Related papers: Diffusive hidden Markov model characterization of …
Time series of conformational dynamics in proteins are usually evaluated with hidden Markov models (HMMs). This approach works well if the number of states and their connectivity is known. However, for the multi-domain protein Hsp90, a…
Active loop extrusion - the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes - is firmly established mechanism responsible for chromatin spatial organization at different…
Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…
The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…
Extracting the intrinsic kinetic information of biological molecule from its single-molecule kinetic data is of considerable biophysical interest. In this work, we theoretically investigate the feasibility of inferring single RNA's…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as…
Over the past few decades, the Hawkes process has become a popular framework for modeling temporal events thanks to its flexibility to capture different dependency structures. The objective of this work is to model call sequences emitted by…
We address the problem of analyzing sets of noisy time-varying signals that all report on the same process but confound straightforward analyses due to complex inter-signal heterogeneities and measurement artifacts. In particular we…
Single-particle tracking allows to infer the motion of single molecules in living cells. When we observe a long trajectory (more than 100 points), it is possible that the particle switches mode of motion over time. Then, fitting a single…
The conformational kinetics of enzymes can be reliably revealed when they are governed by Markovian dynamics. Hidden Markov Models (HMMs) are appropriate especially in the case of conformational states that are hardly distinguishable.…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
A hidden Markov model (HMM) solved recursively by the Viterbi algorithm can be configured to search for persistent, quasimonochromatic gravitational radiation from an isolated or accreting neutron star, whose rotational frequency is unknown…
When analysing gene expression time series data an often overlooked but crucial aspect of the model is that the regulatory network structure may change over time. Whilst some approaches have addressed this problem previously in the…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
We investigate the nonlinear dynamics of a damped Peyrard-Bishop DNA model taking into account long-range interactions with distance dependence |l|^-s on the elastic coupling constant between different DNA base pairs. Considering both…
Experiments, in particular on biological systems, typically probe lower-dimensional observables which are projections of high-dimensional dynamics. In order to infer consistent models capturing the relevant dynamics of the system, it is…