Computational Biophysical Modeling of the Radiation Bystander Effect in Irradiated Cells

It is well known that ionizing radiation can cause damages to cells that interact with it directly. However, many studies have shown that damages also occur in cells that have not experienced direct interaction. This is due to the so-called bystander effect, which is observed when the irradiated cell sends signals that can damage neighboring cells. Due to the complexity of this effect, it is not easy to strictly describe it biophysically, and thus it is also difficult to simulate. This article reviews various approaches to modeling and simulating the bystander effect from the point of view of radiation biophysics. In particular, the last model presented within this article is part of a larger project of modeling the response of a group of cells to ionizing radiation using Monte Carlo methods. The new approach presented here is based on the probability tree, the Poisson distribution of signals and the saturated dose-related probability distribution of the bystander effect’s appearance, which makes the model very broad and universal.

Sampling from Complex Probability Distributions: A Monte Carlo Primer for Engineers

Models which are constructed to represent the uncertainty arising in engineered systems can often be quite complex to ensure they provide a reasonably faithful reflection of the real-world system. As a result, even computation of simple expectations, event probabilities, variances, or integration over utilities for a decision problem can be analytically intractable. Indeed, such models are often sufficiently high dimensional that even traditional numerical methods perform poorly. However, access to random samples drawn from the probability model under study typically simplifies such problems substantially. The methodologies to generate and use such samples fall under the stable of techniques usually referred to as ‘Monte Carlo methods’. This chapter provides a motivation, simple primer introduction to the basics, and sign-posts to further reading and literature on Monte Carlo methods, in a manner that should be accessible to those with an engineering mathematics background. There is deliberately informal mathematical presentation which avoids measure-theoretic formalism. The accompanying lecture can be viewed at https://www.louisaslett.com/Courses/UTOPIAE/.

Linking and link complexity of geometrically constrained pairs of rings

We investigate and compare the effects of two different constraints on the geometrical properties and linking of pairs of polygons on the simple cubic lattice, using Monte Carlo methods. One constraint is to insist that the centres of mass of the two polygons are less than distance $d$ apart, and the other is to insist that the radius of gyration of the \emph{pair} of polygons is less than $R$. The second constraint results in links that are quite spherically symmetric, especially at small values of $R$, while the first constraint gives much less spherically symmetric pairs, prolate at large $d$ and becoming more oblate at smaller $d$. These effects have an influence on the observed values of the linking probability and link spectrum.

Mismatching as a tool to enhance algorithmic performances of Monte Carlo methods for the planted clique model

Over-parametrization was a crucial ingredient for recent developments in inference and machine-learning fields. However a good theory explaining this success is still lacking. In this paper we study a very simple case of mismatched over-parametrized algorithm applied to one of the most studied inference problem: the planted clique problem. We analyze a Monte Carlo (MC) algorithm in the same class of the famous Jerrum algorithm. We show how this MC algorithm is in general suboptimal for the recovery of the planted clique. We show however how to enhance its performances by adding a (mismatched) parameter: the temperature; we numerically find that this over-parametrized version of the algorithm can reach the supposed algorithmic threshold for the planted clique problem.