Related papers: Information processing in biological molecular mac…
Many biological, physical, and social interactions have a particular dependence on where they take place. In living cells, protein movement between the nucleus and cytoplasm affects cellular response (i.e., proteins must be present in the…
We investigate the dependence of the displacements of a molecular motor embedded inside a glassy material on its folding characteristic time. We observe two different time regimes. For slow foldings (regime I) the diffusion evolves very…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
Active systems across scales, ranging from molecular machines to human crowds, are usually modeled as assemblies of self-propelled particles driven by internally generated forces. However, these models often assume memoryless dynamics and…
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…
Within a mathematical model, the process of interaction of the metabolic processes such as glycolysis and gluconeogenesis is studied. As a result of the running of two opposite processes in a cell, the conditions for their interaction and…
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…
Most complex networks serve as conduits for various dynamical processes, ranging from mass transfer by chemical reactions in the cell to packet transfer on the Internet. We collected data on the time dependent activity of five natural and…
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
Biological systems perform an astonishing array of dynamical processes -- including development and repair, regulation, behavior and motor control, sensing and signaling, and adaptation, among others. Powered by the transduction of stored…
Information processing at the molecular scale is limited by thermal fluctuations. This can cause undesired consequences in copying information since thermal noise can lead to errors that can compromise the functionality of the copy. For…
Stochastic chains represent a wide and key variety of phenomena in many branches of science within the context of Information Theory and Thermodynamics. They are typically approached by a sequence of independent events or by a memoryless…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
In these Lecture Notes we aim at clarifying how soft matter physics, and herein notably statistical mechanics and fluid mechanics, can be engaged to understand and manipulate non-equilibrium systems consisting of numerous (microscopic)…
At the dawn of thermodynamics, Carnot's constraint on efficiency of heat engines stimulated the formulation of one of the most universal physical principles, the second law of thermodynamics. In recent years, the field of heat engines…
Biological molecular motors are high-performance nanomachines that convert chemical energy into mechanical motion via chemomechanical coupling. Their reaction cycles typically comprise a series of intermediate chemical states between the…
In this article, we review a general theoretical framework of thermodynamics of information on the basis of Bayesian networks. This framework can describe a broad class of nonequilibrium dynamics of multiple interacting systems with complex…
Fluctuation theorems impose constraints on possible work extraction probabilities in thermodynamical processes. These constraints are stronger than the usual second law, which is concerned only with average values. Here, we show that such…
The two classes of membrane transport, namely, secondary active and passive transport, are understood as different reaction pathways in the same protein structure, described by the 16-state model in this paper. To quantify the thermodynamic…
There are many processes in biology in which mechanical forces are generated. Force-bearing networks can transduce locally developed mechanical signals very extensively over different parts of the cell or tissues. In this article we conduct…