Related papers: Universal pacemaker of genome evolution
Deep learning is changing many areas in molecular physics, and it has shown great potential to deliver new solutions to challenging molecular modeling problems. Along with this trend arises the increasing demand of expressive and versatile…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
A fundamental issue discussed in evolutionary biology is the transition from unicellular to multicellular organisms. Here we develop non-robust models provided in [1] and attempt to get robust models investigated how differentiation of…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
Locomotion is essential for living cells. It enables bacteria and algae to explore space for food, cancer to spread, and immune system to fight infections. Motile cells display trajectories of intriguing complexity, from regular (e.g.…
This paper characterizes the inherent power of evolutionary algorithms. This power depends on the computational properties of the genetic encoding. With some encodings, two parents recombined with a simple crossover operator can sample from…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…
Molecular dynamics (MD) provides insights into atomic-scale processes by integrating over time the equations that describe the motion of atoms under the action of interatomic forces. Machine learning models have substantially accelerated MD…
The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
A punctuated equilibrium model of biological evolution with relative fitness between different species being the fundamental driving force of evolution is introduced. Mutation is modeled as a fitness updating cellular automaton process…
Collective cellular movement plays a crucial role in many processes fundamental to health, including development, reproduction, infection, wound healing, and cancer. The emergent dynamics that arise in these systems are typically thought to…
The evolution model with parallel mutation-selection scheme is solved for the case when selection is accompanied by base substitutions, insertions, and deletions. The fitness is assumed to be either a single-peak function (i.e., having one…
In this paper we study the evolution of the mutation rate for simple organisms in dynamic environments. A model with multiple fitness coding loci tracking a moving fitness peak is developed and an analytical expression for the optimal…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
The evolution of complex cellular life involved two major transitions: the encapsulation of self-replicating genetic entities into cellular units and the aggregation of individual genes into a collectively replicating genome. In this paper,…
While modern physics and biology satisfactorily explain the passage from the Big Bang to the formation of Earth and the first cells to present-day life, respectively, the origins of biochemical life still remain an open question. Since…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
Biological approximations, which are universal for diverse species, are well known. With no other experimental data, their invariance to transformations from one species to another yields exact conservation (with respect to biological…