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The present manuscript revisits one of the earliest approaches to treating molecular systems within the Schr\"odinger formalism of quantum mechanics: the Heitler-London (HL) model. Originally proposed in 1927 and based on a linear…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
The interface between hemoglobin (Hb) and its environment, in particular water, is of great physiological relevance. Here, results from {\it in vitro}, {\it in vivo}, and computational experiments (molecular dynamics simulations) are…
Artificial hydrocarbon networks (AHN) is a novel supervised learning method inspired on the structure and the inner chemical mechanisms of organic compounds. As any other cutting-edge algorithm, there are two challenges to be faced:…
Polymers contain functional groups that participate in hydrogen bond (H-bond) with water molecules, establishing a robust H-bond network that influences bulk properties. This study utilized molecular dynamics (MD) simulations to examine the…
The recombination of hydrogen in the interstellar medium, taking place on surfaces of microscopic dust grains, is an essential process in the evolution of chemical complexity in interstellar clouds. The H_2 formation process has been…
Predicting which proteins interact together from amino-acid sequences is an important task. We develop a method to pair interacting protein sequences which leverages the power of protein language models trained on multiple sequence…
RNA 3D architectures are stabilized by sophisticated networks of (non-canonical) base pair interactions, which can be conveniently encoded as multi-relational graphs and efficiently exploited by graph theoretical approaches and recent…
Background: It is necessary and essential to discovery protein function from the novel primary sequences. Wet lab experimental procedures are not only time-consuming, but also costly, so predicting protein structure and function reliably…
Persistent homology theory is a relatively new but powerful method in data analysis. Using simplicial complexes, classical persistent homology is able to reveal high dimensional geometric structures of datasets, and represent them as…
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…
The prototypical Hydrogen bond in water dimer and Hydrogen bonds in the protonated water dimer, in other small molecules, in water cyclic clusters, and in ice, covering a wide range of bond strengths, are theoretically investigated by…
Grate and co-workers at Pacific Northwest National Laboratory recently developed high information content triazine-based sequence-defined polymers that are robust by not having hydrolyzable bonds and can encode structure and functionality…
We introduce NetworKit, an open-source software package for analyzing the structure of large complex networks. Appropriate algorithmic solutions are required to handle increasingly common large graph data sets containing up to billions of…
Bodge is a free and open-source Python package for constructing large-scale real-space tight-binding models for calculations in condensed matter physics. "Large-scale" means that it should remain performant even for lattices with millions…
Hyaluronan, a sugar polymer found outside the plasma membrane, is a critical component of the extracellular matrix (ECM) scaffold. Hyaluronan's length and moderate negative charge aid in ECM entanglement and solubility. This allows it to…
Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between…
We present an extension of the Poisson-Boltzmann model in which the solute of interest is immersed in an assembly of self-orienting Langevin water dipoles, anions, cations, and hydrophobic molecules, all of variable densities. Interactions…
Interactive molecular graphics applications facilitate analysis of three dimensional protein structures. Naturally, non-interactive 2-D snapshots of the protein structures do not convey the same level of geometric detail. Several 2-D…
Protein phosphorylation involves the reversible modification of a protein (substrate) residue by another protein (kinase). Liquid chromatography-mass spectrometry studies are rapidly generating massive protein phosphorylation datasets…