Related papers: The thermodynamics of computational copying in bio…

A unified thermodynamic formalism describing the efficiency of learning is proposed. First, we derive an inequality, which is more strength than Clausius's inequality, revealing the lower bound of the entropy-production rate of a subsystem.…

Living systems maintain or increase local order by working against the Second Law of Thermodynamics. Thermodynamic consistency is restored as they dissipate heat, thereby increasing the net entropy of their environment. Recently introduced…

Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…

Feedback in sensory biochemical networks can give rise to bifurcations in cells' behavioral response. These bifurcations share many properties with thermodynamic critical points. Evidence suggests that biological systems may operate near…

We develop a physics-based model for classical computation based on autonomous quantum thermal machines. These machines consist of few interacting quantum bits (qubits) connected to several environments at different temperatures. Heat flows…

In the paradigm of thermodynamic computing, instead of behaving deterministically, hardware undergoes a stochastic process in order to sample from a distribution of interest. While it has been hypothesized that thermodynamic computers may…

Cellular ingredient concentrations can be stabilized by adjusting generation and consumption rates through multiple pathways. To explore the portion of cellular metabolism equipped with multiple pathways, we categorize individual metabolic…

Interest in the thermodynamics of computation has revived in recent years, driven by developments in science, economics and technology. Given the consequences of the growing demand for computational power, the idea of reducing the energy…

Biological cells are able to accurately sense chemicals with receptors at their surfaces, allowing cells to move towards sources of attractant and away from sources of repellent. The accuracy of sensing chemical concentration is ultimately…

Cell-cell communication is often achieved by secreted signaling molecules that bind membrane-bound receptors. A common class of such receptors are G-protein coupled receptors, where extracellular binding induces changes on the membrane…

Many biological decision-making processes can be viewed as performing a classification task over a set of inputs, using various chemical and physical processes as "biological hardware." In this context, it is important to understand the…

Stimulus from the environment that guides behavior and informs decisions is encoded in the firing rates of neural populations. Each neuron in the populations, however, does not spike independently: spike events are correlated from cell to…

Predicting future observations plays a central role in machine learning, biology, economics, and many other fields. It lies at the heart of organizational principles such as the variational free energy principle and has even been shown --…

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…

Recent years have shown an increased use of silicon photo-multipliers (SiPM) in experiments as they are of reasonable cost, have relatively low power consumption and are easily available in a variety of form factors allowing for a large…

Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…

This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…

We present the design for a thermodynamic computer that can perform arbitrary nonlinear calculations in or out of equilibrium. Simple thermodynamic circuits, fluctuating degrees of freedom in contact with a thermal bath and confined by a…

Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…

Biological systems have to build models from their sensory data that allow them to efficiently process previously unseen inputs. Here, we study a neural network learning a linearly separable rule using examples provided by a teacher. We…