Related papers: Free Energy Evaluation in Polymer Translocation vi…
We consider the solution of the stochastic heat equation \partial_T \mathcal{Z} = 1/2 \partial_X^2 \mathcal{Z} - \mathcal{Z} \dot{\mathscr{W}} with delta function initial condition \mathcal{Z} (T=0)= \delta_0 whose logarithm, with…
Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and…
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…
Recent advances in Generalized Ensemble simulations and microcanonical analysis allowed the investigation of structural transitions in polymer models over a broad range of local bending and torsion strengths. It is reasonable to argue that…
We analyze a (1+1)-dimension directed random walk model of a polymer dipped in a medium constituted by two immiscible solvents separated by a flat interface. The polymer chain is heterogeneous in the sense that a single monomer may…
We investigate the dynamics of a gas of non-interacting particle-like soliton waves, demonstrating that phase transitions originate from their collective behavior. This is predicted by solving exactly the nonlinear equations and by…
We consider a directed random walk model of a random heterogeneous polymer in the proximity of an interface separating two selective solvents. This model exhibits a localization/delocalization transition. A positive value of the free energy…
We study an undirected polymer chain living on the 1-dimensional integer lattice and carrying i.i.d.\ random charges. Each self-intersection of the polymer contributes to the Hamiltonian an energy that is equal to the product of the charges…
Massless scalar electrodynamics is studied at high temperature and zero chemical potential. I derive the free energy to order $\lambda^2$, $\lambda e^2$ and $e^4$ by effective field theory methods. The first step consists of the…
A polydisperse system contains particles with at least one attribute $\sigma$ (such as particle size in colloids or chain length in polymers) which takes values in a continuous range. It therefore has an infinite number of conserved…
In open systems with strong coupling, the interaction energy between the system and the environment is significant, so thermodynamic quantities cannot be reliably obtained by traditional statistical mechanics methods. The Hamiltonian of…
We consider self-avoiding lattice polygons, in the hypercubic lattice, as a model of a ring polymer adsorbed at a surface and either being desorbed by the action of a force, or pushed towards the surface. We show that, when there is no…
We suggest and discuss a simple model of an ideal gas under the piston to gain an insight into the workings of the Jarzynski identity connecting the average exponential of the work over the non-equilibrium trajectories with the equilibrium…
Using the observation that configurations of N polymers with hard core interactions on a closed random surface correspond to random surfaces with N boundary components we calculate the free energy of a gas of polymers interacting with fully…
Excess contributions to the free energy due to interfaces occur for many problems encountered in the statistical physics of condensed matter when coexistence between different phases is possible (e.g. wetting phenomena, nucleation, crystal…
Monte Carlo simulations are used to study the conformational behavior of a semiflexible polymer confined to cylindrical and conical channels. The channels are sufficiently narrow that the conditions for the Odijk regime are marginally…
One particle in a classical perfect gas is driven out of equilibrium by changing its mass over a short time interval. The work done on the driven particle depends on its collisions with the other particles in the gas. This model thus…
This paper discusses the free energy of complex dislocation microstructures, which is a fundamental property of continuum plasticity. In the past, multiple models of the self energy of dislocations have been proposed in the literature that…
We analyze the free energy for translocation of a polymer from the outside of a spherical vesicle to the inside. The process is assumed to be driven by the adsorption of the polymer on the inner surface of the vesicle. We argue that in the…
Consider the free energy of a $d$-dimensional gas in canonical equilibrium under pairwise repulsive interaction and global confinement, in presence of a volume constraint. When the volume of the gas is forced away from its typical value,…