Related papers: Efficient model chemistries for peptides. II. Basi…
Non-adiabatic effects play an important role in many chemical processes. In order to study the underlying non-adiabatic potential-energy surfaces (PESs), we present a locally-constrained density-functional theory approach, which enables us…
Liquid chromatography with tandem mass spectrometry (LC-MS/MS) based proteomics is a well-established research field with major applications such as identification of disease biomarkers, drug discovery, drug design and development. In…
We present a first principles-quality potential energy surface (PES) describing the inter-atomic forces for hydrogen atoms interacting with free-standing graphene. The PES is a high-dimensional neural network potential that has been…
We summarize and discuss some of the available experimental and theoretical data important for understanding the role played by subsurface sites in dissociative chemisorption calculations for the H$_2$/Pd(111) system. Then we use a…
Peptides are ubiquitous and important biologically derived molecules, that have been found to self-assemble to form a wide array of structures. Extensive research has explored the impacts of both internal chemical composition and external…
We describe a simple ansatz to approximate the low temperature behavior of proteins and peptides by a mean-field-like model which is analytically solvable. For a small peptide some thermodynamic quantities are calculated and compared with…
Lipolysis is a life-essential metabolic process, which supplies fatty acids stored in lipid droplets to the body in order to match the demands of building new cells and providing cellular energy. In this paper, we present a first…
A method to reconstruct the energy landscape of small peptides is presented with reference to a 2d off--lattice model. The starting point is a statistical analysis of the configurational distances between generic minima and directly…
Engineering the free-energy surfaces (FES) of proteins and peptides is central to controlling conformational ensembles and their responses to perturbations. However, predicting how chemical modifications such as point mutations reshape the…
Peptides are biomolecules comprised of amino acids that play an important role in our body. In recent years, peptides have received extensive attention in drug design and synthesis, and peptide prediction tasks help us better search for…
The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary…
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…
In the denser and colder ($\leq$20 K) regions of the interstellar medium (ISM), near-infrared observations have revealed the presence of sub-micron sized dust grains covered by several layers of H\textsubscript{2}O-dominated ices and…
Machine learning interatomic potentials (MLIPs) are often trained with on-the-fly active learning, where sampled configurations from atomistic simulations are added to the training set. However, this approach is limited by the high…
The potential energy surface (PES) of dissociative adsorption of H_2 on Pd(100) is investigated using density functional theory and the full-potential linear augmented plane wave (FP-LAPW) method. Several dissociation pathways are…
Potential Energy Surfaces (PESs) are an indispensable tool to investigate, characterise and understand chemical and biological systems in the gas and condensed phases. Advances in Machine Learning (ML) methodologies have led to the…
There are different environments in the interstellar medium (ISM), depending on the density, temperature and chemical composition. Among them, molecular clouds, often referred to as the cradle of stars, are paradigmatic environments…
Computational studies of electrochemical interfaces based on density-functional theory (DFT) play an increasingly important role in present research on electrochemical processes for energy conversion and storage. The homogeneous background…
Broadly speaking, the calculation of core spectra such as electron energy loss spectra (EELS) at the level of density functional theory (DFT) usually relies one of two approaches: conceptually more complex but computationally efficient…