Quantification of motor network dynamics in Parkinson's disease by means of landscape and flux theory

Mathematical derivation and mechanism analysis of beta oscillations in a cortex-pallidum model

In this paper, we develop a new cortex-pallidum model to study the origin mechanism of Parkinson's oscillations in the cortex. In contrast to many previous models, the globus pallidus internal (GPi) and externa (GPe) both exert direct inhibitory feedback to the cortex. Using Hopf bifurcation analysis, two new critical conditions for oscillations, which can include the self-feedback projection of GPe, are obtained. In this paper, we find that the average discharge rate (ADR) is an important marker of oscillations, which can divide Hopf bifurcations into two types that can uniformly be used to explain the oscillation mechanism. Interestingly, the ADR of the cortex first increases and then decreases with increasing coupling weights that are projected to the GPe. Regarding the Hopf bifurcation critical conditions, the quantitative relationship between the inhibitory projection and excitatory projection to the GPe is monotonically increasing; in contrast, the relationship between different coupling weights in the cortex is monotonically decreasing. In general, the oscillation amplitude is the lowest near the bifurcation points and reaches the maximum value with the evolution of oscillations. The GPe is an effective target for deep brain stimulation to alleviate oscillations in the cortex.

Metastable dynamics of neural circuits and networks

Cortical neurons emit seemingly erratic trains of action potentials or "spikes," and neural network dynamics emerge from the coordinated spiking activity within neural circuits. These rich dynamics manifest themselves in a variety of patterns, which emerge spontaneously or in response to incoming activity produced by sensory inputs. In this Review, we focus on neural dynamics that is best understood as a sequence of repeated activations of a number of discrete hidden states. These transiently occupied states are termed "metastable" and have been linked to important sensory and cognitive functions. In the rodent gustatory cortex, for instance, metastable dynamics have been associated with stimulus coding, with states of expectation, and with decision making. In frontal, parietal, and motor areas of macaques, metastable activity has been related to behavioral performance, choice behavior, task difficulty, and attention. In this article, we review the experimental evidence for neural metastable dynamics together with theoretical approaches to the study of metastable activity in neural circuits. These approaches include (i) a theoretical framework based on non-equilibrium statistical physics for network dynamics; (ii) statistical approaches to extract information about metastable states from a variety of neural signals; and (iii) recent neural network approaches, informed by experimental results, to model the emergence of metastable dynamics. By discussing these topics, we aim to provide a cohesive view of how transitions between different states of activity may provide the neural underpinnings for essential functions such as perception, memory, expectation, or decision making, and more generally, how the study of metastable neural activity may advance our understanding of neural circuit function in health and disease.

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.

Bifurcation analyses and potential landscapes of a cortex-basal ganglia-thalamus model

The dynamics of cortical neuronal activity plays important roles in controlling body movement and is regulated by connection weights between neurons in a cortex–basal ganglia–thalamus (BGCT) loop. Beta‐band oscillation of cortical activity is closely associated with the movement disorder of Parkinson's disease, which is caused by an imbalance in the connection weights of direct and indirect pathways in the BGCT loop. In this study, the authors investigate how the dynamics of cortical activity are modulated by connection weights of direct and indirect pathways in the BGCT loop under low dopamine levels through bifurcation analyses and potential landscapes. The results reveal that cortical activity displays rich dynamics under different connection weights, including one, two, or three stable steady states, one or two stable limit cycles, and the coexistence of one stable limit cycle with one stable steady state or two stable ones. For a low dopamine level, cortical activity exhibits oscillation for larger connection weights of direct and indirect pathways. The stability of these stable dynamics is explored by the potential landscapes.

Non-equilibrium landscape and flux reveal the stability-flexibility-energy tradeoff in working memory

Uncovering the underlying biophysical principles of emergent collective computational abilities, such as working memory, in neural circuits is one of the most essential concerns in modern neuroscience. Working memory system is often desired to be robust against noises. Such systems can be highly flexible for adapting environmental demands. How neural circuits reconfigure themselves according to the cognitive task requirement remains unclear. Previous studies explored the robustness and the flexibility in working memory by tracing individual dynamical trajectories in a limited time scale, where the accuracy of the results depends on the volume of the collected statistical data. Inspired by thermodynamics and statistical mechanics in physical systems, we developed a non-equilibrium landscape and flux framework for studying the neural network dynamics. Applying this approach to a biophysically based working memory model, we investigated how changes in the recurrent excitation mediated by slow NMDA receptors within a selective population and mutual inhibition mediated by GABAergic interneurons between populations affect the robustness against noises. This is realized through quantifying the underlying non-equilibrium potential landscape topography and the kinetics of state switching. We found that an optimal compromise for a working memory circuit between the robustness and the flexibility can be achieved through the emergence of an intermediate state between the working memory states. An optimal combination of both increased self-excitation and inhibition can enhance the flexibility to external signals without significantly reducing the robustness to the random fluctuations. Furthermore, we found that the enhanced performance in working memory is supported by larger energy consumption. Our approach can facilitate the design of new network structure for cognitive functions with the optimal balance between performance and cost. Our work also provides a new paradigm for exploring the underlying mechanisms of many cognitive functions based on non-equilibrium physics.

Nonequilibrium Thermodynamics in Cell Biology: Extending Equilibrium Formalism to Cover Living Systems

We discuss new developments in the nonequilibrium dynamics and thermodynamics of living systems, giving a few examples to demonstrate the importance of nonequilibrium thermodynamics for understanding biological dynamics and functions. We study single-molecule enzyme dynamics, in which the nonequilibrium thermodynamic and dynamic driving forces of chemical potential and flux are crucial for the emergence of non-Michaelis-Menten kinetics. We explore single-gene expression dynamics, in which nonequilibrium dissipation can suppress fluctuations. We investigate the cell cycle and identify the nutrition supply as the energy input that sustains the stability, speed, and coherence of cell cycle oscillation, from which the different vital phases of the cell cycle emerge. We examine neural decision-making processes and find the trade-offs among speed, accuracy, and thermodynamic costs that are important for neural function. Lastly, we consider the thermodynamic cost for specificity in cellular signaling and adaptation.

Non-equilibrium landscape and flux reveal how the central amygdala circuit gates passive and active defensive responses

Uncovering the underlying physical principles of biology is important for understanding the biological function yet challenging. Take an example, the animals' defensive systems are very effective to threats. However, the underlying physical mechanisms are still unclear. We developed a non-equilibrium physics framework in terms of landscape and flux to study a central lateral amygdala (CeL) neural circuit based on experimental findings. We show that the distinct active and passive defensive responses of the animals upon threats are a result of non-equilibrium phase transitions. Such non-equilibrium phase transitions result from thermodynamic symmetry breaking, which is induced dynamically by the non-equilibrium flux. This gives rise to the emergence and selection of passive and active fear defensive responses, which can be quantified by the changes on the topography of the underlying non-equilibrium landscape. We have found the strengthened synaptic transmissions to both the SOM+ and SOM- CeL neurons are necessary for the acquisition and expression of active fear responses. This suggests a way to induce active responses and facilitates the design of new therapeutic strategies for cognitive dysfunction. We have also found that sufficient energy supply is crucial for the ability of selecting the appropriate defensive responses through stabilizing functional states against fluctuations.