Enhanced sampling reveals the main pathway of an organic cascade reactionNormal molecular dynamics simulations are usually unable to simulate chemical reactions due to the low probability of forming the transition state. Therefore, enhanced sampling methods are…Yi Sun, Xu Han, Lijiang Yang·Aug 23, 2022SaveLearn
Building Robust Machine Learning Models for Small Chemical Science Data: The Case of Shear ViscosityShear viscosity, though being a fundamental property of all liquids, is computationally expensive to estimate from equilibrium molecular dynamics simulations. Recently, Machine Learning (ML) methods…Nikhil V. S. Avula, Shivanand K. Veesam, Sudarshan Behera et al.·Aug 23, 2022SaveLearn
Wien effect in interfacial water dissociation through proton-permeable graphene electrodesStrong electric fields can accelerate molecular dissociation reactions. The phenomenon known as the Wien effect was previously observed using high-voltage electrolysis cells that produced fields of…J. Cai, E. Griffin, V. Guarochico-Moreira et al.·Aug 23, 2022SaveLearn
Prediction of good reaction coordinates and future evolution of MD trajectories using Regularized Sparse Autoencoders: A novel deep learning approachIdentifying reaction coordinates(RCs) is an active area of research, given the crucial role RCs play in determining the progress of a chemical reaction. The choice of the reaction coordinate is often…Abhijit Gupta·Aug 22, 2022SaveLearn
Deep Coarse-grained Potentials via Relative Entropy MinimizationNeural network (NN) potentials are a natural choice for coarse-grained (CG) models. Their many-body capacity allows highly accurate approximations of the potential of mean force, promising CG…Stephan Thaler, Maximilian Stupp, Julija Zavadlav·Aug 22, 2022SaveLearn
Generalized nonorthogonal matrix elements for arbitrary excitationsElectronic structure methods that exploit nonorthogonal Slater determinants face the challenge of efficiently computing nonorthogonal matrix elements. In a recent publication, H. G. A. Burton, J.…Hugh G. A. Burton·Aug 22, 2022SaveLearn
Efficient construction of canonical polyadic approximations of tensor networksWe consider the problem of constructing a canonical polyadic (CP) decomposition for a tensor network, rather than a single tensor. We illustrate how it is possible to reduce the complexity of…Karl Pierce, Edward F Valeev·Aug 22, 2022SaveLearn
Hyperradial distribution function of few-body problems: a new arena for extreme value theoryThis work explores classical capture models for few-body systems via a Monte Carlo method in hyperspherical coordinates. In particular, we focus on van der Waals and charged-induced dipole…Yu Wang, Marjan Mirahmadi, Ahmed A. Elkamshishy et al.·Aug 22, 2022SaveLearn
The Calculation of the Rate Constants via a Master Equation approach -- A Comprehensive TutorialIntermolecular hydrogen transfer free radical reactions are common in the combustion process and in a number of organic chemistry reactions. Therefore, evaluating the pressure and…Yi Sun·Aug 19, 2022SaveLearn
Atomistic structure search using local surrogate modeWe describe a local surrogate model for use in conjunction with global structure search methods. The model follows the Gaussian approximation potential (GAP) formalism and is based on a the smooth…Nikolaj Rønne, Mads-Peter V. Christiansen, Andreas Møller Slavensky et al.·Aug 19, 2022SaveLearn
Cross-correlation effects in the solution NMR spectra of near-equivalent spin-1/2 pairsThe NMR spectra of spin-1/2 pairs contains four peaks, with two inner peaks much stronger than the outer peaks in the near-equivalence regime. We have observed that the strong inner peaks have…James W. Whipham, Gamal A. I. Moustafa, Mohamed Sabba et al.·Aug 19, 2022SaveLearn
The three-center two-positron bondComputational studies have shown that one or more positrons can stabilize two repelling atomic anions through the formation of two-center positronic bonds. In the present work, we study the energetic…Jorge Charry, Félix Moncada, Matteo Barborini et al.·Aug 18, 2022SaveLearn
Identifying sequential residue patterns in bitter and umami peptidesThe primary structures of peptides, originating from food proteins, affect their taste. Connecting primary structure to taste, however, is difficult because the size of the peptide sequence space…Arghya Dutta, Tristan Bereau, Thomas A. Vilgis·Aug 18, 2022SaveLearn
