Related papers: Diffusive hidden Markov model characterization of …
Machine learning techniques not only offer efficient tools for modelling dynamical systems from data, but can also be employed as frontline investigative instruments for the underlying physics. Nontrivial information about the original…
Loop extrusion is one of the main processes shaping chromosome organisation across the cell cycle, yet its role in regulating DNA entanglement and nucleoplasm viscoelasticity remains overlooked. We simulate entangled solutions of linear…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
In the present paper we propose to describe gene networks in biological systems using probabilistic algorithms. We describe gene duplication in the process of biological evolution using introduction of the replica procedure for…
DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying…
Biomarker measurements obtained by blood sampling are often used as a non-invasive means of monitoring tumour progression in cancer patients. Diseases evolve dynamically over time, and studying longitudinal observations of specific…
Discrete-space kinetic models, i.e., Markov state models, have emerged as powerful tools for reducing the complexity of trajectories generated from molecular dynamics simulations. These models require configuration-space representations…
DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. The worm-like chain model provides a good description of small to moderate bending fluctuations, but some experiments on strongly-bent shorter molecules…
Brownian motion provides access to hydrodynamic properties of nanoscale objects independent of their optical resolvability. Here, we present a diffusion-based approach to infer effective particle size distributions of DNA-functionalized…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Examples of such systems include DNA-functionalized colloids as well as nanoparticles grafted with antibodies to cell membrane…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time…
The movement of intracellular cargo transported by molecular motors is commonly marked by switches between directed motion and stationary pauses. The predominant measure for assessing movement is effective diffusivity, which predicts the…
We introduce an extension of finite mixture models by incorporating skew-normal distributions within a Hidden Markov Model framework. By assuming a constant transition probability matrix and allowing emission distributions to vary according…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with…
Ecologists often use a hidden Markov model to decode a latent process, such as a sequence of an animal's behaviours, from an observed biologging time series. Modern technological devices such as video recorders and drones now allow…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
Motivated by subdiffusive motion of bio-molecules observed in living cells we study the stochastic properties of a non-Brownian particle whose motion is governed by either fractional Brownian motion or the fractional Langevin equation and…