Related papers: Cooperative Function with Thermal Fluctuations in …
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…
We uncover the dynamics of particles with Gaussian core interactions across melting in pure and disordered two-dimensional (2D) systems. Intriguing signatures of cooperative motion of particles in string-like paths are found at low…
We derive a non-local model for the evolution of temperature in workpieces being joined by linear friction welding. The non-locality arises through the velocity being fixed by the temperature gradient at the weld. Short- and long-time…
Athermal (i.e. zero-temperature) under-constrained systems are typically floppy, but they can be rigidified by the application of external strain, which is theoretically well understood. Here and in the companion paper, we extend this…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in…
Interdependence is a fundamental ingredient to analyze the stability of many real-world complex systems featuring functional liasons. Yet, physical realizations of this coupling are still unknown, due to the lack of a theoretical framework…
The application of thermodynamic reasoning in the study of learning systems has a long tradition. Recently, new tools relating perfect thermodynamic adaptation to the adaptation process have been developed. These results, known as…
The connectivity properties of ad hoc networks have been extensively studied over the past few years, from local observables, to global network properties. In this paper we introduce a novel layer of network dynamics which lives and evolves…
Conventional studies of biomolecular behaviors rely largely on the construction of kinetic schemes. Since the selection of these networks is not unique, a concern is raised whether and under which conditions hierarchical schemes can reveal…
Systems with interacting degrees of freedom play a prominent role in stochastic thermodynamics. Our aim is to use the concept of detached path probabilities and detached entropy production for bipartite Markov processes and elaborate on a…
Training recurrent neural networks is known to be difficult when time dependencies become long. In this work, we show that most standard cells only have one stable equilibrium at initialisation, and that learning on tasks with long time…
A system is glassy when the observation time is much smaller than the equilibration time. A unifying thermodynamic picture of the glassy state is presented. Slow configurational modes are in quasi-equilibrium at an effective temperature. It…
Much of interesting complex biological behaviour arises from collective properties. Important information about collective behaviour lies in the time and space structure of fluctuations around average properties, and two-point correlation…
Parameterized artificial neural networks (ANNs) can be very expressive ansatzes for variational algorithms, reaching state-of-the-art energies on many quantum many-body Hamiltonians. Nevertheless, the training of the ANN can be slow and…
The softmax function is a fundamental component in deep learning. This study delves into the often-overlooked parameter within the softmax function, known as "temperature," providing novel insights into the practical and theoretical aspects…
In microscopic mechanical systems interactions between elastic structures are often mediated by the hydrodynamics of a solvent fluid. At microscopic scales the elastic structures are also subject to thermal fluctuations. Stochastic…
We revisit the problem of inelastic times governing the temperature behavior of the weak localization correction and mesoscopic fluctuations in one- and two-dimensional systems. It is shown that, for dephasing by the electron electron…
Fluctuation relations for the entropy production in non equilibrium stationary states of Ising models are investigated by Monte Carlo simulations. Systems in contact with heat baths at two different temperatures or subject to external…