Related papers: G-quadruplexes and mRNA localization
Recent molecular dynamics simulations show that thermal gradients can induce electric fields in water that are comparable in magnitude to electric fields seen in ionic thin films and biomembranes. This surprising non-equilibrium phenomenon…
All cells must keep time to consistently perform vital biological functions. To that end, the coupling and interrelatedness of diverse subsecond events in the complex cellular environment, such as protein folding or translation rates,…
The collective chemotaxis of multicellular clusters is an important phenomenon in various physiological contexts, ranging from embryonic development to cancer metastasis. Such clusters often display interesting shape dynamics and…
We use density functional theory to describe the phase behaviors of rigid molecules. The construction of kernel function G(x, P, x, P) is discussed. Excluded-volume potential is calculated for two types of molecules with C_{2v} symmetry.…
RNA molecules in living cells form what look like liquid droplets formed by liquid/liquid phase separation. But unlike the molecules in conventional phase separating mixtures, RNA molecules are transported by molecular motors that consume…
The method of molecular dynamics is used to investigate the distribution of DOBAMBC molecules in a capsule with the fixed border layer. Change of an arrangement of molecules in smectic layers depending on an inclination of molecules on…
Localization and delocalization of two photons in an array of cavities are examined. Role of entanglement and relative phase of the initial state in the occurrence of localization or delocalization during time evolution is elucidated.
The shapes of cell membranes are largely regulated by membrane associated, curvature active, proteins. We use a numerical model of the membrane with elongated membrane inclusions, recently developed by us, which posses spontaneous…
Glasses are ubiquitous amorphous solids that remain one of the big mysteries in condensed matter. Despite the vast body of literature on glasses, a unifying approach to link the structure and dynamics of glasses is still missing. A growing…
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase…
A dynamical quark model of hadron and nucleus structure is proposed. In the frame of the model, called the Strongly Correlated Quark Model, quarks and nucleons inside nuclei are arranged in a crystal--like structure.
The charge and potential distributions for insulating particles approaching a substrate with regular insulating structures are studied by particle-in-cell numerical simulations. An elongated particle and substrate with elongated structures…
We study the structural characteristics of complex networks using the representative eigenvectors of the adjacent matrix. The probability distribution function of the components of the representative eigenvectors are proposed to describe…
Channel proteins, that selectively conduct molecules across cell membranes, often exhibit an asymmetric structure. By means of a stochastic model, we argue that channel asymmetry in the presence of non-equilibrium fluctuations, fueled by…
Eukaryotic cell motility is crucial during development, wound healing, the immune response, and cancer metastasis. Some eukaryotic cells can swim, but cells more commonly adhere to and crawl along the extracellular matrix. We study the…
Curved fluid interfaces are investigated on the nanometre length scale by molecular dynamics simulation. Thereby, droplets surrounded by a metastable vapour phase are stabilized in the canonical ensemble. Analogous simulations are conducted…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
We describe the dynamics of a bound state of an attractive $\delta$-well under displacement of the potential. Exact analytical results are presented for the suddenly moved potential. Since this is a quantum system, only a fraction of the…
The organization of live cells into tissues and their subsequent biological function involves inter-cell mechanical interactions, which are mediated by their elastic environment. To model this interaction, we consider cells as spherical…