Related papers: Monte Carlo Simulation and Statistical Analysis of…
Particle-in-cell (PIC) simulations with Monte-Carlo collisions are used in plasma science to explore a variety of kinetic effects. One major problem is the long run-time of such simulations. Even on modern computer systems, PIC codes take a…
We use quantum Monte Carlo methods in the framework of the interacting nuclear shell model to calculate the statistical properties of nuclei at finite temperature and/or excitation energies. With this approach we can carry out realistic…
Evolution is the theory that plants and animals today have come from kinds that have existed in the past. Scientists such as Charles Darwin and Alfred Wallace dedicate their life to observe how species interact with their environment, grow,…
A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is…
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed…
Using a lattice model based on Monte Carlo simulations, we study the role of the reproduction pattern on the fate of an evolving population. Each individual is under the selection pressure from the environment and random mutations. The…
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…
We demonstrate how a genetic algorithm solves the problem of minimizing the resources used for network coding, subject to a throughput constraint, in a multicast scenario. A genetic algorithm avoids the computational complexity that makes…
Networks of genetic expression can be modelled by hypergraphs with the additional structure that real coefficients are given to each vertex-edge incidence. The spectra, i.e. the multiset of the eigenvalues, of such hypergraphs, are known to…
This paper presents our computational methodology using Genetic Algorithms (GA) for exploring the nature of RNA editing. These models are constructed using several genetic editing characteristics that are gleaned from the RNA editing system…
We present a case-study on the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods. Graphics cards, containing multiple Graphics Processing Units (GPUs), are self-contained parallel…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
Here we study how mutations which change physical properties of cell proteins (stability) impact population survival and growth. In our model the genotype is presented as a set of N numbers, folding free energies of cells N proteins.…
Conventional population genetics considers the evolution of a limited number of genotypes corresponding to phenotypes with different fitness. As model phenotypes, in particular RNA secondary structure, have become computationally tractable,…
Convolutional codes are error-correcting linear codes that utilize shift registers to encode. These codes have an arbitrary block size and they can incorporate both past and current information bits. DNA codes represent DNA sequences and…
We have modified the sexual Penna model by introducing the fluctuating environment and fluctuations representing physiological functions of individuals. Additionally, we have introduced the mother care corresponding to the protection…
Supervised learning is limited both by the quantity and quality of the labeled data. In the field of medical record tagging, writing styles between hospitals vary drastically. The knowledge learned from one hospital might not transfer well…
Proteins are responsible for the most diverse set of functions in biology. The ability to extract information from protein sequences and to predict the effects of mutations is extremely valuable in many domains of biology and medicine.…
The Penna model is a model of evolutionary ageing through mutation accumulation where traditionally time and the age of an organism are treated as discrete variables and an organism's genome by a binary bit string. We reformulate the…
Since the early 1970s, stellar population modelling has been one of the basic tools for understanding the physics of unresolved systems from observation of their integrated light. Models allow us to relate the integrated spectra (or…