Related papers: Efficient model chemistries for peptides. II. Basi…
Electrolyte solutions play critical role in a vast range of important applications, yet an accurate and scalable method of predicting their properties without fitting to experiment has remained out of reach, despite over a century of…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
Hydrophobic polyelectrolytes have been predicted to adopt an unique pearl-necklace conformation in aqueous solvents. We present in this Letter an attempt to characterise quantitatively this conformation with a focus on $D_p$, the pearl…
Ab initio electronic structure methods give accurate results for small systems, but do not scale well to large systems. Chemical insight tells us that molecular functional groups will behave approximately the same way in all molecules,…
Porous electrode theory (PET) provides essential insights into electrochemical states, but its computational complexity hinders real-time control and obscures scaling relations. To bridge the gap between high-fidelity simulations and…
The goal of the present work is to obtain accurate potential energy surfaces (PES) for high-dimensional molecular systems with a small number of ${\it ab}$ ${\it initio}$ calculations in a system-agnostic way. We use probabilistic modeling…
Atomic basis sets are widely employed within quantum mechanics based simulations of matter. We introduce a machine learning model that adapts the basis set to the local chemical environment of each atom, prior to the start of self…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…
Electronically-active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from $\pi$-conjugated oligopeptides composed of an aromatic core…
A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is explored, in which parameters are embedded into a low-cost, low-level (LL) ab initio model and adjusted to obtain agreement…
Chemical accuracy serves as an important metric for assessing the effectiveness of the numerical method in Kohn--Sham density functional theory. It is found that to achieve chemical accuracy, not only the Kohn--Sham wavefunctions but also…
Density functional theory is used to describe electrolyte solutions in contact with electrodes of planar or spherical shape. For the electrolyte solutions we consider the so-called civilized model, in which all species present are treated…
Machine Learning Interatomic Potentials (MLIPs) sometimes fail to reproduce the physical smoothness of the quantum potential energy surface (PES), leading to erroneous behavior in downstream simulations that standard energy and force…
The issues we attempt to tackle here are what the first peptides did look like when they emerged on the primitive earth, and what simple catalytic activities they fulfilled. We conjecture that the early functional peptides were short (3 to…
Segments with the amino acid sequence EKAYLRT appear in natural occurring proteins both in $\alpha$-helices and $\beta$-sheets. For this reason, we have use this peptide to study how secondary structure formation in proteins depends on the…
We perform a generalized-ensemble simulation of a small peptide taking the interactions among all atoms into account. From this simulation we obtain thermodynamic quantities over a wide range of temperatures. In particular, we show that the…
Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…
We explore the performance of a statistical learning technique based on Gaussian Process (GP) regression as an efficient non-parametric method for constructing multi-dimensional potential energy surfaces (PES) for polyatomic molecules.…
We present the implementation of a variational finite element solver in the HelFEM program for benchmark calculations on diatomic systems. A basis set of the form $\chi_{nlm}(\mu,\nu,\phi)=B_{n}(\mu)Y_{l}^{m}(\nu,\phi)$ is used, where…
The two most recently published potential energy surfaces (PESs) for the HeH$_2$ complex, the so-called MR (Muchnick and Russek) and BMP (Boothroyd, Martin, and Peterson) surfaces, are quantitatively evaluated and compared through the…