Related papers: Free energy approach to micellization and aggregat…
Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed…
We report on recent progress in the study of evolution processes involving degenerate parabolic equations what may exhibit free boundaries. The equations we have selected follow to recent trends in diffusion theory: considering anomalous…
Lipid membrane with freely exposed edge is regarded as smooth surface with curved boundary. Exterior differential forms are introduced to describe the surface and the boundary curve. The total free energy is defined as the sum of Helfrich's…
We derive a coarse grained, free-energy functional which describes droplet configurations arising on nucleation of a product crystal within a parent. This involves a new `slow' vacancy mode that lives at the parent-product interface. A…
We prove reversed Hardy-Littlewood-Sobolev inequalities by carefully studying the natural associated free energies with direct methods of calculus of variations. Tightness is obtained by a dyadic argument, which quantifies the relative…
We study the phase behavior of a nematic liquid crystal confined between a flat substrate with strong anchoring and a patterned substrate whose structure and local anchoring strength we vary. By first evaluating an effective surface free…
A variational approach for the free energy is used to study the three-dimensional anisotropic XY model in the presence of a crystal field. The magnetization and the phase diagrams as a function of the parameters of the Hamiltonian are…
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of "bridging" potential energy…
The multistate Bennett acceptance ratio (MBAR) method is a prevalent approach for computing free energies of thermodynamic states. In this work, we introduce BayesMBAR, a Bayesian generalization of the MBAR method. By integrating…
The free energy, or equivalently the ground state energy in finite volume, may be calculated from forward scattering amplitudes using a formula due to Dashen, Ma, and Bernstein. However a naive treatment leads to singularities when…
We have studied the structure and free energy landscape of a semi-flexible lattice-polymer in the presence of a surface. At low temperatures coexistence of two-dimensional integer-folded crystals is observed. As the temperature is increased…
We simulate the homogeneous nucleation of ice from supercooled liquid water at 220 K in the isobaric-isothermal ensemble using the MW monatomic water potential. Monte Carlo simulations using umbrella sampling are performed in order to…
With the help of metadynamics it is possible to calculate efficiently the free energy of systems displaying high energy barriers as a function of few selected "collective variables". In doing this, the contribution of all the other degrees…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Understanding how different classes of molecules move across biological membranes is a prerequisite to predicting a solute's permeation rate, which is a critical factor in the fields of drug design and pharmacology. We use biased Molecular…
The solid-liquid interface free energy \gamma sl is a key parameter controlling nucleation and growth during solidification and other phenomena. There are intrinsic difficulties in obtaining accurate experimental values, and the previous…
The Jarzynski equality and the fluctuation theorem relate equilibrium free energy differences to non-equilibrium measurements of the work. These relations extend to single-molecule experiments that have probed the finite-time thermodynamics…
We report a numerical study of the rate of crystal nucleation in a binary suspension of oppositely charged colloids. Two different crystal structures compete in the thermodynamic conditions under study. We find that the crystal phase that…
Recent very large molecular dynamics simulations of homogeneous nucleation with $(1-8) \cdot 10^9$ Lennard-Jones atoms [Diemand et al. J. Chem. Phys. {\bf 139}, 074309 (2013)] allow us to accurately determine the formation free energy of…
Free energies as a function of a selected set of collective variables are commonly computed in molecular simulation and of significant value in understanding and engineering molecular behavior. These free energy surfaces are most commonly…