Related papers: The Effective Geometry Monte Carlo Algorithm: Appl…
This work generalizes the discrete implicit Monte-Carlo (DIMC) method for modeling the radiative transfer equation from a gray treatment to an frequency-dependent one. The classic implicit Monte-Carlo (IMC) algorithm, that has been used for…
Molecular Communication (MC) architectures suffer from molecular build-up in the channel if they do not have appropriate reuptake mechanisms. The molecular build-up either leads to intersymbol interference (ISI) or reduces the transmission…
To better understand the capture process by a nanopore, we introduce an efficient Kinetic Monte Carlo (KMC) algorithm that can simulate long times and large system sizes by mapping the dynamic of a point-like particle in a 3D spherically…
Monte-Carlo Diffusion Simulations (MCDS) have been used extensively as a ground truth tool for the validation of microstructure models for Diffusion-Weighted MRI. However, methodological pitfalls in the design of the biomimicking…
Approximate inference in probabilistic graphical models (PGMs) can be grouped into deterministic methods and Monte-Carlo-based methods. The former can often provide accurate and rapid inferences, but are typically associated with biases…
Recently, molecular communication (MC) has been studied as a micro-scale communication between cells or molecular robots. In previous works, the MC channels in unbounded environment was analyzed. However, many of the experimentally…
We benchmark and analyze the error of energy conservation (EC) scheme for Particle in cell/Monte-Carlo Couple (PIC/MCC) algorithms by a radio frequency discharging simulation. The plasma heating behaviors and electron distributing functions…
Stochastic differential equations (SDEs) or diffusions are continuous-valued continuous-time stochastic processes widely used in the applied and mathematical sciences. Simulating paths from these processes is usually an intractable problem,…
Piecewise deterministic Markov process samplers are attractive alternatives to Metropolis--Hastings algorithms. A central design question is how to incorporate partial velocity refreshment to ensure ergodicity without injecting excessive…
We present a novel way of performing kinetic Monte Carlo simulations which does not require an {\it a priori} list of diffusion processes and their associated energetics and reaction rates. Rather, at any time during the simulation,…
The Expectation--Maximization (EM) algorithm is a simple meta-algorithm that has been used for many years as a methodology for statistical inference when there are missing measurements in the observed data or when the data is composed of…
In order to find the equilibrium geometries of molecules and solids and to perform ab initio molecular dynamics, it is necessary to calculate the forces on the nuclei. We present a correlated sampling method to efficiently calculate…
This paper presents a stochastic analysis of the time-variant channel impulse response (CIR) of a three dimensional diffusive mobile molecular communication (MC) system where the transmitter, the absorbing receiver, and the molecules can…
A simple Monte Carlo (MC) algorithm for the simulation of the passage of low-energy gamma rays and electrons through any material medium is presented. The algorithm includes several approximations that accelerate the simulation while…
In this paper, a diffusion-based molecular communication channel is modeled in presence of a probabilistic absorber. The probabilistic absorber is an absorber which absorbs molecules upon collision with probability q. With random walk…
Monte Carlo (MC) simulation is commonly considered to be the most accurate dose calculation method in radiotherapy. However, its efficiency still requires improvement for many routine clinical applications. In this paper, we present our…
Molecular communication (MC) is a new communication engineering paradigm where molecules are employed as information carriers. MC systems are expected to enable new revolutionary applications such as sensing of target substances in…
Molecular communication is an emerging paradigm for systems that rely on the release of molecules as information carriers. Communication via molecular diffusion is a popular strategy that is ubiquitous in nature and very fast over distances…
Molecular Communication (MC) is an important nanoscale communication paradigm, which is employed for the interconnection of the nanomachines (NMs) to form nanonetworks. A transmitter NM (TN) sends the information symbols by emitting…
In this work, we present an extensive computational study on the Ziff-Gulari-Barshad (ZGB) model extended in order to include the spatial diffusion of oxygen atoms and carbon monoxide molecules, both adsorbed on the surface. In our…