Related papers: Cooperative Function with Thermal Fluctuations in …
A theory which uses data of the static pair-correlation function is developed to calculate quantities associated with the viscous slowing down of supercooled liquids. We calculate value of the energy fluctuations that determine the number…
Allosteric regulation is central to many biochemical processes. Allosteric sites provide a target to fine-tune protein activity, yet we lack computational methods to predict them. Here, we present an efficient graph-theoretical approach for…
Are "turn-on" and "turn-off" functions in protein-protein interaction networks exact opposites of each other? To answer this question, we implement a minimal model for the evolution of functional protein-interaction networks using a…
Randomly coupled Ising spins constitute the classical model of collective phenomena in disordered systems, with applications covering ferromagnetism, combinatorial optimization, protein folding, stock market dynamics, and social dynamics.…
Contractile biopolymer networks, such as the actomyosin meshwork of animal cells, are ubiquitous in living organisms. The active gel theory, which provides the thermodynamic framework for these materials, has been mostly used in conjunction…
The limit of small entropy production is reached in relaxing systems long after preparation, and in stationary driven systems in the limit of small driving power. Surprisingly, for extended systems this limit is not in general the…
Mechanical properties of disordered networks can be significantly tailored by modifying a small fraction of their bonds. This procedure has been used to design and build mechanical metamaterials with a variety of responses. A long-range…
Allostery, the phenomenon by which the perturbation of a molecule at one site alters its behavior at a remote functional site, enables control over biomolecular function. Allosteric modulation is a promising avenue for drug discovery and is…
Advances in manufacturing and characterization of complex molecular systems have created a need for new methods for design at molecular length scales. Emerging approaches are increasingly relying on the use of Artificial Intelligence (AI),…
We study ballistic thermal transport in Heisenberg spin chain with nearest-neighbor ferromagnetic interactions at low temperatures. Explicit expressions for transmission coefficients are derived for thermal transport in a periodic spin…
As a function of connectivity, spring networks exhibit a critical transition between floppy and rigid phases at an isostatic threshold. For connectivity below this threshold, fiber networks were recently shown theoretically to exhibit a…
The structure of social networks is a key determinant in fostering cooperation and other altruistic behavior among naturally selfish individuals. However, most real social interactions are temporal, being both finite in duration and spread…
Combining simulations and theory I study the interplay between bundle elastic degrees of freedom and crosslink binding propensity. By slowly driving bundles into a deformed configuration, and depending on the mechanical stiffness of the…
Using a thermodynamically consistent, mesoscopic model for modern complementary metal-oxide-semiconductor transistors, we study an array of logical circuits and explore how their function is constrained by recent thermodynamic uncertainty…
Reinforcement Learning offers a framework to learn to choose actions in order to achieve some goal. However, at the nano-scale, thermal fluctuations hamper the learning process. We analyze this regime using the general framework of Markov…
The mechanical behaviors of polycrystalline solids are determined by the interplay between phenomena governed by two different thermodynamic temperatures: the configurational effective temperature that controls the density of dislocations,…
We observe many-body pairing in a two-dimensional gas of ultracold fermionic atoms at temperatures far above the critical temperature for superfluidity. For this, we use spatially resolved radio-frequency spectroscopy to measure pairing…
We show that a protein can be trained to recognise multiple conformations, analogous to an associative memory, and provide capacity calculations based on energy fluctuations and information theory. Unlike the linear capacity of a Hopfield…
We study a neural network model of interacting stochastic discrete two--state cellular automata on a regular lattice. The system is externally tuned to a critical point which varies with the degree of stochasticity (or the effective…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…