Related papers: Allocating dissipation across a molecular machine …
Information molecules play a crucial role in molecular communication (MC), acting as carriers for information transfer. A common approach to get information molecules in MC involves harvesting them from the environment; however, the…
Chemically active droplets provide simple models for cell-like systems that can grow and divide. Such active droplet systems are driven away from thermodynamic equilibrium and turn over chemically, which corresponds to a simple metabolism.…
We study the energy flow due to the motion of topological solitons in nonlinear extended systems in the presence of damping and driving. The total field momentum contribution to the energy flux, which reduces the soliton motion to that of a…
In this article, we focus on a periodic resource allocation problem applied to a dynamical system which comes from a biological system. More precisely, we consider a system with $N$ resources and $N$ activities, each activity use the…
Nonequilibrium, ``fast switching'' estimates of equilibrium free energy differences, Delta F, are often plagued by poor convergence due to dissipation. We propose a method to improve these estimates by generating trajectories with reduced…
The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular…
Active matter constantly dissipates energy to power the self-propulsion of its microscopic constituents. This opens the door to designing innovative cyclic engines without any equilibrium equivalent. We offer a consistent thermodynamic…
All cells must sustain ionic motive forces (IMFs) -- the electrochemical gradients of permeant ions, together with the membrane potential they produce -- to regulate intracellular pH, drive secondary transport, and power ATP synthesis.…
The pump process of the ratchet model inspired by the $F_o$ rotatory motor of ATP synthase is investigated. In this model there are two kinds of characteristic time. One is dynamical, the relaxation time of the system. Others are chemical,…
Living systems need to be highly responsive, and also to keep fluctuations low. These goals are incompatible in equilibrium systems due to the Fluctuation Dissipation Theorem (FDT). Here, we show that biological sensory systems, driven far…
Biological and living organisms sense and process information from their surroundings, typically having access only to a subset of external observables for a limited amount of time. In this work, we uncover how biological systems can…
We calculate and verify with simulations the ratio between the average translational and rotational energies of systems with rough, inelastic particles, either forced or freely cooling. The ratio shows non-equipartition of energy. In…
Finding a transformation between two unknown probability distributions from finite samples is crucial for modeling complex data distributions and performing tasks such as sample generation, domain adaptation and statistical inference. One…
Synthetic nanoscale complexes capable of mechanical movement are often studied theoretically using discrete-state models that involve instantaneous transitions between metastable states. A number of general results have been derived within…
The development of sophisticated experimental means to control nanoscale systems has motivated efforts to design driving protocols which minimize the energy dissipated to the environment. Computational models are a crucial tool in this…
Near equilibrium, thermodynamic intuition suggests that fast, irreversible processes will dissipate more energy and entropy than slow, quasistatic processes connecting the same initial and final states. Here, we test the hypothesis that…
A solvable model is proposed and analyzed to reveal the mechanism underlying the diffusion enhancement recently reported for a model of molecular motors and predicted to be observed in the biological rotary motor $\rm F_1$-ATPase. It turns…
Biological machines like molecular motors and enzymes operate in dynamic cycles representable as stochastic flows on networks. Current stochastic dynamics describes such flows on fixed networks. Here, we develop a scalable approach to…
The peak performance of any SpMV depends primarily on the available memory bandwidth and its effective use. GPUs, ASICs, and new FPGAs have higher and higher bandwidth; however, for large scale and highly sparse matrices, SpMV is still a…
Unlike many physical nonequilibrium systems, in biological systems, the coupling to external energy sources is not a fixed parameter but adaptively controlled by the system itself. We do not have theoretical frameworks that allow for such…