Related papers: The thermodynamics of computational copying in bio…

Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…

The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…

Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…

In recent years considerable portion of the computer science community has focused its attention on understanding living cell biochemistry and efforts to understand such complication reaction environment have spread over wide front, ranging…

Optimal (reversible) processes in thermodynamics can be modelled as step-by-step processes, where the system is successively thermalized with respect to different Hamiltonians by an external thermal bath. However, in practice interactions…

To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…

Biomolecules stochastically occupy different possible configurations with probabilities given by non-equilibrium steady-state distributions. These distributions are determined by the transition rate constants between different…

Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…

In view of ever-changing conditions both in the external world and in intrinsic brain states, maintaining the robustness of computations poses a challenge, adequate solutions to which we are only beginning to understand. At the level of…

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…

Improved understanding of molecular systems has only emphasised the sophistication of networks within the cell. Simultaneously, the advance of nucleic acid nanotechnology, a platform within which reactions can be exquisitely controlled, has…

Due to large fluctuations in cellular environments, transfer of information in biological processes without regulation is inherently error-prone. The mechanistic details of error-reducing mechanisms in biological copying processes have been…

Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory…

Cells must continuously sense and respond to time-varying environmental stimuli. These signals are transmitted and processed by biochemical signalling networks. However, the biochemical reactions making up these networks are intrinsically…

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…

Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…

Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not…

Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool…

In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…

This letter exposes a tight connection between the thermodynamic efficiency of information processing and predictive inference. A generalized lower bound on dissipation is derived for partially observable information engines which are…