The dense medium created in Au + Au collisions at the Relativistic Heavy-Ion Collider significantly suppresses particle production from hard-scattering processes and their characteristic back-to-back angular correlation. We present a simple model of jet absorption in dense matter that incorporates a realistic nuclear geometry. Our calculations are performed at the jet level and assume independent jet fragmentation in the vacuum. This model describes quantitatively the centrality dependence of the observed suppression of the high p T hadron yield and of the back-to-back angular correlations. The azimuthal anisotropy of high p T particle production cannot be accounted for using a realistic nuclear geometry.

The driving force of the dynamical system can be decomposed into the gradient of a potential landscape and curl flux (current). The fluctuation-dissipation theorem (FDT) is often applied to near equilibrium systems with detailed balance. The response due to a small perturbation can be expressed by a spontaneous fluctuation. For non-equilibrium systems, we derived a generalized FDT that the response function is composed of two parts: (1) a spontaneous correlation representing the relaxation which is present in the near equilibrium systems with detailed balance; (2) a correlation related to the persistence of the curl flux in steady state, which is also in part linked to a internal curvature of a gauge field. The generalized FDT is also related to the fluctuation theorem. In the equal time limit, the generalized FDT naturally leads to non-equilibrium thermodynamics where the entropy production rate can be decomposed into spontaneous relaxation driven by gradient force and house keeping contribution driven by the non-zero flux that sustains the non-equilibrium environment and breaks the detailed balance.The global stability is essential in understanding the dynamical non-equilibrium systems. The driving force of the dynamical system often is not integrable and can not be written in terms of the gradient of a potential. The driving force however can be decomposed into the gradient of a potential and a curl flux (current) [1]. The potential is related to the steady state probability and the gradient force gives the normal dynamics analogous to equilibrium system, while the curl flux force is directly linked to the non-equilibrium contribution from detailed balance breaking. For non-equilibrium dynamics, the dual description with both potential and flux is necessary.In addition, the fluctuation-dissipation theorem (FDT) plays a central role for systems in near equilibrium systems with detail balance [2,3]. It links the fluctuations of the system quantified by the correlation function with the response of the system quantified by the response function. Many efforts have been made to extend the FDT to non-equilibrium systems [4][5][6][7][8][9][10][11][12][13][14][15][16]. It was found that the FDT involves the correlation function of a variable that is conjugate with entropy [17]. Furthermore, by choosing proper observables, the FDT for non-equilibrium systems can be uncovered [18].

Understanding differentiation, a biological process from a multipotent stem or progenitor state to a mature cell is critically important. We developed a theoretical framework to quantify the underlying potential landscape and pathways for cell development and differentiation. We proposed a new mechanism of differentiation and found the differentiated states can emerge from the slow binding/unbinding of regulatory proteins to gene promoters. With slow promoter binding/unbinding, we found multiple meta-stable differentiated states, which can explain the origin of multiple states observed in recent experiments. The kinetic time for the differentiation and reprogramming strongly depends on the time scale of the promoter binding/unbinding processes. We discovered an optimal speed for differentiation for certain promoter binding/unbinding rates. Future experiments might be able to tell if cells differentiate at that optimal speed. We also quantified irreversible kinetic pathways for the differentiation and reprogramming, which captures the non-equilibrium dynamics in multipotent stem or progenitor cells.