Microcanonical Thermodynamics of Small Ideal Gas Systems

We consider the thermal, mechanical, and chemical contact of two subsystems composed of ideal gases, both of which are not in the thermodynamic limit. After contact, the combined system is isolated, and the entropy is determined through the use of its standard connection to the phase space density (PSD), where only those microstates at a given energy value are counted. The various intensive properties of these small systems that follow from a derivative of the PSD, such as the temperature, pressure, and chemical potential (evaluated via a backward difference), while equal when the two subsystems are in equilibrium are nevertheless found not to behave in accordance with what is expected from macroscopic thermodynamics. Instead, it is the entropy, defined from its connection to the PSD, that still controls the behavior of these small (nonextensive) systems. We also analyze the contact of these two subsystems utilizing an alternative entropy definition, through its proposed connection to the phase space volume (PSV), where all microstates at or below a given energy value are counted. We show that certain key properties of these small systems obtained with the PSV either do not become equal or do not consistently describe the two subsystems when in contact, suggesting that the PSV should not be used for analyzing the behavior of small isolated systems.

Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit

Signaling networks are spatiotemporally organized to sense diverse inputs, process information, and carry out specific cellular tasks. In β cells, Ca2+, cyclic adenosine monophosphate (cAMP), and Protein Kinase A (PKA) exist in an oscillatory circuit characterized by a high degree of feedback. Here, we describe a mode of regulation within this circuit involving a spatial dependence of the relative phase between cAMP, PKA, and Ca2+. We show that in mouse MIN6 β cells, nanodomain clustering of Ca2+-sensitive adenylyl cyclases (ACs) drives oscillations of local cAMP levels to be precisely in-phase with Ca2+ oscillations, whereas Ca2+-sensitive phosphodiesterases maintain out-of-phase oscillations outside of the nanodomain. Disruption of this precise phase relationship perturbs Ca2+ oscillations, suggesting the relative phase within an oscillatory circuit can encode specific functional information. This work unveils a novel mechanism of cAMP compartmentation utilized for localized tuning of an oscillatory circuit and has broad implications for the spatiotemporal regulation of signaling networks.

Computational Modeling Reveals Frequency Modulation of Calcium-cAMP/PKA Pathway in Dendritic Spines

Dendritic spines are the primary excitatory postsynaptic sites that act as subcompartments of signaling. Ca²⁺ is often the first and most rapid signal in spines. Downstream of calcium, the cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) pathway plays a critical role in the regulation of spine formation, morphological modifications, and ultimately, learning and memory. Although the dynamics of calcium are reasonably well-studied, calcium-induced cAMP/PKA dynamics, particularly with respect to frequency modulation, are not fully explored. In this study, we present a well-mixed model for the dynamics of calcium-induced cAMP/PKA dynamics in dendritic spines. The model is constrained using experimental observations in the literature. Further, we measured the calcium oscillation frequency in dendritic spines of cultured hippocampal CA1 neurons and used these dynamics as model inputs. Our model predicts that the various steps in this pathway act as frequency modulators for calcium, and the high frequency of calcium input is filtered by adenylyl cyclase 1 and phosphodiesterases in this pathway such that cAMP/PKA only responds to lower frequencies. This prediction has important implications for noise filtering and long-timescale signal transduction in dendritic spines. A companion manuscript presents a three-dimensional spatial model for the same pathway.

Mechanical and geometrical determinants of wall stress in abdominal aortic aneurysms: A computational study

An aortic aneurysm (AA) is a focal dilatation of the aortic wall. Occurrence of AA rupture is an all too common event that is associated with high levels of patient morbidity and mortality. The decision to surgically intervene prior to AA rupture is made with recognition of significant procedural risks, and is primarily based on the maximal diameter and/or growth rate of the AA. Despite established thresholds for intervention, rupture occurs in a notable subset of patients exhibiting sub-critical maximal diameters and/or growth rates. Therefore, a pressing need remains to identify better predictors of rupture risk and ultimately integrate their measurement into clinical decision making. In this study, we use a series of finite element-based computational models that represent a range of plausible AA scenarios, and evaluate the relative sensitivity of wall stress to geometrical and mechanical properties of the aneurysmal tissue. Taken together, our findings encourage an expansion of geometrical parameters considered for rupture risk assessment, and provide perspective on the degree to which tissue mechanical properties may modulate peak stress values within aneurysmal tissue.