Keun-Young Kim

Potential energy landscape and robustness of a gene regulatory network: toggle switch.

Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers. It leads to the robustness of the biological basins of the gene switches. The technique used here is general and can be applied to explore the potential energy landscape of the gene networks.

Coherent/incoherent metal transition in a holographic model

A bstractWe study AC electric (σ), thermoelectric (α), and thermal κ¯

The chiral model of Sakai-Sugimoto at finite baryon density

\left(\overline{\kappa}\right)

Dense Holographic QCD in the Wigner-Seitz Approximation

conductivities in a holographic model, which is based on 3+1 dimensional Einstein-Maxwell-scalar action. There is momentum relaxation due to massless scalar fields linear to spatial coordinate. The model has three field theory parameters: temperature (T), chemical potential (μ), and effective impurity (β). At low frequencies, if β < μ, all three AC conductivities (σ, α,κ¯

Baryonic response of dense holographic QCD

\overline{\kappa}

Electromagnetic baryon form factors from holographic QCD

) exhibit a Drude peak modified by pair creation contribution (coherent metal). The parameters of this modified Drude peak are obtained analytically. In particular, if β ≪ μ the relaxation time of electric conductivity approaches to 23μ/β2