Related papers: Evolution of the Ubiquitin-Activating Enzyme Uba1 …
A theoretical study of cell evolution is presented here. By using a toolbox containing an intracellular catalytic reaction network model and a mutation-selection process, four distinct phases of self-organization were unveiled. First, the…
Known as one of the hallmarks of cancer [30], cancer cell invasion of human body tissue is a complicated spatio-temporal multiscale process which enables a localised solid tumour to transform into a systemic, metastatic and fatal disease.…
We investigated melting transitions in biological membranes in their native state that include their membrane proteins. These membranes originated from \textit{E. coli}, \textit{B. subtilis}, lung surfactant and nerve tissue from the spinal…
The evolutionary origins of ageing and age-associated diseases continue to pose a fundamental question in biology. This study is concerned with a recently proposed framework, which conceptualises development and ageing as a continuous…
The evolution of various competing cell types in tissues, and the resulting persistent tissue population, is studied numerically and analytically in a particle-based model of active tissues. Mutations change the properties of cells in…
The evolution of multiplicity distribution of a species which undergoes chemical reactions can be described with the help of a master equation. We study the master equation for a fixed temperature, because we want to know how fast different…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…
We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate…
We incorporate hydrodynamic interactions in a structure-based model of ubiquitin and demonstrate that the hydrodynamic coupling may reduce the peak force when stretching the protein at constant speed, especially at larger speeds.…
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…
Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature…
To maintain a constant cell size, dividing cells have to coordinate cell cycle events with cell growth. This coordination has for long been supposed to rely on the existence of size thresholds determining cell cycle progression [1]. In…
Bacterial attachment to a fluid interface can lead to the formation of a film with physicochemical properties that evolve with time. We study the time evolution of interface (micro)mechanics for interfaces between oil and bacterial…
Organisms have increased in complexity through a series of major evolutionary transitions, in which formerly autonomous entities become parts of a novel higher-level entity. One intriguing feature of the higher-level entity after some major…
We investigate the evolution of a single qubit subject to a continuous unitary dynamics and an additional interrupting influence which occurs periodically. One may imagine a dynamically evolving closed quantum system which becomes open at…
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…
Neural networks show a progressive increase in complexity during the time course of evolution. From diffuse nerve nets in Cnidaria to modular, hierarchical systems in macaque and humans, there is a gradual shift from simple processes…
Membrane phase behavior induced by the binding of curvature-inducing proteins is studied by a combination of analytical and numerical approaches. In thermal equilibrium under the detailed balance between binding and unbinding, the membrane…
We propose an approach of open-ended evolution via the simulation of swarm dynamics. In nature, swarms possess remarkable properties, which allow many organisms, from swarming bacteria to ants and flocking birds, to form higher-order…
Biological forces govern essential cellular and molecular processes in all living organisms. Many cellular forces, e.g. those generated in cyclic conformational changes of biological machines, have repetitive components. However, little is…