Related papers: Design principles for biochemical oscillations wit…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
We propose a principle of consistency between different hierarchical levels of biological systems. Given a consistency between molecule replication and cell reproduction, universal statistical laws on cellular chemical abundances are…
Free energy calculations are at the heart of physics-based analyses of biochemical processes. They allow us to quantify molecular recognition mechanisms, which determine a wide range of biological phenomena from how cells send and receive…
How biological networks achieve robust control despite relying on imperfect, local information remains an important open question. Here, we identify thermodynamic constraints that can curtail non-equilibrium steady-state responses so…
Power systems are susceptible to natural threats including hurricanes and floods. Modern power grids are also increasingly threatened by cyber attacks. Existing approaches that help improve power system security and resilience may not be…
Living organisms are non-equilibrium, fluctuating, dynamic systems containing multi-step biological signaling cascades (BSC) with the ability to transduce changes in the concentration of extracellular molecules such as cytokines into…
The energy system studies include a wide range of issues from short term (e.g. real-time, hourly, daily and weekly operating decisions) to long term horizons (e.g. planning or policy making). The decision making chain is fed by input…
When cells measure concentrations of chemical signals, they may average multiple measurements over time in order to reduce noise in their measurements. However, when cells are in a environment that changes over time, past measurements may…
We show that noise-induced oscillations in a gene circuit model display stochastic coherence, that is, a maximum in the regularity of the oscillations as a function of noise amplitude. The effect is manifest as a system-size effect in a…
Rate processes are simple and analytically tractable models for many dynamical systems which switch stochastically between a discrete set of quasi stationary states but they may also approximate continuous processes by coarse grained,…
The traditional framework of quantum metrology commonly assumes unlimited access to resources, overlooking resource constraints in realistic scenarios. As such, the optimal strategies therein can be infeasible in practice. Here, we…
While most work on the quantum simulation of chemistry has focused on computing energy surfaces, a similarly important application requiring subtly different algorithms is the computation of energy derivatives. Almost all molecular…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
The second law of thermodynamics implies that no macroscopic system may oscillate indefinitely without consuming energy. The question of the number of possible oscillations and the coherent quality of these oscillations remain unanswered.…
Noisy fluctuations are ubiquitous in complex systems. They play a crucial or delicate role in the dynamical evolution of gene regulation, signal transduction, biochemical reactions, among other systems. Therefore, it is essential to…
To reduce computational complexity, macro-energy system models commonly implement reduced time-series data. For renewable energy systems dependent on seasonal storage and characterized by intermittent renewables, like wind and solar,…
We consider some crucial problems related to the secure and reliable operation of power systems with high renewable penetrations: how much reserve should we procure, how should reserve resources distribute among different locations, and how…
Recent progress in diverse intelligence has shown simple learning capacities below the organism level - single cells and even molecular networks. However, there are still many knowledge gaps around learning capacity above the organism…
Computational exploration of the compositional spaces of materials can provide guidance for synthetic research and thus accelerate the discovery of novel materials. Most approaches employ high-throughput sampling and focus on reducing the…
In order to respond to environmental signals, cells often use small molecular circuits to transmit information about their surroundings. Recently, motivated by concrete examples in signaling and gene regulation, a body of work has focused…