Related papers: On the Calculation of Puckering Free Energy Surfac…
We present the results of a combined metadynamics--umbrella sampling investigation of the puckered conformers of pyranoses described using the gromos 45a4 force field. The free energy landscape of Cremer--Pople puckering coordinates has…
Cyclic molecules are ubiquitous across applications in chemistry and biology. Their restricted conformational flexibility provides structural pre-organization that is key to their function in drug discovery and catalysis. However, reliably…
We present the results of a combined metadynamics-umbrella sampling investigation of the puckered conformers of pyranoses described using the gromos 45a4 force field. The free energy landscape of Cremer-Pople puckering coordinates has been…
A puckered sheet is a freestanding crystalline membrane with an embedded array of bistable buckled units. Recent work has shown that the bistable units behave like spins in a two-dimensional compressible Ising antiferromagnet with, however,…
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…
The conformational behavior of a coarse-grained finite polymer chain near an attractive spherical surface was investigated by means of multicanonical Monte Carlo computer simulations. In a detailed analysis of canonical equilibrium data…
We calculate the universal part of the free energy of certain finite two- dimensional regions at criticality by use of conformal field theory. Two geometries are considered: a section of a circle ("pie slice") of angle \phi and a helical…
We derive an exact analytic expression for the high-temperature limit of the Casimir interaction between two Drude spheres of arbitrary radii. Specifically, we determine the Casimir free energy by using the scattering approach in the…
The properties of spin polarized pure neutron matter and symmetric nuclear matter are studied using the finite range simple effective interaction, upon its parametrization revisited. Out of the total twelve parameters involved, we now…
Accurate free-energy estimation is essential in molecular simulation, yet the periodic boundary conditions (PBC) commonly used in computer simulations have rarely been explicitly exploited. Equilibrium methods such as umbrella sampling,…
Single molecule pulling experiments provide information about interactions in biomolecules that cannot be obtained by any other method. However, the reconstruction of the molecule's free energy profile from the experimental data is still a…
We study numerical conformal mapping of multiply connected planar domains with boundaries consisting of unions of finitely many circular arcs, so called polycircular domains. We compute the conformal capacities of condensers defined by…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
Particles interacting with short-ranged potentials have attracted increasing interest, partly for their ability to model mesoscale systems such as colloids interacting via DNA or depletion. We consider the free energy landscape of such…
Circular-harmonic spectra are a compact representation of local image features in two dimensions. It is well known that the computational complexity of such transforms is greatly reduced when polar separability is exploited in steerable…
We study the geometric properties of the energy landscape of coarse-grained, off-lattice models of polymers by endowing the configuration space with a suitable metric, depending on the potential energy function, such that the dynamical…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
Recent polarized proton experiments at Brookhaven National Laboratory are used as a basis for a model of the energy dependence of the analyzing power of proton-carbon elastic scattering. In addition to their practical value for polarimetry,…
This work addresses the question of whether it is possible to define simple pair-wise interaction terms to approximate free energies of proteins or polymers. Rather than ask how reliable a potential of mean force is, one can ask how…
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,…