30 citations · 192 across the 13 of their papers we have counts for
13 papers
Attraction-Induced Cluster Fragmentation and Local Alignment in Active Particle Systems
Sota Shimamura, Nen Saito, Shuji Ishihara
We numerically studied active Brownian particles with attractive interactions. Contrary to our intuition, the attractive force between particles disrupts the formation of a single…
Active Deformable Cells Undergo Cell Shape Transition Associated with Percolation of Topological Defects
Nen Saito, Shuji Ishihara
Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for understanding tissue homeostasis and stabl…
Rare-Event Sampling Analysis Uncovers the Fitness Landscape of the Genetic Code
Yuji Omachi, Nen Saito, Chikara Furusawa
The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). Wh…
The advantage of leakage of essential metabolites and resultant symbiosis of diverse species
Jumpei F Yamagishi, Nen Saito, Kunihiko Kaneko
Microbial communities display extreme diversity. A variety of strains or species coexist even when limited by a single resource. It has been argued that metabolite secretion create…
Symbiotic Cell Differentiation and Cooperative Growth in Multicellular Aggregates
Jumpei F Yamagishi, Nen Saito, Kunihiko Kaneko
As cells grow and divide under a given environment, they become crowded and resources are limited, as seen in bacterial biofilms and multicellular aggregates. These cells often sho…
Motif Analysis for Small-Number Effects in Chemical Reaction Dynamics
Nen Saito, Yuki Sughiyama, Kunihiko Kaneko
The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-…
Theoretical Analysis of Discreteness-Induced Transition in Autocatalytic Reaction Dynamics
Nen Saito, Kunihiko Kaneko
Transitions in the qualitative behavior of chemical reaction dynamics with a decrease in molecule number have attracted much attention. Here, a method based on a Markov process wit…
Multicanonical MCMC for Sampling Rare Events
Yukito Iba, Nen Saito, Akimasa Kitajima
Multicanonical MCMC (Multicanonical Markov Chain Monte Carlo; Multicanonical Monte Carlo) is discussed as a method of rare event sampling. Starting from a review of the generic fra…
Evolution of Genetic Redundancy : The Relevance of Complexity in Genotype-Phenotype Mapping
Nen Saito, Shuji Ishihara, Kunihiko Kaneko
Genetic redundancy is ubiquitous and can be found in any organism. However, it has been argued that genetic redundancy reduces total population fitness, and therefore, redundancy i…
The Baldwin effect under multi-peaked fitness landscapes: Phenotypic fluctuation accelerates evolutionary rate
Nen Saito, Shuji Ishihara, Kunihiko Kaneko
Phenotypic fluctuations and plasticity can generally affect the course of evolution, a process known as the Baldwin effect. Several studies have recast this effect and claimed that…
Robustness Leads Close to the Edge of Chaos in Coupled Map Networks: toward the understanding of biological networks
Nen Saito, Macoto Kikuchi
Dynamics in biological networks are in general robust against several perturbations. We investigate a coupled map network as a model motivated by gene regulatory networks and desig…
Probability of graphs with large spectral gap by multicanonical Monte Carlo
Nen Saito, Yukito Iba
Graphs with large spectral gap are important in various fields such as biology, sociology and computer science. In designing such graphs, an important question is how the probabili…
Multicanonical sampling of rare events in random matrices
Nen Saito, Yukito Iba, Koji Hukushima
A method based on multicanonical Monte Carlo is applied to the calculation of large deviations in the largest eigenvalue of random matrices. The method is successfully tested with…