efficiency and…
As an extension of the former study on 2-dimensional systems, we simulate phase behavior of polymer-grafted colloidal particles in 3 dimensions by molecular Monte Carlo technique in the canonical ensemble. We use a spherically symmetric…
We tackle the problem of efficiently approximating the volume of convex polytopes, when these are given in three different representations: H-polytopes, which have been studied extensively, V-polytopes, and zonotopes (Z-polytopes). We…
In the framework of detector development, Monte Carlo simulations play a key role in the evaluation of the expected performance and the full understanding of the behavior in beam conditions. In particular, a software which simulates the…
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their…
We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias…
Monte Carlo generation of high energy particle collisions is a critical tool for both theoretical and experimental particle physics, connecting perturbative calculations to phenomenological models, and theory predictions to full detector…
Successful computer studies of glass-forming materials need to overcome both the natural tendency to structural ordering and the dramatic increase of relaxation times at low temperatures. We present a comprehensive analysis of eleven…
We present a new approach to path integral Monte Carlo (PIMC) simulations based on the worm algorithm, originally developed for lattice models and extended here to continuous-space many-body systems. The scheme allows for efficient…
In a variety of biological situations, swimming cells have to move through complex fluids. Similarly, mucociliary clearance involves the transport of polymeric fluids by beating cilia. Here, we consider the extent to which complex fluids…
A new general purpose Monte Carlo event generator with self-adapting grid consisting of simplices is described. In the process of initialization, the simplex-shaped cells divide into daughter subcells in such a way that: (a) cell density is…
In this paper, we propose a novel approach to Bayesian experimental design for non-exchangeable data that formulates it as risk-sensitive policy optimization. We develop the Inside-Out SMC$^2$ algorithm, a nested sequential Monte Carlo…
We present a new, biased Monte Carlo scheme for simulating complex, cyclic peptides. Backbone atoms are equilibrated with a biased rebridging scheme, and side-chain atoms are equilibrated with a look-ahead configurational bias Monte Carlo.…
One of the many secrets to the success and prevalence of insects is their versatile, robust, and complex exoskeleton morphology. A fundamental challenge in insect-inspired robotics has been the fabrication of robotic exoskeletons that can…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
Machine learning inference pipelines commonly encountered in data science and industries often require real-time responsiveness due to their user-facing nature. However, meeting this requirement becomes particularly challenging when certain…
Many cells face search problems, such as finding food, mates or shelter, where their success depends on their search strategy. In contrast to other unicellular organisms, the slime mold Physarum polycephalum forms a giant network-shaped…