相关论文: Experimental Free Energy Surface Reconstruction Fr…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
Quantum electrodynamics near a boundary is investigated by considering the inertial mass shift of an electron near a dielectric or conducting surface. We show that in all tractable cases the shift can be written in terms of integrals over…
The Jarzynski Equality is a well-known and widely used identity, relating the free energy difference between two states of a system to the work done over some arbitrary, nonequilibrium transformation between the two states. Despite being…
We consider the paradigm of an overdamped Brownian particle in a potential well, which is modulated through an external protocol, in the presence of stochastic resetting. Thus, in addition to the short range diffusive motion, the particle…
Non-equilibrium path integral methods for computing quantum free energy differences are applied to a quantum particle trapped in a harmonic well of uniformly changing strength with the purpose of establishing the convergence properties of…
We present a new ternary free energy lattice Boltzmann model. The distinguishing feature of our model is that we are able to analytically derive and independently vary all fluid-fluid surface tensions and the solid surface contact angles.…
We propose a method of free energy calculation for a system of interacting particles arranged in a Bravais lattice. It will be shown how to treat divergences for infinite unbounded systems with "catastrophic" potetntials like Coulomb and…
Recent advances in ultrafast electron emission, microscopy, and diffraction have demonstrated a remarkable ability to manipulate free electrons with quantum coherence using light beams. Here, we present a framework for exploring free…
The elastic deformation of a soft solid induced by capillary forces crucially relies on the excess stress inside the solid-liquid interface. While for a liquid-liquid interface this "surface stress" is strictly identical to the "surface…
We study a phase-field variational model for the solvaiton of charged molecules with an implicit solvent. The solvation free-energy functional of all phase fields consists of the surface energy, solute excluded volume and solute-solvent van…
Considerable progress has recently been made in controling the motion of free atomic particles by means of light pressure exerted by laser radiation. The free fall of atoms and bouncing on a reflecting surface made from evanescent wave…
In single-molecule force spectroscopy experiments, a biomolecule is attached to a force probe via polymer linkers, and the total extension -- of molecule plus apparatus -- is monitored as a function of time. In a typical unfolding…
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…
Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the…
A free-energy functional that contains both the symmetry conserved and symmetry broken parts of the direct pair correlation function has been used to investigate the freezing of a system of hard spheres into crystalline and amorphous…
Binding energy of symmetric nuclear matter can be accessed straightforwardly with the textbook mass-formula and a sample of nuclear masses. We show that, with a minimally modified formula (along the lines of the droplet model), the symmetry…
We present a detailed comparison of computational efficiency and precision for several free energy difference ($\Delta F$) methods. The analysis includes both equilibrium and non-equilibrium approaches, and distinguishes between…
We examine the renormalized free energy of the free Dirac fermion and the free scalar on a (2+1)-dimensional geometry $\mathbb{R} \times \Sigma$, with $\Sigma$ having spherical topology and prescribed area. Using heat kernel methods, we…
External biasing forces are often applied to enhance sampling in regions of phase space which would otherwise be rarely observed. While the typical goal of these experiments is to calculate the potential of mean force (PMF) along the…
In a recent paper by Iglesias, Rumpf and Scherzer (Found. Comput. Math. 18(4), 2018) a variational model for deformations matching a pair of shapes given as level set functions was proposed. Its main feature is the presence of anisotropic…