Related papers: Universal pacemaker of genome evolution
Cancer has been characterized as a constellation of hundreds of diseases differing in underlying mutations and depending on cellular environments. Carcinogenesis as a stochastic physical process has been studied for over sixty years, but…
Quantum walks are the quantum-mechanical analog of random walks, in which a quantum `walker' evolves between initial and final states by traversing the edges of a graph, either in discrete steps from node to node or via continuous evolution…
A central goal of evolutionary biology is to explain the origins and distribution of diversity across life. Beyond species or genetic diversity, we also observe diversity in the circuits (genetic or otherwise) underlying complex functional…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
We present a detailed study of the evolution of GMCs in a galactic disc simulation. We follow individual GMCs (defined in our simulations by a total column density criterion), including their level of star formation, from their formation to…
We introduce the notion of universal memcomputing machines (UMMs): a class of brain-inspired general-purpose computing machines based on systems with memory, whereby processing and storing of information occur on the same physical location.…
All-atom molecular simulation serves as a quintessential ``computational microscope'' for understanding the machinery of life, yet it remains fundamentally limited by the trade-off between quantum-mechanical (QM) accuracy and biological…
This paper proposes an extension of the traditional Central Dogma of molecular biology to a more dynamic model termed the Central Dogma Cycle (CDC) and a broader network called the Central Dogma Cyclic Network (CDCN). While the Central…
Epigenetics is a driving force of important and ubiquitous phenomena in nature such as cell differentiation or even metamorphosis. Oppositely to its widespread role, understanding the biophysical principles that allow epigenetics to control…
The distributed genome hypothesis states that the set of genes in a population of bacteria is distributed over all individuals that belong to the specific taxon. It implies that certain genes can be gained and lost from generation to…
Metabolic networks are known to be scale free but the evolutionary origin of this structural property is not clearly understood. One way of studying the dynamical process is to compare the metabolic networks of species that have arisen at…
The profound impact of Darwin's theory of evolution on biology has led to the acceptance of the theory in many complex systems that lie well beyond its original domain. Culture is one example that also exhibits key Darwinian evolutionary…
The evolution of molecular dynamics (MD) simulations has been intimately linked to that of computing hardware. For decades following the creation of MD, simulations have improved with computing power along the three principal dimensions of…
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.…
Due to the asymmetric nature of the nucleotides, the extant informational biomolecule, DNA, is constrained to replicate unidirectionally on a template. As a product of molecular evolution that sought to maximize replicative potential, DNA's…
We study the stochastic dynamics of sequences evolving by single site mutations, segmental duplications, deletions, and random insertions. These processes are relevant for the evolution of genomic DNA. They define a universality class of…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
One popular assumption regarding biological systems is that traits have evolved to be optimized with respect to function. This is a standard goal in evolutionary computation, and while not always embraced in the biological sciences, is an…
When a system is brought to a metastable state, nuclei of the equilibrium phase form and grow. This is the well-known nucleation and growth of first-order phase transitions. Near a critical point of a continuous phase transition, critical…
The computer revolution has been driven by a sustained increase of computational speed of approximately one order of magnitude (a factor of ten) every five years since about 1950. In natural sciences this has led to a continuous increase of…