Related papers: Information Transmission and Processing in G-Prote…
How biological networks achieve robust control despite relying on imperfect, local information remains an important open question. Here, we identify thermodynamic constraints that can curtail non-equilibrium steady-state responses so…
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…
Recent experimental results suggest that the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble, at least for small fast folding proteins. To investigate the extent of the…
Many driven systems alternate between bursts of activity and quiescence and can become trapped in an absorbing state, such as complete inactivity in reaction-diffusion processes or extinction in predator-prey dynamics. It is generally…
Controlling crystallographic orientation in quasi-van der Waals (vdW) epitaxy remains a fundamental challenge, especially for material systems located near the boundary between weakly and strongly coupled growth regimes. In such marginal…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…
In nervous system information is conveyed by sequence of action potentials (spikes-trains). As MacKay and McCulloch proposed, spike-trains can be represented as bits sequences coming from Information Sources. Previously, we studied…
Neurotensin receptor 1 (NTSR1), a member of the Class A G protein-coupled receptor superfamily, plays an important role in modulating dopaminergic neuronal activity and eliciting opioid-independent analgesia. Recent studies suggest that…
Signal transduction is an important and basic mechanism to cell life activities. The stochastic state transition of receptor induces the release of signaling molecular, which triggers the state transition of other receptors. It constructs a…
We describe optimized coherent control methods for two-photon transitions in atoms of a ladder-type three-state energy configuration. Our approach is based on the spatial coherent control scheme which utilizes counter-propagating ultrashort…
This paper deals with the theory of structure, stability, robustness, and stabilization for an appealing class of nonlinear systems which arises in the analysis of chemical networks. The results given here extend, but are also heavily based…
Fluctuations-driven complex oscillations are experimentally observed in cellular systems such as hepatocytes, cardiac cells, neuronal cells, etc. These systems are generally operating in regimes far from thermodynamic equilibrium. To study…
We study nonequilibrium steady states of lattice gases with nearest-neighbor interactions that are driven between two reservoirs. Density profiles in these systems exhibit oscillations close to the reservoirs. We demonstrate that an…
When plotted in linear transformations of the Michaelis-Menten equation, ion uptake in plants has been shown to be multiphasic, i.e. to be represented by a series of straight lines separated by discontinuous transitions (Nissen 1971, 1974,…
In this paper, we take a brief look at the advantages and disadvantages of dominant frameworks in consciousness studies -- functionalist and causal structure theories, and use it to motivate a new non-equilibrium thermodynamic framework of…
We study information flow on a weighted graph whose topology evolves according to a spectral curvature measure $\mathcal{R}$. The model (FIU) defines $\mathcal{R}$ from the diagonal of the graph Green function, propagates energy with…
The nuclear pore supports molecular communication between cytoplasm and nucleus in eukaryotic cells. Selective transport of proteins is mediated by soluble receptors, whose regulation by the small GTPase Ran leads to cargo accumulation in,…
The dynamics of a packages diffusion process within a selforganized network is analytically studied by means of an extended $f$% -spin facilitated kinetic Ising model (Fredrickson-Andersen model) using a Fock-space representation for the…
We give a mathematical criterion for the concept of information flow within closed quantum systems described by quantum registers. We define the concepts of separations and entanglements over quantum registers and use them with the quantum…