Related papers: G-quadruplexes and mRNA localization
Aberrantly regulated cell motility is a hallmark of cancer cells. A hybrid agent-based model has been developed to investigate the synergistic and antagonistic cell motility-impacting effects of three microenvironment variables…
RNA velocity is an important model that combines cellular spliced and unspliced RNA counts to infer dynamical properties of various regulatory functions. Despite its wide applicability and many variants used in practice, the model has not…
Many of the most important processes in cells take place on and across membranes. With the rise of an impressive array of powerful quantitative methods for characterizing these membranes, it is an opportune time to reflect on the structure…
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…
Particle localization is an essential ingredient in quantum Hall physics [1,2]. In conventional high mobility two-dimensional electron systems Coulomb interactions were shown to compete with disorder and to play a central role in particle…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
Dynamic heterogeneity is expected to be a key concept for understanding the origin of slow dynamics near the glass transition. In previous studies, quantitative evaluations of dynamic heterogeneity have been attempted using two different…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
The dynamics of two-dimensional fluids confined within a random matrix of obstacles is investigated using both colloidal model experiments and molecular dynamics simulations. By varying fluid and matrix area fractions in the experiment, we…
During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…
Signaling molecules play an important role for many cellular functions. We investigate here a general system of two membrane reaction-diffusion equations coupled to a diffusion equation inside the cell by a Robin-type boundary condition and…
Uncertainty relations for particle motion in curved spaces are discussed. The relations are shown to be topologically invariant. New coordinate system on a sphere appropriate to the problem is proposed. The case of a sphere is considered in…
It has been recently argued that the depletion attraction may play an important role in different aspects of the cellular organization, ranging from the organization of transcriptional activity in transcription factories to the formation of…
We have employed molecular dynamics simulations based on the TIP4P/2005 water model to investigate the local structural, dynamical, and dielectric properties of the two recently reported body-centered-cubic and face-centered-cubic plastic…
Liquid-liquid phase separation has emerged as a fundamental mechanism underlying intracellular organization, with evidence for it being reported in numerous different systems. However, there is a growing concern regarding the lack of…
The dipole moment is a physical quantity indicating the polarity of a molecule and is determined by reflecting the electrical properties of constituent atoms and the geometric properties of the molecule. Most embeddings used to represent…
Flow instabilities play important roles in a wide range of engineering, geophysical, and astrophysical flows, ranging from supernova explosion in crab nebula, formation of clouds in sky, waves on ocean, to inertial confinement fusion…
We consider the lateral diffusion of a protein interacting with the curvature of the membrane. The interaction energy is minimized if the particle is at a membrane position with a certain curvature that agrees with the spontaneous curvature…
Molecules have seemed like a natural fit to deep learning's tendency to handle a complex structure through representation learning, given enough data. However, this often continuous representation is not natural for understanding chemical…
Molecular structure is often considered as emerging from the decoherence effect of the environment. Electrons are part of the environment of the nuclei in a molecule. In this work, their contribution to the classical-like geometrical…