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Collective behaviour in living systems is observed across many scales, from bacteria to insects, to fish shoals. Zebrafish have emerged as a model system amenable to laboratory study. Here we report a three-dimensional study of the…

When studying the dynamics of trait distribution of populations in a heterogeneous environment, classical models from quantitative genetics choose to look at its system of moments, specifically the first two ones. Additionally, in order to…

We are interested in supporting software evolution caused by changing requirements and/or environmental settings. For example, users of a system may require new functionality (changing requirements), or performance enhancements to cope with…

A macroscopic theory for describing cellular states during steady-growth is presented, which is based on the consistency between cellular growth and molecular replication, as well as the robustness of phenotypes against perturbations.…

One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…

Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…

In order to recognize environmental effects on the evolution of dwarf galaxies in clusters of galaxies, it is first necessary to quantify the properties of objects which have evolved in relative isolation. With oxygen abundance as the gauge…

We discuss the efficacy of evolutionary method for the purpose of structural analysis of amorphous solids. At present ab initio molecular dynamics (MD) based melt-quench technique is used and this deterministic approach has proven to be…

In this research, we present a generalized quasispecies model in which population growth is governed by an arbitrary nonlinear function incorporating time delays. We begin by demonstrating that, under the constant population constraint, the…

The perfect phylogeny mixture (PPM) model is useful due to its simplicity and applicability in scenarios where mutations can be assumed to accumulate monotonically over time. It is the underlying model in many tools that have been used, for…

The aim of this paper is two-fold. First, we propose a new computational method to investigate the particularities of evolution. Second, we apply this method to a model of gene regulatory networks (GRNs) and explore the evolution of…

Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show…

Natural selection explains how life has evolved over millions of years from more primitive forms. The speed at which this happens, however, has sometimes defied formal explanations when based on random (uniformly distributed) mutations.…

Cell biomechanics involve a great number of complex phenomena that are fundamental to the evolution of life itself and other associated processes, ranging from the very early stages of embryo-genesis to the maintenance of damaged structures…

The mass discrepancy problem, observed in high-mass stars within eclipsing binaries, highlights systematic differences between dynamical and evolutionary mass estimates, challenging the accuracy of stellar evolution models. We aim to…

Genome length varies widely among organisms, from compact genomes of prokaryotes to vast and complex genomes of eukaryotes. In this study, we theoretically identify the evolutionary pressures that may have driven this divergence in genome…

The rheological response, in particular the non-linear response, to oscillatory shear is experimentally investigated in colloidal glasses. The glasses are highly concentrated binary hard-sphere mixtures with relatively large size…

Evolutionary computation methods have been successfully applied to neural networks since two decades ago, while those methods cannot scale well to the modern deep neural networks due to the complicated architectures and large quantities of…

A fundamental task in developmental biology is to identify the mechanisms which drive morphogenesis. In many cases, pattern formation is driven by the positional information determined by both the gradient of maternal factors and hard-wired…

Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…