相关论文: The energy costs of biological insulators
The connection between optimal biological function and energy use, measured for example by the rate of metabolite consumption, is a current topic of interest in the systems biology literature which has been explored in several different…
One of the primary computational requirements of a cellular system is the ability to transfer information between spatially separated components. To accomplish this, biology uses diverse physical channels including production or release of…
Retroactivity arises when the coupling of a molecular network $\mathcal{U}$ to a downstream network $\mathcal{D}$ results in signal propagation back from $\mathcal{D}$ to $\mathcal{U}$. The phenomenon represents a breakdown in modularity of…
Oscillation is an important cellular process that regulates timing of different vital life cycles. However, in the noisy cellular environment, oscillations can be highly inaccurate due to phase fluctuations. It remains poorly understood how…
All cells must sustain ionic motive forces (IMFs) -- the electrochemical gradients of permeant ions, together with the membrane potential they produce -- to regulate intracellular pH, drive secondary transport, and power ATP synthesis.…
Biological synaptic transmission is unreliable, and this unreliability likely degrades neural circuit performance. While there are biophysical mechanisms that can increase reliability, for instance by increasing vesicle release probability,…
Active matter constantly dissipates energy to power the self-propulsion of its microscopic constituents. This opens the door to designing innovative cyclic engines without any equilibrium equivalent. We offer a consistent thermodynamic…
A ubiquitous building block of signaling pathways is a cycle of covalent modification (e.g., phosphorylation and dephosphorylation in MAPK cascades). Our paper explores the kind of information processing and filtering that can be…
A variety of biomolecular systems rely on exploratory dynamics to reach target locations or states within a cell. Without a mechanism to remotely sense and move directly towards a target, the system must sample over many paths, often…
In order to transmit biochemical signals, biological regulatory systems dissipate energy with concomitant entropy production. Additionally, signaling often takes place in challenging environmental conditions. In a simple model regulatory…
Life is a nonequilibrium phenomenon: metabolism provides a continuous supply of energy that drives nearly all cellular processes. However, very little is known about how much energy different cellular processes use, i.e. their energetic…
Digital computers implement computations using circuits, as do many naturally occurring systems (e.g., gene regulatory networks). The topology of any such circuit restricts which variables may be physically coupled during the operation of a…
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…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation. Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes, all require energy consumption.…
Molecular motors fulfill critical functions within all living beings. Understanding their underlying working principles is therefore of great interest. Here we develop a simple model inspired by the two-component biomolecular motor Fo-F1…
We study the current rectification of particles moving in a pulsating channel under the in uence of an applied force. We have shown the existence of diferent rectification scenarios in which entropic and energetic effects compete. The…
Cells use biochemical networks to translate environmental information into intracellular responses. These responses can be highly dynamic, but how the information is encoded in these dynamics remains poorly understood. Here we investigate…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
The recent advent of photonic topological insulators has opened the door to using the robustness of topologically protected transport (originated in the domain of condensed matter physics) in optical devices and in quantum simulation.…