Robust and scalable uncertainty estimation with conformal prediction for machine-learned interatomic potentialsUncertainty quantification (UQ) is important to machine learning (ML) force fields to assess the level of confidence during prediction, as ML models are not inherently physical and can therefore…Yuge Hu, Joseph Musielewicz, Zachary Ulissi et al.·Aug 17, 2022SaveLearn
XPS core-level chemical shift by ab initio many-body theoryX-ray photoemission spectroscopy (XPS) provides direct information on the atomic composition and stoichiometry by measuring core electron binding energies. Moreover, according to the shift of the…Iskander Mukatayev, Florient Moevus, Benoît Sklénard et al.·Aug 17, 2022SaveLearn
DPA-1: Pretraining of Attention-based Deep Potential Model for Molecular SimulationMachine learning assisted modeling of the inter-atomic potential energy surface (PES) is revolutionizing the field of molecular simulation. With the accumulation of high-quality electronic structure…Duo Zhang, Hangrui Bi, Fu-Zhi Dai et al.·Aug 17, 2022SaveLearn
Centroid Molecular Dynamics Can Be Greatly Accelerated Through Neural Network Learned Centroid Forces Derived from Path Integral Molecular DynamicsFor nearly the past 30 years, Centroid Molecular Dynamics (CMD) has proven to be a viable classical-like phase space formulation for the calculation of quantum dynamical properties. However,…Timothy D. Loose, Patrick G. Sahrmann, Gregory A. Voth·Aug 16, 2022SaveLearn
HCl, DCl and TCl diatomic molecules in their ground state: predicting Born-Oppenheimer rovibrational spectraThe analytic Born-Oppenheimer (B-O) potential curve for the ground state X1+ of the molecule (H,D,T)Cl is constructed for the whole range of internuclear distances R ∈ [0,∞) with…Horacio Olivares-Pilón, Alexander V. Turbiner·Aug 16, 2022SaveLearn
Why Ortho- and Para-Hydroxy Metabolites Can Scavenge Free Radicals that the Parent Atorvastatin Cannot? Important Pharmacologic Insight from Quantum ChemistryThe pharmaceutical success of atorvastatin (ATV), a widely employed drug against the "bad" cholesterol (LDL) and cardiovascular diseases, traces back to its ability to scavenge free radicals.…Ioan Baldea·Aug 16, 2022SaveLearn
Unified definition of exciton coherence length for exciton-phonon coupled molecular aggregatesExciton coherence length (ECL) is an essential concept to characterize the nature of exciton in molecular aggregates for photosynthesis, organic photovoltaics, and light-emitting diodes. ECL has been…Tong Jiang, Jiajun Ren, Zhigang Shuai·Aug 16, 2022SaveLearn
Periodic Coupled-Cluster Green's Function for Photoemission Spectra of Realistic SolidsWe present an efficient implementation of coupled-cluster Green's function (CCGF) method for simulating photoemission spectra of periodic systems. We formulate the periodic CCGF approach with…Katelyn Laughon, Jason M. Yu, Tianyu Zhu·Aug 16, 2022SaveLearn
Current rectification by nanoparticles in bipolar nanoporesBipolar nanochannels comprising two domains of positively and negatively charged walls along the pore axis are known to rectify current when exposed to an electric potential bias. We find that…Andrés Córdoba, Joan M. Montes de Oca, Johnson Dhanasekaran et al.·Aug 15, 2022SaveLearn
Catalysis in Click Chemistry Reactions Controlled by Cavity Quantum Vacuum Fluctuations: The Case of endo/exo Diels-Alder ReactionAchieving control over chemical reaction's rate and stereoselectivity realizes one of the Holy Grails in chemistry that can revolutionize chemical and pharmaceutical industries. Strong…Fabijan Pavošević, Robert L. Smith, Angel Rubio·Aug 14, 2022SaveLearn
Reliable emulation of complex functionals by active learning with error controlA statistical emulator can be used as a surrogate of complex physics-based calculations to drastically reduce the computational cost. Its successful implementation hinges on an accurate…Xinyi Fang, Mengyang Gu, Jianzhong Wu·Aug 13, 2022SaveLearn
On the classical reaction rate and the first-time problems of Brownian motionWe have developed efficient techniques to solve the first-time problems of Brownian motion. Based on a time-scale separation of recrossings, we show that Eyring's transmission coefficient ()…Aihua Zhang, Sun Choi·Aug 13, 2022SaveLearn