Related papers: Reaction Coordinates for Conformational Transition…
We have investigated plasma-surface interactions with molecular dynamics (MD) simulations. It, however, is high cost computation and is limited to simulations for materials of nanometer order. In order to overcome the limitation, a…
We present a local density approximation (LDA) for one-dimensional (1D) systems interacting via the soft-Coulomb interaction based on quantum Monte-Carlo calculations. Results for the ground-state energies and ionization potentials of…
Machine learning-based models to predict product state distributions from a distribution of reactant conditions for atom-diatom collisions are presented and quantitatively tested. The models are based on function-, kernel- and grid-based…
Molecule-and-text cross-modal representation learning has emerged as a promising direction for enhancing the quality of molecular representation, thereby improving performance in various scientific fields. However, most approaches employ a…
We present an overview of the reaction coordinate approach to handling strong system-reservoir interactions in quantum thermodynamics. This technique is based on incorporating a collective degree of freedom of the reservoir (the reaction…
Short-range corrections to long-range selected configuration interaction calculations are derived from perturbation theory considerations and applied to harmonium (with two to six electrons for some low-lying states). No fitting to…
Molecular representation learning has attracted much attention recently. A molecule can be viewed as a 2D graph with nodes/atoms connected by edges/bonds, and can also be represented by a 3D conformation with 3-dimensional coordinates of…
Applications of machine learning in chemistry are often limited by the scarcity and expense of labeled data, restricting traditional supervised methods. In this work, we introduce a framework for molecular reasoning using general-purpose…
Accurate diagnostic tests are essential for effective screening and treatment. However, individual biomarkers often fail to provide sufficient diagnostic accuracy, as they typically capture only one aspect of the complex disease process.…
A machine learned (ML) model for predicting product state distributions from specific initial states (state-to-distribution or STD) for reactive atom-diatom collisions is presented and quantitatively tested for the N($^4$S)+O$_{2}$(X$^3…
The atmospheric reaction of H$_2$S with Cl has been reinvestigated to check if, as previously suggested, only explicit dynamical computations can lead to an accurate evaluation of the reaction rate because of strong recrossing effects and…
We analyze the combined effect of the long range Coulomb (LRC) interaction and of surface energy on first order density-driven phase transitions in the presence of a compensating rigid background. We study mixed states formed by regions of…
We propose a cross-entropy minimization method for finding the reaction coordinate from a large number of collective variables in complex molecular systems. This method is an extension of the likelihood maximization approach describing the…
Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical…
We extend the non-parametric framework of reaction coordinate optimization to non-equilibrium ensembles of (short) trajectories. For example, we show how, starting from such an ensemble, one can obtain an equilibrium free energy profile…
Exploration of structure-property relationships as a function of dopant concentration is commonly based on mean field theories for solid solutions. However, such theories that work well for semiconductors tend to fail in materials with…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
We present an efficient method for rigorous quantum calculations of cross sections for atom-molecule reactive scattering in the presence of a dc electric field. The wavefunction of the reaction complex is expanded in an overcomplete set of…
We propose Adjustable Molecular Representation (AdaMR), a new large-scale uniform pre-training strategy for small-molecule drugs, as a novel unified pre-training strategy. AdaMR utilizes a granularity-adjustable molecular encoding strategy,…
The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic…