Related papers: Enzyme localization can drastically affect signal …

Biochemical covalent modification networks exhibit a remarkable suite of steady state and dynamical properties such as multistationarity, oscillations, ultrasensitivity and absolute concentration robustness. This paper focuses on conditions…

Many real-world networks are embedded in space, and their resilience in the presence of reinforced nodes has not been studied. Here we model such networks using a spatial network model that have an exponential distribution of link length…

Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-grained models of cellular networks in simple organisms. In…

Knowing the location of a protein within the cell is important for understanding its function, role in biological processes, and potential use as a drug target. Much progress has been made in developing computational methods that predict…

Local changes in pH are known to significantly alter the state and activity of proteins and in particular enzymes. pH variations induced by pulses propagating along soft interfaces (e.g. the lipid bilayer) would therefore constitute an…

The motion of a eukaryotic cell presents a variety of interesting and challenging problems from both a modeling and a computational perspective. The processes span many spatial scales (from molecular to tissue) as well as disparate time…

Eukaryotic cells adhere to extracellular matrix during the normal development of the organism, forming static adhesion as well as during cell motility. We study this process by considering a simplified coarse-grained model of a vesicle that…

Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…

Liquid-liquid phase separation is now recognized as a common mechanism for regulating enzyme activity in cells. Insights from studies in cells are complemented by in vitro studies aimed at developing better understanding of mechanisms…

Electrochemical communication is a mechanism that enables intercellular interaction among bacteria within communities. Bacteria achieves synchronization and coordinates collective actions at the population level through the utilization of…

We describe the possibility of drastically boosting the spontaneous emission of a collection of two-level quantum emitters by embedding them in an epsilon-near-zero (ENZ) environment, consisting of a plasmonic waveguide operated at cut-off.…

Proteins with multiple binding sites play important roles in cell signaling systems by nucleating protein complexes in which, for example, enzymes and substrates are co-localized. Proteins that specialize in this function are called by a…

One of the most important steps in the developmental process of the bacteria cell at the cellular level is the determination of the middle of the cell and the proper placement of the septum, these being essential to the division of the…

We investigate the effect of a two-level jump process or random telegraph noise on a square wave driven tight-binding lattice. In the absence of the noise, the system is known to exhibit dynamical localization for specific ratios of the…

The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…

The progress of the successive rounds of catalytic conversion of substrates into product(s) by a single enzyme is characterized by the distribution of turnover times. Establishing the most general form of dependence of this distribution on…

Electron transport properties through single conjugated molecules sandwiched between two non-superconducting electrodes are studied by the use of Green's function technique. Based on the tight-binding model, we do parametric calculations to…

The hormone auxin is actively transported throughout plants via protein machineries including the dedicated transporter known as PIN. The associated transport is ordered with nearby cells driving auxin flux in similar directions. Here we…

We study the environment-assisted enhancement of the excitation-transport efficiency across a network of interacting quantum particles or sites. Our study reveals a crucial influence of the network configuration - and especially its degree…

Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…