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Register a new userInteracting Elastic Lattice Polymers: a Study of the Free-Energy of Globular Rings
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We introduce and implement a Monte Carlo scheme to study the equilibrium statistics of polymers in the globular phase. It is based on a model of interacting elastic lattice polymers and allows a sufficiently good sampling of long and compact configurations, an essential prerequisite to study the scaling behaviour of free energies. By simulating interacting self-avoiding rings at several temperatures in the collapsed phase, we estimate both the bulk and the surface free energy. Moreover from the corresponding estimate of the entropic exponent $alpha-2$ we provide evidence that, unlike for swollen and $Theta$-point rings, the hyperscaling relation is not satisfied for globular rings.
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A compressed knotted ring polymer in a confining cavity is modelled by a knotted lattice polygon confined in a cube in ${mathbb Z}^3$. The GAS algorithm [17] is used to sample lattice polygons of fixed knot type in a confining cube and to estimate the free energy of confined lattice knots. Lattice polygons of knot types the unknot, the trefoil knot, and the figure eight knot, are sampled and the free energies are estimated as functions of the concentration of monomers in the confining cube. The data show that the free energy is a function of knot type at low concentrations, and (mean-field) Flory-Huggins theory [12,15] is used to model the free energy as a function of monomer concentration. The Flory interaction parameter of knotted lattice polygons in ${mathbb Z}^3$ is also estimated.
An analysis of extensive simulations of interacting self-avoiding polygons on cubic lattice shows that the frequencies of different knots realized in a random, collapsed polymer ring decrease as a negative power of the ranking order, and suggests that the total number of different knots realized grows exponentially with the chain length. Relative frequencies of specific knots converge to definite values because the free energy per monomer, and its leading finite size corrections, do not depend on the ring topology, while a subleading correction only depends on the crossing number of the knots.
Extensions of statistical mechanics are routinely being used to infer free energies from the work performed over single-molecule nonequilibrium trajectories. A key element of this approach is the ubiquitous expression dW/dt=partial H(x,t)/ partial t which connects the microscopic work W performed by a time-dependent force on the coordinate x with the corresponding Hamiltonian H(x,t) at time t. Here we show that this connection, as pivotal as it is, cannot be used to estimate free energy changes. We discuss the implications of this result for single-molecule experiments and atomistic molecular simulations and point out possible avenues to overcome these limitations.
We present a Monte Carlo method that allows efficient and unbiased sampling of Hamiltonian walks on a cubic lattice. Such walks are self-avoiding and visit each lattice site exactly once. They are often used as simple models of globular proteins, upon adding suitable local interactions. Our algorithm can easily be equipped with such interactions, but we study here mainly the flexible homopolymer case where each conformation is generated with uniform probability. We argue that the algorithm is ergodic and has dynamical exponent z=0. We then use it to study polymers of size up to 64^3 = 262144 monomers. Results are presented for the effective interaction between end points, and the interaction with the boundaries of the system.
The properties of the interface between solid and melt are key to solidification and melting, as the interfacial free energy introduces a kinetic barrier to phase transitions. This makes solidification happen below the melting temperature, in out-of-equilibrium conditions at which the interfacial free energy is ill-defined. Here we draw a connection between the atomistic description of a diffuse solid- liquid interface and its thermodynamic characterization. This framework resolves the ambiguities in defining the solid-liquid interfacial free energy above and below the melting temperature. In addition, we introduce a simulation protocol that allows solid-liquid interfaces to be reversibly created and destroyed at conditions relevant for experiments. We directly evaluate the value of the interfacial free energy away from the melting point for a simple but realistic atomic potential, and find a more complex temperature dependence than the constant positive slope that has been generally assumed based on phenomenological considerations and that has been used to interpret experiments. This methodology could be easily extended to the study of other phase transitions, from condensation to precipitation. Our analysis can help reconcile the textbook picture of classical nucleation theory with the growing body of atomistic studies and mesoscale models of solidification.
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