Machine learning for active matter
The availability of large datasets has boosted the application of machine learning in many
fields and is now starting to shape active-matter research as well. Machine learning …
fields and is now starting to shape active-matter research as well. Machine learning …
Learning dynamical models of single and collective cell migration: a review
D Brückner, CP Broedersz - Reports on Progress in Physics, 2024 - iopscience.iop.org
Single and collective cell migration are fundamental processes critical for physiological
phenomena ranging from embryonic development and immune response to wound healing …
phenomena ranging from embryonic development and immune response to wound healing …
[HTML][HTML] Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics
Advances in single-cell technologies allow scrutinizing of heterogeneous cell states,
however, detecting cell-state transitions from snap-shot single-cell transcriptome data …
however, detecting cell-state transitions from snap-shot single-cell transcriptome data …
[HTML][HTML] A combination of machine learning and infrequent metadynamics to efficiently predict kinetic rates, transition states, and molecular determinants of drug …
JM Lamim Ribeiro, D Provasi, M Filizola - The Journal of Chemical …, 2020 - pubs.aip.org
Determining the drug-target residence time (RT) is of major interest in drug discovery given
that this kinetic parameter often represents a better indicator of in vivo drug efficacy than …
that this kinetic parameter often represents a better indicator of in vivo drug efficacy than …
A dimension reduction approach for energy landscape: identifying intermediate states in metabolism‐EMT network
X Kang, C Li - Advanced Science, 2021 - Wiley Online Library
Dimension reduction is a challenging problem in complex dynamical systems. Here, a
dimension reduction approach of landscape (DRL) for complex dynamical systems is …
dimension reduction approach of landscape (DRL) for complex dynamical systems is …
Energy landscape decomposition for cell differentiation with proliferation effect
Complex interactions between genes determine the development and differentiation of cells.
We establish a landscape theory for cell differentiation with proliferation effect, in which the …
We establish a landscape theory for cell differentiation with proliferation effect, in which the …
Controlling Uncertainty of Empirical First-Passage Times in the Small-Sample Regime
R Bebon, A Godec - Physical Review Letters, 2023 - APS
We derive general bounds on the probability that the empirical first-passage time τ¯ n≡∑ i=
1 n τ i/n of a reversible ergodic Markov process inferred from a sample of n independent …
1 n τ i/n of a reversible ergodic Markov process inferred from a sample of n independent …
Topological metric detects hidden order in disordered media
Recent advances in microscopy techniques make it possible to study the growth, dynamics,
and response of complex biophysical systems at single-cell resolution, from bacterial …
and response of complex biophysical systems at single-cell resolution, from bacterial …
[HTML][HTML] Conformational state switching and pathways of chromosome dynamics in cell cycle
The cell cycle is a process and function of a cell with different phases essential for cell
growth, proliferation, and replication. It depends on the structure and dynamics of the …
growth, proliferation, and replication. It depends on the structure and dynamics of the …
Estimation of non-equilibrium transition rate from gene expression data
F Chen, Y Bai, C Li - Briefings in Bioinformatics, 2023 - academic.oup.com
The dynamical properties of many complex physical and biological systems can be
quantified from the energy landscape theory. Previous approaches focused on estimating …
quantified from the energy landscape theory. Previous approaches focused on estimating …