Landscape Framework and Global Stability for Stochastic Reaction Diffusion and General Spatially Extended Systems with Intrinsic Fluctuations

Quantifying cancer cell plasticity with gene regulatory networks and single-cell dynamics

Phenotypic plasticity of cancer cells can lead to complex cell state dynamics during tumor progression and acquired resistance. Highly plastic stem-like states may be inherently drug-resistant. Moreover, cell state dynamics in response to therapy allow a tumor to evade treatment. In both scenarios, quantifying plasticity is essential for identifying high-plasticity states or elucidating transition paths between states. Currently, methods to quantify plasticity tend to focus on 1) quantification of quasi-potential based on the underlying gene regulatory network dynamics of the system; or 2) inference of cell potency based on trajectory inference or lineage tracing in single-cell dynamics. Here, we explore both of these approaches and associated computational tools. We then discuss implications of each approach to plasticity metrics, and relevance to cancer treatment strategies.

Nonequilibrium Equation of State for Open Hamiltonian Systems Maintained in Nonequilibrium Steady States

We establish the nonequilibrium equation of state in the stochastic thermodynamics framework for open Hamiltonian systems in contact with multiple heat baths governed by the Langevin equation and the Fokker-Planck equation. The derived nonequilibrium equation of state is an integral part of the nonequilibrium steady-state thermodynamics, and it reduces to the equilibrium equation of state when all the heat baths have the same temperature. We find that the nonequilibrium equation of state can be separated into two parts. One part has the form of the equilibrium equation of state, with the equilibrium temperature replaced by the average temperature of the heat baths. The other part depends on the temperature differences of the heat baths and represents nonequilibrium corrections. For systems with harmonic potentials, the nonequilibrium correction part is linear in the temperature differences of the heat baths. For more general open Hamiltonian systems, it may contain higher powers of the temperature differences. Another important feature of the nonequilibrium equation of state is that, in addition to the temperatures of the heat baths, it also depends on the friction coefficients arising from system-bath interactions in general. This suggests that it represents a relational condition between the system and the heat baths instead of the intrinsic properties of the system itself. In addition, when the potential energy is a homogeneous function, we find that the product of the generalized force and the generalized coordinate is proportional to the nonequilibrium internal energy, which is an alternative form of the nonequilibrium equation of state. Our findings may provide insights into the nonequilibrium equation of state for more general nonequilibrium open systems, including active matter and living organisms. Results in this work with suitable extension may find potential applications in nanoelectronics and biophysics including molecular motors and cells.

Perspectives on the landscape and flux theory for describing emergent behaviors of the biological systems

We give a review on the landscape theory of the equilibrium biological systems and landscape-flux theory of the nonequilibrium biological systems as the global driving force. The emergences of the behaviors, the associated thermodynamics in terms of the entropy and free energy and dynamics in terms of the rate and paths have been quantitatively demonstrated. The hierarchical organization structures have been discussed. The biological applications ranging from protein folding, biomolecular recognition, specificity, biomolecular evolution and design for equilibrium systems as well as cell cycle, differentiation and development, cancer, neural networks and brain function, and evolution for nonequilibrium systems, cross-scale studies of genome structural dynamics and experimental quantifications/verifications of the landscape and flux are illustrated. Together, this gives an overall global physical and quantitative picture in terms of the landscape and flux for the behaviors, dynamics and functions of biological systems.

Landscape-Flux Framework for Nonequilibrium Dynamics and Thermodynamics of Open Hamiltonian Systems Coupled to Multiple Heat Baths

We establish a nonequilibrium dynamic and thermodynamic formalism in the landscape-flux framework for open Hamiltonian systems in contact with multiple heat baths governed by stochastic dynamics. To systematically characterize nonequilibrium steady states, the nonequilibrium trinity construct is developed, which consists of detailed balance breaking, nonequilibrium potential landscape, and irreversible probability flux. We demonstrate that the temperature difference of the heat baths is the physical origin of detailed balance breaking, which generates the nonequilibrium potential landscape characterizing the nonequilibrium statistics and creates the irreversible probability flux signifying time irreversibility, with the latter two aspects closely connected. It is shown that the stochastic dynamics of the system can be formulated in the landscape-flux form, where the reversible force drives the conservative Hamiltonian dynamics, the irreversible force consisting of a landscape gradient force and an irreversible flux force drives the dissipative dynamics, and the stochastic force adds random fluctuations to the dynamics. The possible connection of the nonequilibrium trinity construct to nonequilibrium phase transitions is also suggested. A set of nonequilibrium thermodynamic equations, applicable to both nonequilibrium steady states and transient relaxation processes, is constructed. We find that an additional thermodynamic quantity, named the mixing entropy production rate, enters the nonequilibrium thermodynamic equations. It arises from the interplay between detailed balance breaking and transient relaxation, and it also relies on the conservative dynamics. At the nonequilibrium steady state, the heat flow, entropy flow, and entropy production are demonstrated to be thermodynamic manifestations of the nonequilibrium trinity construct. The general nonequilibrium formalism is applied to a class of solvable systems consisting of coupled harmonic oscillators. A more specific example of two harmonic oscillators coupled to two heat baths is worked out in detail. The example may facilitate connection with experiments.