The homogeneous and heterogeneous nucleation of a Lennard-Jones liquid is investigated using the umbrella sampling method. The free energy cost of forming a nucleating droplet is determined as a function of the quench depth, and the saddle point nature of the droplets is verified using an intervention technique. The structure and symmetry of the nucleating droplets are found for a range of temp...

Supramolecular polymerization has been traditionally focused on the thermodynamic equilibrium state, where one-dimensional assemblies reside at the global minimum of the Gibbs free energy. The pathway and rate to reach the equilibrium state are irrelevant, and the resulting assemblies remain unchanged over time. In the past decade, the focus has shifted to kinetically trapped (non-dissipative n...

Recent years have witnessed major advances in our understanding of nonequilibrium processes. The Jarzynski equality, for example, provides a link between equilibrium free energy differences and finite-time nonequilibrium dynamics. We propose a generalization of this relation to non-Hamiltonian dynamics, relevant for active matter systems, continuous feedback, and computer simulation. Surprising...

Theories of phase change and self-assembly often invoke the idea of a "quasiequilibrium," a regime in which the nonequilibrium association of building blocks results nonetheless in a structure whose properties are determined solely by an underlying free energy landscape. Here we study a prototypical example of multicomponent self-assembly, a one-dimensional fiber grown from red and blue blocks....

Using both numerical simulations and exact expressions for the free energy and microcanonical entropy for a modified Hamiltonian mean-field (HMF) model, we show that when two similar systems with the same intensive parameters but with negative specific heat are weakly coupled, they undergo a process in which the total entropy increases irreversibly. We find that the final equilibrium is such th...

This paper analyzes equilibrium superhelical cruciform formation in a topologial domain of DNA containing inverted repeat sequences. The cruciform conformation is shown to he stable when the molecule is sufficiently negatively supercoiled but not when it is positively supercoiled. For a particular sequence containing a single inverted repeat, onset of stability occurs at a degree of negative su...

A theory is introduced to describe self-assembly of liquid crystalline AB diblock copolymers, consisting of a homopolymer (A) and a side-chain liquid crystalline polymer (B). We derive the free energy of the liquid crystalline micellar solutions and examine the equilibrium solution properties: critical micelle concentration (CMC), nematic-isotropic phase transition (NIT) of the rigid side-chain...

Using an algorithm for simulating equilibrium configurations, we study a fluctuating helical polymer either (i) contained in a cylindrical pore or (ii) wound around a cylindrical rod. We work in the regime where both the contour length and the persistence length of the helical polymer are much larger than the diameter of the cylinder. In case (i) we calculate the free energy of confinement and ...

The equilibrium unfolding of hen lysozyme at pH 2 was studied as a function of pressure (0.1~700MPa) and temperature (-10°C~50°C) using Trp fluorescence as monitor supplemented by variable pressure 1H NMR spectroscopy (0.1~400MPa). The unfolding profiles monitored by the two methods allowed the two-state equilibrium analysis between the folded (N) and unfolded (U) conformers. The free energy di...

The potential of mean force (PMF) calculation in single molecule manipulation experiments performed via the steered molecular dynamics (SMD) technique is a computationally very demanding task because the analyzed system has to be perturbed very slowly to be kept close to equilibrium. Faster perturbations, far from equilibrium, increase dissipation and move the average work away from the underly...