We present a revision to the well known Störmer-Verlet algorithm for simulating second order differential equations. The revision addresses the inclusion of linear friction with associated stochastic noise, and we analytically demonstrate that the new algorithm correctly reproduces diffusive behavior of a particle in a flat potential. For a harmonic oscillator, our algorithm provides the exact Boltzmann distribution for any value of damping, frequency, and time step for both underdamped and overdamped behavior within the usual stability limit of the Verlet algorithm. Given the structure and simplicity of the method we conclude that this approach can trivially be adapted for contemporary applications, including molecular dynamics with extensions such as molecular constraints.PACS numbers:

We use a simple and efficient computer model to investigate the physical properties of bilayer membranes. The amphiphilic molecules are modeled as short rigid trimers with finite range pair interactions between them. The pair potentials have been designed to mimic the hydrophobic interactions, and to allow the simulation of the membranes without the embedding solvent as if the membrane is in vacuum. We find that upon decreasing the area density of the molecules the membrane undergoes a solid-fluid phase transition, where in the fluid phase the molecules can diffuse within the membrane plane. The surface tension and the bending modulus of the fluid membranes are extracted from the analysis of the spectrum of thermal undulations. At low area densities we observe the formation of pores in the membrane through which molecules can diffuse from one layer to the other. The appearance of the pores is explained using a simple model relating it to the area dependence of the free energy.

We compare Monte Carlo simulations of knotted and unknotted polymers whose ends are connected to two parallel walls. The force f exerted on the polymer is measured as a function of the separation R between the walls. For unknotted polymers of several monomer numbers N , the product f N ν is a simple function of R/N ν , where ν ≃ 0.59. By contrast, knotted polymers exhibit strong finite size effects which can be interpreted in terms of a new length scale related to the size of the knot. Based on this interpretation, we conclude that the number of monomers forming the knot scales as N t , with t = 0.4 ± 0.1.