Related papers: An allosteric model for circadian KaiC phosphoryla…
In a recent series of ground-breaking experiments, Nakajima et al. [Science 308, 414-415 (2005)] showed that the three cyanobacterial clock proteins KaiA, KaiB, and KaiC are sufficient in vitro to generate circadian phosphorylation of KaiC.…
By incubating the mixture of three cyanobacterial proteins, KaiA, KaiB, and KaiC, with ATP in vitro, Kondo and his colleagues reconstituted the robust circadian rhythm of the phosphorylation level of KaiC (Science, 308; 414-415 (2005)).…
The simple circadian oscillator found in cyanobacteria can be reconstituted in vitro using three proteins-KaiA, KaiB and KaiC. The total phosphorylation level of KaiC oscillates with a circadian period. Recent experiments elucidated the…
It is possible that there are post-translational circadian oscillators that continue functioning in the absence of negative feedback transcriptional repression in many cell types from diverse organisms. Apart from the KaiABC system from…
In this Supporting information we provide background information on our model of the bacterial flagellar motor. We also derive the analytical solution of our coarse-grained model of the switching dynamics and explain the hybrid stochastic…
The KaiABC circadian clock from cyanobacteria is the only known three-protein oscillatory system which can be reconstituted outside the cell and which displays sustained periodic dynamics in various molecular state variables. Despite many…
Circadian clocks must be able to entrain to time-varying signals to keep their oscillations in phase with the day-night rhythm. On the other hand, they must also exhibit input compensation: their period must remain about one day in…
Biological oscillators are very diverse but can be classified based on dynamical motifs such as the types of feedback loops present. The S. Elongatus circadian clock is a remarkable phosphorylation-based oscillator that can be reconstituted…
Quasi steady state assumptions are often used to simplify complex systems of ordinary differential equations in modelling of biochemical processes. The simplified system is designed to have the same qualitative properties as the original…
We illustrate the use of tools (asymptotic theories of standard error quantification using appropriate statistical models, bootstrapping, model comparison techniques) in addition to sensitivity that may be employed to determine the…
A simplified mathematical model of oral hydrocortisone delivery in adrenal insufficiency is described; the model is based on three components (gastric hydrocortisone, free serum cortisol and bound serum cortisol) and is formulated in terms…
We study the approach to equilibrium of systems of gas particles in terms of relative entropy. The systems are modeled by the Kac master equation in arbitrary dimensions. First, we study the Kac system coupled to a thermostat, and secondly…
This report presents the detailed steps of establishing the composite load model in the power system. The derivations of estimation the ZIP model and IM model parameters are proposed in this report. This is a supplementary material for the…
The landscape of computational modeling in cancer systems biology is diverse, offering a spectrum of models and frameworks, each with its own trade-offs and advantages. Ideally, models are meant to be useful in refining hypotheses, to…
This paper continues our previous work on a nanostructural evolution model for Fe-C alloys under irradiation, using Object Kinetic Monte Carlo modeling techniques. We here present a number of sensitivity studies of parameters of the model,…
Experimental information on low energy $\pi K$ scattering would shed light on the poorly known OZI suppressed sector of ChPT. I describe recent work aimed at generating such information based on available experimental data by setting up and…
A new class of methods is introduced for solving the Kohn-Sham equations of density functional theory, based on constructing a mapping dynamically between the Kohn-Sham system and an auxiliary system. The resulting auxiliary density…
The Kohn-Sham (KS) system is an auxiliary system whose effective potential is unknown in most cases. It is in principle determined by the ground state density, and it has been found numerically for some low-dimensional systems by inverting…
We introduce a variational structure for the Fourier-Cattaneo (FC) system which is a second-order hyperbolic system. This variational structure is inspired by the large-deviation rate functional for the Kac process which is closely linked…
Quantum Fisher information (QFI) plays a vital role in quantum precision measurement, quantum information, many-body physics, and other domains. Obtaining the QFI from experiment for a quantum state reveals insights such as the limits of…