Related papers: A Three-State Thermodynamically Consistent Cross-B…
In this work, we study the impact of non-Gaussian alpha-stable Levy motion on transitions between metastable equilibrium states (or attractors) in a stochastic Stommel two-box model for thermohaline circulation (THC). By maximizing the…
This work is devoted to the consistent modeling of a three-phase mixture of a gas, a liquid and its vapor. Since the gas and the vapor are mis-cible, the mixture is subjected to a non-symmetric constraint on the volume. Adopting the Gibbs…
An adiabatic approach is developed for the problem of boundary friction between two atomically smooth and incommensurate solid surfaces, separated by a monolayer of lubricant atoms. This method permits to consider very slow macroscopic…
A coarse-grained molecular simulation approach originally developed for entangled polymeric liquids is extended to model the mechanical behavior of long-fiber networks. The model, based on the slip-link picture of chain entanglements,…
We present a hybrid computational method for simulating the dynamics of macromolecules in solution which couples a mesoscale solver for the fluctuating hydrodynamics (FH) equations with molecular dynamics to describe the macromolecule. The…
A recently introduced particle-based model for fluid dynamics with continuous velocities is generalized to model immiscible binary mixtures. Excluded volume interactions between the two components are modeled by stochastic multiparticle…
Randomly crosslinked macromolecules undergo a liquid-to-amorphous solid phase transition at a critical crosslink concentration. This transition has two main signatures: the random localization of a fraction of the monomers and the emergence…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
The steady-state nucleation rate and flux of composite nucleus at the saddle point is studied by extending the theory of binary nucleation. The Fokker-Planck equation that describes the nucleation flux is derived using the Master equation…
A new formulation of time-dependent Relaxed Magnetohydrodynamics (RxMHD) is derived variationally from Hamilton's Action Principle using microscopic conservation of mass, and macroscopic conservation of total magnetic helicity, cross…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
Mechanical stretching of secondary structures is studied through molecular dynamics simulations of a Go-like model. Force vs. displacement curves are studied as a function of the stiffness and velocity of the pulling device. The succession…
We investigate a one-dimensional water-like lattice model with Van der Waals and hydrogen-bond interactions, allowing for particle number fluctuations through a chemical potential. The model, defined on a chain with periodic boundary…
Inspired by the Melan equation we propose a model for suspension bridges with two cables linked to a deck, through inextensible hangers. We write the energy of the system and we derive from variational principles two nonlinear and nonlocal…
We obtain macroscopic adiabatic thermodynamic transformations by space-time scalings of a microscopic Hamiltonian dynamics subject to random collisions with the environment. The microscopic dynamics is given by a chain of oscillators…
For a single enzyme or molecular motor operating in an aqueous solution of non-equilibrated solute concentrations, a thermodynamic description is developed on the level of an individual trajectory of transitions between states. The concept…
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…
The chaperonin GroEL-GroES, a machine which helps some proteins to fold, cycles through a number of allosteric states, the $T$ state, with high affinity for substrate proteins (SPs), the ATP-bound $R$ state, and the $R^{\prime\prime}$…