Related papers: Allocating dissipation across a molecular machine …
Biological systems fundamentally exist out of equilibrium in order to preserve organized structures and processes. Many changing cellular conditions can be represented as transitions between nonequilibrium steady states, and organisms have…
We discuss the distributed matching scheme in accelerators where control of transverse beam phase space, oscillation, and transport is accomplished by flexible distribution of focusing elements beyond dedicated matching sections. Besides…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
We propose a two-dimensional model for a complete description of the dynamics of molecular motors, including both the processive movement along track filaments and the dissociation from the filaments. The theoretical results on the…
Production of energy (metabolism) and its distribution is vital for living organisms, both at individual level - between different functions of an organism, as well as between species of communities at different organizational levels,…
Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
Adiabatic quantum computation employs a slow change of a time-dependent control function (or functions) to interpolate between an initial and final Hamiltonian, which helps to keep the system in the instantaneous ground state. When the…
The simplest mechanism for molecular electron pumps is discussed which is based on nonadiabatic electron tunnelling and nonequilibrium conformational fluctuations. Such fluctuations can be induced, e.g. by random binding of negatively…
Both natural and engineered supply networks exhibit universal structural patterns, such as the formation of loops, yet the principles governing optimal structures remain unclear. These patterns can be interpreted as solutions of…
Mixtures of active and passive particles are ubiquitous at the microscale. Many essential microbial processes involve interactions with dead or immotile cells or passive crowders. When passive objects are immersed in active baths, their…
When exposed to a thermal gradient, reaction networks can convert thermal energy into the chemical selection of states that would be unfavourable at equilibrium. The kinetics of reaction paths, and thus how fast they dissipate available…
By analytically solving some simple models of phase-ordering kinetics, we suggest a mechanism for the onset of non-equilibrium behaviour in colloid-polymer mixtures. These mixtures can function as models of atomic systems; their physics…
A system of impulsive differential equations with state-dependent impulses is used to model the growth of a single population on two limiting essential resources in a self-cycling fermentor. Potential applications include water purification…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
We consider the thermodynamics of chemical coupling from the viewpoint of free energy transduction efficiency. In contrast to an external parameter-driven stochastic energetics setup, the dynamic change of the equilibrium distribution…
Modern foundation models often undergo iterative ``bootstrapping'' in their post-training phase: a model generates synthetic data, an external verifier filters out low-quality samples, and the high-quality subset is used for further…
We study the current rectification of particles moving in a pulsating channel under the in uence of an applied force. We have shown the existence of diferent rectification scenarios in which entropic and energetic effects compete. The…
We review a recently developed micellization theory, which is based on a free-energy approach and offers several advantages over the conventional one, based on mass action and rate equations. As all the results are derived from a single…
The interaction between natural selection and random mutation is frequently debated in recent years. Does similar dilemma also exist in the evolution of real networks such as biological networks? In this paper, we try to discuss this issue…
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…