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The main objective of this and its accompanying articles is to derive a mathematical theory associated with the thermohaline circulations (THC). This article provides a general transition and stability theory for the Boussinesq system,…
Amorphous solids yield at a critical value $\Sigma_c$ of the imposed stress $\Sigma$ through a dynamical phase transition. While sharp in athermal systems, the presence of thermal fluctuations leads to the rounding of the transition and…
The use of the osmotic thermodynamic model, combined with a series of methane and carbon dioxide gas adsorption experiments at various temperatures, has allowed shedding some new light on the fascinating phase behavior of flexible…
For over three decades, the front-capturing level-set method has demonstrated its prowess for the simulation, at the mesoscopic scale, of numerous mechanisms in the context of microstructure evolution occurring during complex…
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,…
The equilibrium configuration of an engineering structure, able to withstand a certain loading condition, is usually associated with a local minimum of the underlying potential energy. However, in the nonlinear context, there may be other…
We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so…
The Suspension Balance Model (SBM) [J. Fluid Mech. \textbf{275}, 157 (1994)] for two-phase flows uses the momentum balance of the particle phase as a closure for the particle flux, showing that particle migration is driven by the divergence…
Markov State Modeling has recently emerged as a key technique for analyzing rare events in thermal equilibrium molecular simulations and finding metastable states. Here we export this technique to the study of friction, where strongly…
Friction experiments were conducted on hydrogel thin films sliding against a rigid sphere in a low velocity regime where molecular adsorption at the sliding interface sets the friction force, through a dissipative…
Transitions between solid-like and fluid-like states in living tissues have been found in steps of embryonic development and in stages of disease progression. Our current understanding of these transitions has been guided by experimental…
The homogeneous state of a binary mixture of smooth inelastic hard disks or spheres is analyzed. The mixture is driven by a thermostat composed by two terms: a stochastic force and a drag force proportional to the particle velocity. The…
In this work, we analyse the stick-slip motion of a soft elastomeric block on a smooth, hard surface under the application of shear, which is induced by a puller moving at a steady velocity. The frictional stress is generated by make-break…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…
The application of a sufficiently strong strain perpendicular to the pitch axis of a monodomain cholesteric elastomer unwinds the cholesteric helix. Previous theoretical analyses of this transition ignored the effects of Frank elasticity…
We study the phase transition in the holographic entanglement entropy for various confining models. This transition occurs for the entanglement entropy of a strip at a critical value of the strip width. Our main interest is to examine the…
We derive a self-consistent hydrodynamic theory of coupled binary-fluid-surfactant systems from the underlying microscopic physics using Rayleigh's variational principle. At the microscopic level, surfactant molecules are modelled as…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
We present a theoretical treatment of energy transfer in a molecular motor described in terms of overdamped Brownian motion on a multidimensional tilted periodic potential. The tilt acts as a thermodynamic force driving the system out of…