Related papers: Efficient model chemistries for peptides. II. Basi…
The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase…
Analysis of the geometric properties of a mean-field HP model on a square lattice for protein structure shows that structures with large number of switch backs between surface and core sites are chosen favorably by peptides as unique ground…
Both molecular mechanical and quantum mechanical calculations play an important role in describing the behavior and structure of molecules. In this work, we compare for the same peptide systems the results obtained from folding molecular…
Within the Poisson-Boltzmann (PB) approach electrolytes in contact with planar, spherical, and cylindrical electrodes are analyzed systematically. The dependences of their capacitance $C$ on the surface charge density $\sigma$ and the ionic…
The NH2 + O reaction represents a critical oxidation pathway in ammonia and hydrazine combustion, yet significant discrepancies persist in reported kinetics. Here, we generate a full-dimensional ground-state potential energy surface (PES)…
Multipole moments are the first order responses of the energy to spatial derivatives of the electric field strength. The quality of density functional theory (DFT) prediction of molecular multipole moments thus characterizes errors in…
The interpolation of high-dimensional potential energy surfaces (PESs) is commonly done with physically-inspired deep-neural network models. In this work, we illustrate that Gaussian Processes (GPs) are also capable of interpolating…
The rapid emergence of universal Machine Learning Interatomic Potentials (uMLIPs) has transformed materials modeling. However, a comprehensive understanding of their generalization behavior across configurational space remains an open…
The FCC structure of Pd$\rm_{1-x}$Ag$\rm_{x}$ ($\rm{x}=$ 0.25, 0.50, 0.75) alloys is considered as a fuel cell component in this study. We have looked into its qualities as a component of a fuel cell to see whether it could be potentially…
We present a generally-applicable computational framework for the efficient and accurate characterization of molecular structural patterns and acid properties in explicit solvent using H$_2$O$_2$ and CH$_3$SO$_3$H in phenol as an example.…
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic…
A central problem of materials science is to determine whether a hypothetical material is stable without being synthesized, which is mathematically equivalent to a global optimization problem on a highly non-linear and multi-modal potential…
We present a systematic Density Functional Theory (DFT) study of geometries and energies of the nucleic acid DNA bases (guanine, adenine, cytosine and thymine) and 30 different DNA base-pairs. We use a recently developed linear-scaling DFT…
The description of fluid mixtures molecular behavior is significant for various industry fields due to the complex composition of fluid found in nature. Statistical mechanics approaches use intermolecular interaction potential to predict…
Peptide therapeutics, including macrocycles, peptide inhibitors, and bioactive linear peptides, play a crucial role in therapeutic development due to their unique physicochemical properties. However, predicting these properties remains…
The relative energies of different phases or polymorphs of molecular solids can be small, less than a kiloJoule/mol. Reliable description of such energy differences requires high quality treatment of electron correlations, typically beyond…
Full dimensional potential energy surfaces (PESs) based on machine learning (ML) techniques provide means for accurate and efficient molecular simulations in the gas- and condensed-phase for various experimental observables ranging from…
This work reports an efficient density-fitting implementation of the density-based basis-set correction (DBBSC) method in the MOLPRO software. This method consists in correcting the energy calculated by a wave-function method with a given…
We have performed exhaustive multicanonical Monte Carlo simulations of three 12-residue synthetic peptides in order to investigate the thermodynamic and structural properties as well as the characteristic helix-coil transitions. In these…
We define a generalized finite element method for the discretization of elliptic partial differential equations in heterogeneous media. An adaptive local finite element basis (AL basis) on a coarse mesh which does not resolve the matrix of…