相关论文: Modeling Dual Pathways for the Metazoan Spindle As…

Many active fluid systems encountered in biology are set in total geometric confinement. Cytoplasmic streaming in plant cells is a prominent and ubiquitous example, in which cargo-carrying molecular motors move along polymer filaments and…

Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…

Dysregulation in signal transduction pathways can lead to a variety of complex disorders, including cancer. Computational approaches such as network analysis are important tools to understand system dynamics as well as to identify critical…

Signal transduction in biological cells is effected by signaling pathways that typically include multiple feedback loops. Here we analyze information transfer through a prototypical signaling module with biochemical feedback. The module…

Biopolymer self-assembly pathways are central to biological activity, but are complicated by the ability of the monomeric subunits of biopolymers to adopt different conformational states. As a result, biopolymer nucleation often involves a…

Experiments show that the movement of eukaryotic cells is regulated by a process of phase separation of two competing enzymes on the cell membrane, that effectively amplifies shallow external gradients of chemical attractant. Notably, the…

Using molecular dynamics simulation, we investigate transport properties of a classical two-dimensional electron system confined in a microchannel with a narrow constriction. As a function of the confinement strength of the constriction,…

The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…

Nonlinear systems driven by recurrent signals are known to exhibit complex dynamical responses which, in the physiological context, can have important functional consequences. One of the simplest biological systems that is exposed to such…

During metastatic dissemination, streams of cells collectively migrate through a network of narrow channels within the extracellular matrix, before entering into the blood stream. This strategy is believed to outperform other migration…

During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. Establishing a stable overlap region is essential for maintenance of…

Modeling and simulation are transforming all fields of biology. Tools like AlphaFold have revolutionized structural biology, while molecular dynamics simulations provide invaluable insights into the behavior of macromolecules in solution or…

Transport of molecular motors along protein filaments in a half-closed geometry is a common feature of biologically relevant processes in cellular protrusions. Using a lattice gas model we study how the interplay between active and…

To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…

Two identical autonomous dynamical systems coupled in a master-slave configuration can exhibit anticipated synchronization (AS) if the slave also receives a delayed negative self-feedback. Recently, AS was shown to occur in systems of…

Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…

The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view,…

We investigate the two-photon transport through a waveguide side-coupling to a whispering-gallery-atom system. Using the Lehmann-Symanzik-Zimmermann (LSZ) reduction approach, we present the general formula for the two-photon processes…

Rhythmic activity is ubiquitous in biological systems from the cellular to organism level. Reconstructing the instantaneous phase is the first step in analyzing the essential mechanism leading to a synchronization state from the observed…

We describe a method for coupling an embedded domain in a magnetohydrodynamic (MHD) simulation with a particle-in-cell (PIC) method. In this two-way coupling we follow the work of Daldorff et al. in which the PIC domain receives its initial…