相关论文: Dynamical hysteresis in multisite protein modifica…
The position of an interface (domain wall) in a medium with random pinning defects is not determined unambiguously by a current value of the driving force even in average. Based on general theory of the interface motion in a random medium…
The natural impedance, or dynamic relationship between force and motion, of a human operator can determine the stability of exoskeletons that use interaction-torque feedback to amplify human strength. While human impedance is typically…
Understanding the relationship between protein sequence, function, and stability is a fundamental problem in biology. While high-throughput methods have produced large numbers of sequence-function pairs, functional assays do not distinguish…
Multistationarity in molecular systems underlies switch-like responses in cellular decision making. Determining whether and when a system displays multistationarity is in general a difficult problem. In this work we completely determine the…
On the microscopic level, biological signal transmission relies on coordinated structural changes in allosteric proteins that involve sensor and effector modules. The timescales and microscopic details of signal transmission in proteins are…
Many cell types exhibit oscillatory activity, such as repetitive action potential firing due to the Hodgkin-Huxley dynamics of ion channels in the cell membrane or reveal intracellular inositol triphosphate (IP$_3$) mediated calcium…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
Multistationarity in biological systems is a mechanism of cellular decision making. In particular, signaling pathways regulated by protein phosphorylation display features that facilitate a variety of responses to different biological…
Biological tissue integrity is actively maintained by cells. It is essential to comprehend how cells accomplish this in order to stage tissue diseases. However, addressing the complexity of a cell's system of interrelated mechanisms poses a…
Mechanical cues like the rigidity of the substrate are main determinants for the decision making of adherent cells. Here we use a mechano-chemical model to predict the cellular response to varying substrate stiffness. The model equations…
Multisite phosphorylation plays an important role in regulating switchlike protein activity and has been used widely in mathematical models. With the development of new experimental techniques and more molecular data, molecular…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
Post-translational modifications of histone proteins are an important factor in epigenetic control that serve to regulate transcription, depending on the particular modification states of the histone proteins. We study the stochastic…
We are looking at local protein interaction networks from the perspective of directed, labeled graphs with quantitative values for monotonic changes in concentrations. These systems can be used to perform stability analysis for a stable…
Multicellular tissues are the building blocks of many biological systems and organs. These tissues are not static, but dynamically change over time. Even if the overall structure remains the same there is a turnover of cells within the…
Multisite phosphorylation plays an important role in intracellular signaling. There has been much recent work aimed at understanding the dynamics of such systems when the phosphorylation/dephosphorylation mechanism is distributive, that is,…
Our study unveils the precise role of the underlying potential in regulating the fundamental processes of dynamic hysteresis, which manifests in numerous natural and designed systems. We identify that it is possible to induce symmetry…
The dynamics of motor protein molecules that have two subunits is investigated using simple discrete stochastic models. Exact steady-state analytical expressions are obtained for velocities and dispersions for any number of intermediate…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
A simple way to get insights about the possible functional motions of a protein is to perform a normal mode analysis (NMA). Indeed, it has been shown that low-frequency modes thus obtained are often closely related to domain motions…