Related papers: Information processing in biological molecular mac…
Biological organisms are open, adaptve systems that can respond to changes in environment in specific ways. Adaptation and response can be posed as an optimization problem, with a tradeoff between the benefit obtained from a response and…
Quantum memory effects can be related to a bidirectional exchange of information between an open system and its environment, which in turn modifies the state and dynamical behavior of the last one. Nevertheless, non-Markovianity can also be…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
A novel mechanism of reaction-induced active molecular motion, not involving any kind of self-propulsion, is proposed and analyzed. Because of the momentum exchange with the surrounding solvent, conformational transitions in…
Small systems in a thermodynamic medium --- like colloids in a suspension or the molecular machinery in living cells --- are strongly affected by the thermal fluctuations of their environment. Physicists model such systems by means of…
We describe a minimal model of an autonomous Maxwell demon, a device that delivers work by rectifying thermal fluctuations while simultaneously writing information to a memory register. We solve exactly for the steady-state behavior of our…
Biological functions in each animal cell depend on coordinated operations of a wide variety of molecular motors. Some of the these motors transport cargo to their respective destinations whereas some others are mobile workshops which…
The mathematical formulation of the model for molecular movement of single motor proteins driven by cyclic biochemical reactions in an aqueous environment leads to a drifted Brownian motion characterized by coupled diffusion equations. In…
Complex systems are often characterized by the interplay of multiple interconnected dynamical processes operating across a range of temporal scales. This phenomenon is widespread in both biological and artificial scenarios, making it…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
Molecular motors play pivotal roles in organizing the interior of cells. A motor efficient in cargo transport would move along cytoskeletal filaments with a high speed and a minimal error in transport distance (or time) while consuming a…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
So far, feedback-driven systems have been discussed using (i) measurement and control, (ii) a tape interacting with a system or (iii) by identifying an implicit Maxwell demon in steady state transport. We derive the corresponding second…
We extend the principles of information thermodynamics to study energy and information exchanges between coupled systems composed of one part undergoing a Markov jump process and another underdamped diffusion. We derive integral fluctuation…
Second law of thermodynamics can be apparently violated for systems whose dynamics depends on acquired information by measurement. However, when one consider measurement and erasure process together along with the system it saves the second…
Information engines can convert thermal fluctuations of a bath at temperature $T$ into work at rates of order $k_\mathrm{B}T$ per relaxation time of the system. We show experimentally that such engines, when in contact with a bath that is…
Biological nanomachines are nanometer-size macromolecular complexes that catalyze chemical reactions in the presence of substrate molecules. The catalytic functions carried out by such nanomachines in the cytoplasm, and biological membranes…
Spontaneous directed motion, a hallmark of cell biology, is unusual in classical statistical physics. Here we study, using both numerical and analytical methods, organized motion in models of the cytoskeleton in which constituents are…
Living microorganisms have evolved dedicated sensory machinery to detect environmental perturbations, processing these signals through biochemical networks to guide behavior. Replicating such capabilities in synthetic active matter remains…
Living systems are often described utilizing informational analogies. An important open question is whether information is merely a useful conceptual metaphor, or intrinsic to the operation of biological systems. To address this question,…