Related papers: Free Energy of Multiple Overlapping Chains
Pre-calculated libraries of molecular fragment configurations have previously been used as a basis for both equilibrium sampling (via "library-based Monte Carlo") and for obtaining absolute free energies using a polymer-growth formalism.…
Using computer simulations, we validate a simple free energy model that can be analytically solved to predict the equilibrium size of self-limiting clusters of particles in the fluid state governed by a combination of short-range attractive…
A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures…
The analytical solution of the recently proposed ideal chain polymer mean-spherical approximation (Yu.Kalyuzhnyi, Mol.Phys., 94, 735(1998)) is presented for the multicomponent mixture of charged hard-sphere linear chain flexible molecules.…
A simple theory for glassy polymeric mechanical response which accounts for large scale chain relaxation is presented. It captures the crossover from perfect-plastic response to strong strain hardening as the degree of polymerization $N$…
We examine the phase transition of polymer adsorption as well as the underlying kinetics of polymer binding from dilute solutions on a structureless solid surface. The emphasis is put on the properties of regular multiblock copolymers,…
We study theoretically situations where competition arises between an interdiffusion process and a cross-linking chemical reaction at interfaces between pieces of the same polymer material. An example of such a situation is observable in…
Constant temperature molecular dynamics simulations were used to study solutions of flexible polyelectrolyte chains at nonzero concentrations with explicit counterions and unscreened coulombic interactions. Counterion condensation, measured…
A common approach to study nucleation rates is the estimation of free-energy barriers. This usually requires knowledge about the shape of the forming droplet, a task that becomes notoriously difficult in macromolecular setups starting with…
RNA molecules form a sequence-specific self-pairing pattern at low temperatures. We analyze this problem using a random pairing energy model as well as a random sequence model that includes a base stacking energy in favor of helix…
The freely jointed chain is often applied to model the thermodynamics of single polymer chains, but the traditional formulation of the model lacks internal energy changes due to bond stretching. For this reason, the extensible freely…
We consider a binary system of small and large spheres of finite size in a continuous medium interacting via a non-negative potential. We work in the canonical ensemble and compute upper and lower bound for the free energy at finite and…
During fast diffusion-influenced polymerization, nonequilibrium behavior of the polymer chains and the surrounding reactive monomers has been reported recently. Based on the laws of thermodynamics, the emerging nonequilibrium structures…
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy,…
Molecular dynamics simulations were performed for a polymer melt. In quiescent states, the inter-chain interaction energy supported by each particle takes relatively large values persistently for long times if the particle is close to an…
A variational approach is used to calculate free energy and conformational properties in polyelectrolytes. The true bond and Coulomb potentials are approximated by a trial isotropic harmonic energy containing monomer-monomer force constants…
We propose a scaling ansatz for the elastic energy of a system near the critical jamming transition in terms of three relevant fields: the compressive strain $\Delta \phi$ relative to the critical jammed state, the shear strain $\epsilon$,…
Macromolecular crowding can influence polymer shapes, which is important for understanding the thermodynamic stability of polymer solutions and the structure and function of biopolymers (proteins, RNA, DNA) under confinement. We explore the…
We discuss interfaces in spin glasses. We present new theoretical results and a numerical method to characterize overlap interfaces and the stability of the spin-glass phase in extended disordered systems. We use this definition to…
The translocation time of a polymer chain through an interaction energy gradient nanopore was studied by Monte Carlo simulations and the Fokker-Planck equation with double-absorbing boundary conditions. Both the simulation and calculation…