相关论文: Tracing the minimum-energy path on the free-energy…
Free energy of crystal phases is commonly evaluated by thermodynamic integration (TDI) along a reversible path that involves an external potential. A persistent problem in this method is that a significant hysteresis is observed due to…
We address the problem of constructing accurate mathematical models of the dynamics of complex systems projected on a collective variable. To this aim we introduce a conceptually simple yet effective algorithm for estimating the parameters…
Recently, Lattelais et al. (2009) have interpreted aggregated observations of molecular isomers to suggest that there exists a "minimum energy principle'', such that molecular formation will favor more stable molecular isomers for…
Due to the development of efficient algorithms and the improvement of computer power it is now possible to map out potential energy surfaces (PES) of reactions at surfaces in great detail. This achievement has been accompanied by an…
A new method for finding the minimum free energy pathway (MFEP) of ions and small molecule transportation through a protein based on the three-dimensional reference interaction site model (3D-RISM) theory combined with the string method has…
In this work a method is proposed for computing step free energies for faceted solid-liquid interfaces based on atomistic simulations. The method is demonstrated in an application to (111) interfaces in elemental Si, modeled with the…
The van der Waals and Casimir-Polder interaction energy of an atom with an infinitely thin sphere with finite conductivity is investigated in the framework of the hydrodynamic approach at finite temperature. This configuration models the…
Path optimization methods have been widely used and highly successful for the analysis of chemical reactions. Yet, they can fail to capture intrinsically multidimensional features of potential energy surfaces (PES). We introduce the nudged…
A vast array of phenomena, ranging from chemical reactions to phase transformations, are analysed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used,…
Mapping the chemical reaction pathways and their corresponding activation barriers is a significant challenge in molecular simulation. Given the inherent complexities of 3D atomic geometries, even generating an initial guess of these paths…
A new potential energy surface (PES) and dynamical study are presented of the reactive process between H2CO + OH towards the formation of HCO + H2O and HCOOH + H. In this work a source of spurious long range interactions in symmetry adapted…
Probing the reaction mechanisms of supramolecular processes in soft- and biological matter, such as protein aggregation, is inherently challenging. These processes emerge from the simultaneous action of multiple molecular mechanisms, each…
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…
This work describes the formalism for estimating thermonuclear reaction rates for astrophysical applications, emphasizing modern statistical approaches such as Monte-Carlo sampling and Bayesian models. We discuss related topics including…
We propose a method that exploits sparse representation of potential energy surfaces (PES) on a polynomial basis set selected by compressed sensing. The method is useful for studies involving large numbers of PES evaluations, such as the…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
We prove that the lowest free energy of a classical interacting system at temperature $T$ with a prescribed density profile $\rho(x)$ can be approximated by the local free energy $\int f_T(\rho(x))dx$, provided that $\rho$ varies slowly…
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…
By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent…
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…