Related papers: Mechanochemical action of the dynamin protein
For a model glass-former we demonstrate via computer simulations how macroscopic dynamic quantities can be inferred from a PEL analysis. The essential step is to consider whole superstructures of many PEL minima, called metabasins, rather…
Evolution of the amino acid sequences of transthyretin (TTR) can provide additional information about its dynamics that both complements and extends the already extensive static structural data. Protein dynamics is largely driven by…
Microtubules are a major component of the cytoskeleton distinguished by highly dynamic behavior both in vitro and in vivo. We propose a general mathematical model that accounts for the growth, catastrophe, rescue and nucleation processes in…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
Microtubules are biological protein polymers with critical and diverse functions. Their structures share some similarities with photosynthetic antenna complexes, particularly in the ordered arrangement of photoactive molecules with large…
We model the dynamical states of the C-termini of tubulin dimers that comprise neuronal microtubules. We use molecular dynamics and other computational tools to explore the time-dependent behavior of conformational states of a C-terminus of…
Membrane organization is essential for cellular functions such as signal transduction and membrane trafficking. A major challenge is to understand the lateral heterogeneous structures in membranes and membrane fluidity in the presence of…
The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with…
Many-body dissipative particle dynamics (MDPD) offers a significant speed-up in the simulation of various systems, including soft matter, in comparison with molecular dynamics (MD) simulations based on Lennard-Jones nteractions, which is…
Microphase separation of membrane components is thought to play an important role in many physiological processes, from cell signaling to endocytosis and cellular trafficking. Here, we study how variations in the membrane composition can be…
Random lateral translocation of lipids and proteins is a universal process on membrane surfaces. Local aggregation or organization of lipids and proteins can be induced when this lateral random diffusion is mediated by the electrostatic…
A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a `protein-like' dynamical transition in nonbiological aqueous environments. To this aim we exploit the popular colloidal…
Active filaments, such as microtubules with attached cargo-carrying motor proteins, are important dynamic structures for fluid transport in and around living cells. The mathematical models of active filaments appearing in the literature…
We have developed several distinct model systems of microtubule-based 3D active isotropic fluids and have compared their dynamical and structural properties. The non-equilibrium dynamics of these fluids is powered by three different types…
Motor proteins are active enzyme molecules that play a crucial role in many biological processes. They transform the chemical energy into the mechanical work and move unidirectionally along rigid cytoskeleton filaments. Single-molecule…
Recent Molecular Dynamics simulations of glass-forming liquids revealed superdiffusive fluctuations associated with the position of a tracer particle (TP) driven by an external force. Such anomalous response, whose mechanism remains…
The reaction-diffusion waves of proteins are known to be involved in fundamental cellular functions, such as cell migration, cell division, and vesicular transportation. In some of these phenomena, pattern formation on the membranes is…
Membrane shape fluctuations induce attractive interactions between rigid inclusions. Previous analytical studies showed that the fluctuation-induced pair interactions are rather small compared to thermal energies, but also that multi-body…
The extraction of membrane tubes by molecular motors is known to play an important role for the transport properties of eukaryotic cells. By studying a generic class of models for the tube extraction, we discover a rich phase diagram. In…
Active networks composed of biopolymers and motor proteins provide versatile biomimetic systems that have advanced active matter physics and deepened our understanding of cytoskeletal dynamics and self-organization under diverse stimuli. In…