Related papers: Information processing in biological molecular mac…
How do organisms recognize their environment by acquiring knowledge about the world, and what actions do they take based on this knowledge? This article examines hypotheses about organisms' adaptation to the environment from machine…
Biochemical reaction networks in living cells usually involve reversible covalent modification of signaling molecules, such as protein phosphorylation. Under conditions of small molecule numbers, as is frequently the case in living cells,…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
Organisms are nonequilibrium, stationary systems self-organized via spontaneous symmetry breaking and undergoing metabolic cycles with broken detailed balance in the environment. The thermodynamic free-energy principle describes an…
Mechanics and biochemical signaling are both often deregulated in cancer, leading to cancer cell phenotypes that exhibit increased invasiveness, proliferation, and survival. The dynamics and interactions of cytoskeletal components control…
In this PhD thesis, we explore and apply methods inspired by the free energy principle to two important areas in machine learning and neuroscience. The free energy principle is a general mathematical theory of the necessary…
We show that the correlated stochastic fluctuation of the friction coefficient can give rise to long-range directional motion of a particle undergoing Brownian random walk in a constant periodic energy potential landscape. The occurrence of…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
The glassy cytoplasm, crowded with bio-macromolecules, is fluidized in living cells by mechanical energy derived from metabolism. Characterizing the living cytoplasm as a non-equilibrium system is crucial in elucidating the intricate…
The excess work required to drive a stochastic system out of thermodynamic equilibrium through a time-dependent external perturbation is directly related to the amount of entropy produced during the driving process, allowing excess work and…
Motor enzymes catalyze chemical reactions, like the hydrolysis of ATP, and in the process they also perform work. Recent studies indicate that motor enzymes perform work with specific intermediate steps in their catalyzed reactions,…
On the one hand, the dissipated heat of a thermodynamic work extraction process upper bounds the non-predictive information, which the associated system encodes about its environment. Thus, emergent information processing capabilities can…
Dynamics of molecular motors that move along linear lattices and interact with them via reversible destruction of specific lattice bonds is investigated theoretically by analyzing exactly solvable discrete-state ``burnt-bridge'' models.…
In many assembly line processes like metabolic and signaling networks in biological systems, the products of the first enzyme is the reactant for the next enzyme in the network. Working of multiple machines leads to efficient utilization of…
Dual-process theories play a central role in both psychology and neuroscience, figuring prominently in fields ranging from executive control to reward-based learning to judgment and decision making. In each of these domains, two mechanisms…
Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
Information-driven engines that rectify thermal fluctuations are a modern realization of the Maxwell-demon thought experiment. We introduce a simple design based on a heavy colloidal particle, held by an optical trap and immersed in water.…
The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…
Maintained by environmental fluxes, biological systems are thermodynamic processes that operate far from equilibrium without detailed-balance dynamics. Yet, they often exhibit well defined nonequilibrium steady states (NESSs). More…